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August 12, 2022 14:29
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<github.com:microbiomedata/nmdc-schema>: git diff v3.2.0 v6.0.3 -- src/schema/*
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| diff --git a/src/schema/basic_slots.yaml b/src/schema/basic_slots.yaml | |
| index 17c8bf3..1fa4bda 100644 | |
| --- a/src/schema/basic_slots.yaml | |
| +++ b/src/schema/basic_slots.yaml | |
| @@ -29,7 +29,7 @@ slots: | |
| description: >- | |
| A unique identifier for a thing. | |
| Must be either a CURIE shorthand for a URI or a complete URI | |
| - #required: false # for now we setting this to false until we develop an id template | |
| + #required: false # for now we are setting this to false until we develop an id template | |
| name: | |
| multivalued: false | |
| @@ -61,7 +61,7 @@ slots: | |
| range: string | |
| multivalued: false | |
| description: >- | |
| - A name given to the entity that differs from the name/label programatically assigned to it. | |
| + A name given to the entity that differs from the name/label programmatically assigned to it. | |
| For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. | |
| However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study. | |
| exact_mappings: | |
| @@ -91,7 +91,7 @@ slots: | |
| multivalued: true | |
| description: >- | |
| A list of alternative descriptions for the entity. | |
| - The distinction between desciption and alternative descriptions is application-specific. | |
| + The distinction between description and alternative descriptions is application-specific. | |
| alternative identifiers: | |
| range: string | |
| diff --git a/src/schema/bioscales.yaml b/src/schema/bioscales.yaml | |
| new file mode 100644 | |
| index 0000000..beeaef1 | |
| --- /dev/null | |
| +++ b/src/schema/bioscales.yaml | |
| @@ -0,0 +1,206 @@ | |
| +id: https://microbiomedata/schema/bioscales | |
| +name: NMDC-Bioscales | |
| +title: NMDC Schema support for Bioscales analytes | |
| +description: >- | |
| + NMDC Schema support for Bioscales analytes | |
| +license: https://creativecommons.org/publicdomain/zero/1.0/ | |
| + | |
| +prefixes: | |
| + nmdc: https://microbiomedata/meta/ | |
| + mixs: https://w3id.org/gensc/ | |
| + wgs: http://www.w3.org/2003/01/geo/wgs84_pos | |
| + qud: http://qudt.org/1.1/schema/qudt# | |
| + dcterms: http://purl.org/dc/terms/ | |
| + schema: http://schema.org/ | |
| + MS: http://purl.obolibrary.org/obo/MS_ | |
| + igsnvoc: https://igsn.org/voc/v1/ | |
| + linkml: https://w3id.org/linkml/ | |
| + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# | |
| + sio: http://semanticscience.org/resource/SIO_ | |
| + skos: http://www.w3.org/2004/02/skos/core# | |
| + | |
| +default_prefix: nmdc | |
| +default_range: string | |
| + | |
| +default_curi_maps: | |
| + - obo_context | |
| + - idot_context | |
| + | |
| +imports: | |
| + - linkml:types | |
| + - core | |
| +slots: | |
| + zinc: | |
| + name: zinc | |
| + aliases: | |
| + - zinc | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mg/kg (ppm) | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of zinc in the sample | |
| + title: zinc | |
| + examples: | |
| + - value: 2.5 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + manganese: | |
| + name: manganese | |
| + aliases: | |
| + - manganese | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mg/kg (ppm) | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of manganese in the sample | |
| + title: manganese | |
| + examples: | |
| + - value: 24.7 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + | |
| + ammonium nitrogen: | |
| + name: ammonium nitrogen | |
| + aliases: | |
| + - ammonium nitrogen | |
| + - NH4-N | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mg/kg | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of ammonium nitrogen in the sample | |
| + title: ammonium nitrogen | |
| + examples: | |
| + - value: 2.3 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + | |
| + nitrate nitrogen: | |
| + name: nitrate nitrogen | |
| + aliases: | |
| + - nitrate nitrogen | |
| + - NO3-N | |
| + notes: | |
| + - often below some specified limit of detection | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mg/kg | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of nitrate nitrogen in the sample | |
| + title: nitrate nitrogen | |
| + examples: | |
| + - value: 0.29 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + | |
| + nitrite nitrogen: | |
| + name: nitrite nitrogen | |
| + aliases: | |
| + - nitrite nitrogen | |
| + - NO2-N | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mg/kg | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of nitrite nitrogen in the sample | |
| + title: nitrite nitrogen | |
| + examples: | |
| + - value: 1.2 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + | |
| + | |
| + lbc_thirty: | |
| + name: lbc_thirty | |
| + notes: | |
| + - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit | |
| + aliases: | |
| + - lbc_thirty | |
| + - lbc30 | |
| + - lime buffer capacity (at 30 minutes) | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: ppm CaCO3/pH | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: lime buffer capacity, determined after 30 minute incubation | |
| + title: lime buffer capacity (at 30 minutes) | |
| + examples: | |
| + - value: 543 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| + see_also: https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF | |
| + | |
| + | |
| + lbceq: | |
| + name: lbceq | |
| + notes: | |
| + - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit | |
| + aliases: | |
| + - lbceq | |
| + - lime buffer capacity (at 5-day equilibrium) | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: ppm CaCO3/pH | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: lime buffer capacity, determined at equilibrium after 5 day incubation | |
| + title: lime buffer capacity (after 5 day incubation) | |
| + examples: | |
| + - value: 1575 mg/kg | |
| +# source: https://www.ornl.gov/content/bio-scales-0 | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: quantity value | |
| \ No newline at end of file | |
| diff --git a/src/schema/core.yaml b/src/schema/core.yaml | |
| index 23449ab..656b5d9 100644 | |
| --- a/src/schema/core.yaml | |
| +++ b/src/schema/core.yaml | |
| @@ -30,14 +30,14 @@ imports: | |
| - linkml:types | |
| - basic_slots | |
| - prov | |
| - | |
| + | |
| subsets: | |
| - environment: {} | |
| - investigation: {} | |
| - mixs extension: {} | |
| - nucleic acid sequence source: {} | |
| - sequencing: {} | |
| - soil: {} | |
| + environment: { } | |
| + investigation: { } | |
| + mixs extension: { } | |
| + nucleic acid sequence source: { } | |
| + sequencing: { } | |
| + soil: { } | |
| types: | |
| @@ -56,7 +56,7 @@ types: | |
| base: float | |
| see_also: | |
| - https://en.wikipedia.org/wiki/Decimal_degrees | |
| - | |
| + | |
| language code: | |
| description: >- | |
| A language code conforming to ISO_639-1 | |
| @@ -73,7 +73,7 @@ types: | |
| - UO:0000000 | |
| - | |
| + | |
| classes: | |
| named thing: | |
| @@ -84,7 +84,7 @@ classes: | |
| - name | |
| - description | |
| - alternative identifiers | |
| - | |
| + | |
| ontology class: | |
| is_a: named thing | |
| @@ -103,7 +103,7 @@ classes: | |
| description: >- | |
| An optional string that specified the type of object. | |
| required: false | |
| - | |
| + | |
| quantity value: | |
| is_a: attribute value | |
| description: >- | |
| @@ -151,16 +151,29 @@ classes: | |
| - add additional fields e.g for institution | |
| - deprecate "has raw value" in favor of "name" | |
| slot_usage: | |
| + orcid: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: Open Researcher and Contributor ID for this person. See https://orcid.org | |
| + email: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: Email address for this person. | |
| has raw value: | |
| description: >- | |
| - The full name of the Investgator in format FIRST LAST. | |
| + The full name of the Investigator in format FIRST LAST. | |
| notes: >- | |
| May eventually be deprecated in favor of "name". | |
| name: | |
| description: >- | |
| - The full name of the Investgator. | |
| + The full name of the Investigator. | |
| It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional. | |
| - | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: First name, middle initial, and last name of this person. | |
| person: | |
| is_a: named thing | |
| @@ -175,7 +188,7 @@ classes: | |
| MAG bin: | |
| slots: | |
| - - type # custom slot that specifies object type | |
| + - type # custom slot that specifies object type | |
| attributes: | |
| bin name: | |
| range: string | |
| @@ -242,7 +255,7 @@ classes: | |
| description: >- | |
| TODO: Yuri to fill in | |
| range: float | |
| - | |
| + | |
| peptide quantification: | |
| description: >- | |
| This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information | |
| @@ -342,7 +355,7 @@ classes: | |
| - MESH | |
| exact_mappings: | |
| - biolink:ChemicalSubstance | |
| - | |
| + | |
| gene product: | |
| is_a: named thing | |
| description: >- | |
| @@ -362,7 +375,7 @@ classes: | |
| A basic string value | |
| slots: | |
| - language | |
| - | |
| + | |
| url value: | |
| is_a: attribute value | |
| description: >- | |
| @@ -390,7 +403,7 @@ classes: | |
| A value that is a boolean | |
| slots: | |
| - has boolean value | |
| - | |
| + | |
| controlled term value: | |
| is_a: attribute value | |
| description: >- | |
| @@ -415,19 +428,19 @@ classes: | |
| - schema:GeoCoordinates | |
| slots: | |
| - | |
| + | |
| language: | |
| range: language code | |
| description: >- | |
| Should use ISO 639-1 code e.g. "en", "fr" | |
| attribute: | |
| - aliases: ['field', 'property', 'template field', 'key', 'characteristic'] | |
| + aliases: [ 'field', 'property', 'template field', 'key', 'characteristic' ] | |
| abstract: true | |
| description: >- | |
| A attribute of a biosample. Examples: depth, habitat, material. | |
| For NMDC, attributes SHOULD be mapped to terms within a MIxS template | |
| - | |
| + | |
| has raw value: | |
| description: >- | |
| The value that was specified for an annotation in raw form, i.e. a string. E.g. "2 cm" or "2-4 cm" | |
| @@ -435,7 +448,7 @@ slots: | |
| required: false | |
| domain: attribute value | |
| range: string | |
| - | |
| + | |
| has unit: | |
| description: >- | |
| Links a quantity value to a unit | |
| @@ -496,10 +509,10 @@ slots: | |
| pointer to an ontology class | |
| slot_uri: rdf:type | |
| inlined: true | |
| - | |
| + | |
| orcid: | |
| description: >- | |
| - The ORICD of a person. | |
| + The ORCID of a person. | |
| domain: person value | |
| range: string | |
| @@ -514,7 +527,7 @@ slots: | |
| description: >- | |
| One or more other email addresses for an entity. | |
| range: string | |
| - | |
| + | |
| profile image url: | |
| description: >- | |
| A url that points to an image of a person. | |
| @@ -522,15 +535,15 @@ slots: | |
| range: string | |
| has input: | |
| - aliases: ['input'] | |
| + aliases: [ 'input' ] | |
| domain: named thing | |
| - range: named thing | |
| + range: named thing | |
| multivalued: true | |
| description: >- | |
| An input to a process. | |
| - | |
| + | |
| has output: | |
| - aliases: ['output'] | |
| + aliases: [ 'output' ] | |
| domain: named thing | |
| range: named thing | |
| multivalued: true | |
| @@ -538,7 +551,7 @@ slots: | |
| An output biosample to a processing step | |
| part of: | |
| - aliases: ['is part of'] | |
| + aliases: [ 'is part of' ] | |
| range: named thing | |
| domain: named thing | |
| multivalued: true | |
| @@ -550,7 +563,7 @@ slots: | |
| is_a: attribute | |
| description: >- | |
| Example: NERSC-Cori | |
| - | |
| + | |
| url: | |
| is_a: attribute | |
| range: string | |
| @@ -567,7 +580,7 @@ slots: | |
| range: string | |
| description: >- | |
| Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1 | |
| - | |
| + | |
| file size bytes: | |
| is_a: attribute | |
| range: bytes | |
| @@ -609,11 +622,11 @@ slots: | |
| range: string | |
| multivalued: true | |
| description: >- | |
| - A list of websites that are assocatiated with the entity. | |
| + A list of websites that are associated with the entity. | |
| publications: | |
| range: string | |
| multivalued: true | |
| description: >- | |
| - A list of publications that are assocatiated with the entity. | |
| - The publicatons SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible. | |
| + A list of publications that are associated with the entity. | |
| + The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible. | |
| diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml | |
| index 92b171b..e9afdf2 100644 | |
| --- a/src/schema/mixs.yaml | |
| +++ b/src/schema/mixs.yaml | |
| @@ -1,7361 +1,14295 @@ | |
| -id: https://microbiomedata/schema/mixs | |
| name: mixs-schema | |
| title: MIxS Schema | |
| - | |
| +id: https://microbiomedata/schema/mixs | |
| imports: | |
| - - core | |
| - | |
| +- core | |
| +default_prefix: https://microbiomedata/schema/mixs/ | |
| +enums: | |
| + arch_struc_enum: | |
| + name: arch_struc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + building: | |
| + text: building | |
| + shed: | |
| + text: shed | |
| + home: | |
| + text: home | |
| + biol_stat_enum: | |
| + name: biol_stat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + wild: | |
| + text: wild | |
| + natural: | |
| + text: natural | |
| + semi-natural: | |
| + text: semi-natural | |
| + inbred line: | |
| + text: inbred line | |
| + breeder's line: | |
| + text: breeder's line | |
| + hybrid: | |
| + text: hybrid | |
| + clonal selection: | |
| + text: clonal selection | |
| + mutant: | |
| + text: mutant | |
| + biotic_relationship_enum: | |
| + name: biotic_relationship_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + free living: | |
| + text: free living | |
| + parasite: | |
| + text: parasite | |
| + commensal: | |
| + text: commensal | |
| + symbiont: | |
| + text: symbiont | |
| + build_docs_enum: | |
| + name: build_docs_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + building information model: | |
| + text: building information model | |
| + commissioning report: | |
| + text: commissioning report | |
| + complaint logs: | |
| + text: complaint logs | |
| + contract administration: | |
| + text: contract administration | |
| + cost estimate: | |
| + text: cost estimate | |
| + janitorial schedules or logs: | |
| + text: janitorial schedules or logs | |
| + maintenance plans: | |
| + text: maintenance plans | |
| + schedule: | |
| + text: schedule | |
| + sections: | |
| + text: sections | |
| + shop drawings: | |
| + text: shop drawings | |
| + submittals: | |
| + text: submittals | |
| + ventilation system: | |
| + text: ventilation system | |
| + windows: | |
| + text: windows | |
| + build_occup_type_enum: | |
| + name: build_occup_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + office: | |
| + text: office | |
| + market: | |
| + text: market | |
| + restaurant: | |
| + text: restaurant | |
| + residence: | |
| + text: residence | |
| + school: | |
| + text: school | |
| + residential: | |
| + text: residential | |
| + commercial: | |
| + text: commercial | |
| + low rise: | |
| + text: low rise | |
| + high rise: | |
| + text: high rise | |
| + wood framed: | |
| + text: wood framed | |
| + health care: | |
| + text: health care | |
| + airport: | |
| + text: airport | |
| + sports complex: | |
| + text: sports complex | |
| + building_setting_enum: | |
| + name: building_setting_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + urban: | |
| + text: urban | |
| + suburban: | |
| + text: suburban | |
| + exurban: | |
| + text: exurban | |
| + rural: | |
| + text: rural | |
| + ceil_cond_enum: | |
| + name: ceil_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + new: | |
| + text: new | |
| + visible wear: | |
| + text: visible wear | |
| + needs repair: | |
| + text: needs repair | |
| + damaged: | |
| + text: damaged | |
| + rupture: | |
| + text: rupture | |
| + ceil_finish_mat_enum: | |
| + name: ceil_finish_mat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + drywall: | |
| + text: drywall | |
| + mineral fibre: | |
| + text: mineral fibre | |
| + tiles: | |
| + text: tiles | |
| + PVC: | |
| + text: PVC | |
| + plasterboard: | |
| + text: plasterboard | |
| + metal: | |
| + text: metal | |
| + fiberglass: | |
| + text: fiberglass | |
| + stucco: | |
| + text: stucco | |
| + mineral wool/calcium silicate: | |
| + text: mineral wool/calcium silicate | |
| + wood: | |
| + text: wood | |
| + ceil_texture_enum: | |
| + name: ceil_texture_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + crows feet: | |
| + text: crows feet | |
| + crows-foot stomp: | |
| + text: crows-foot stomp | |
| + double skip: | |
| + text: double skip | |
| + hawk and trowel: | |
| + text: hawk and trowel | |
| + knockdown: | |
| + text: knockdown | |
| + popcorn: | |
| + text: popcorn | |
| + orange peel: | |
| + text: orange peel | |
| + rosebud stomp: | |
| + text: rosebud stomp | |
| + Santa-Fe texture: | |
| + text: Santa-Fe texture | |
| + skip trowel: | |
| + text: skip trowel | |
| + smooth: | |
| + text: smooth | |
| + stomp knockdown: | |
| + text: stomp knockdown | |
| + swirl: | |
| + text: swirl | |
| + ceil_type_enum: | |
| + name: ceil_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + cathedral: | |
| + text: cathedral | |
| + dropped: | |
| + text: dropped | |
| + concave: | |
| + text: concave | |
| + barrel-shaped: | |
| + text: barrel-shaped | |
| + coffered: | |
| + text: coffered | |
| + cove: | |
| + text: cove | |
| + stretched: | |
| + text: stretched | |
| + cur_land_use_enum: | |
| + name: cur_land_use_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + cities: | |
| + text: cities | |
| + farmstead: | |
| + text: farmstead | |
| + industrial areas: | |
| + text: industrial areas | |
| + roads/railroads: | |
| + text: roads/railroads | |
| + rock: | |
| + text: rock | |
| + sand: | |
| + text: sand | |
| + gravel: | |
| + text: gravel | |
| + mudflats: | |
| + text: mudflats | |
| + salt flats: | |
| + text: salt flats | |
| + badlands: | |
| + text: badlands | |
| + permanent snow or ice: | |
| + text: permanent snow or ice | |
| + saline seeps: | |
| + text: saline seeps | |
| + mines/quarries: | |
| + text: mines/quarries | |
| + oil waste areas: | |
| + text: oil waste areas | |
| + small grains: | |
| + text: small grains | |
| + row crops: | |
| + text: row crops | |
| + vegetable crops: | |
| + text: vegetable crops | |
| + horticultural plants (e.g. tulips): | |
| + text: horticultural plants (e.g. tulips) | |
| + marshlands (grass,sedges,rushes): | |
| + text: marshlands (grass,sedges,rushes) | |
| + tundra (mosses,lichens): | |
| + text: tundra (mosses,lichens) | |
| + rangeland: | |
| + text: rangeland | |
| + pastureland (grasslands used for livestock grazing): | |
| + text: pastureland (grasslands used for livestock grazing) | |
| + hayland: | |
| + text: hayland | |
| + meadows (grasses,alfalfa,fescue,bromegrass,timothy): | |
| + text: meadows (grasses,alfalfa,fescue,bromegrass,timothy) | |
| + shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus): | |
| + text: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus) | |
| + successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries): | |
| + text: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub | |
| + dogwoods,blackberries) | |
| + shrub crops (blueberries,nursery ornamentals,filberts): | |
| + text: shrub crops (blueberries,nursery ornamentals,filberts) | |
| + vine crops (grapes): | |
| + text: vine crops (grapes) | |
| + conifers (e.g. pine,spruce,fir,cypress): | |
| + text: conifers (e.g. pine,spruce,fir,cypress) | |
| + hardwoods (e.g. oak,hickory,elm,aspen): | |
| + text: hardwoods (e.g. oak,hickory,elm,aspen) | |
| + intermixed hardwood and conifers: | |
| + text: intermixed hardwood and conifers | |
| + tropical (e.g. mangrove,palms): | |
| + text: tropical (e.g. mangrove,palms) | |
| + rainforest (evergreen forest receiving greater than 406 cm annual rainfall): | |
| + text: rainforest (evergreen forest receiving greater than 406 cm annual rainfall) | |
| + swamp (permanent or semi-permanent water body dominated by woody plants): | |
| + text: swamp (permanent or semi-permanent water body dominated by woody plants) | |
| + crop trees (nuts,fruit,christmas trees,nursery trees): | |
| + text: crop trees (nuts,fruit,christmas trees,nursery trees) | |
| + depos_env_enum: | |
| + name: depos_env_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Continental - Alluvial: | |
| + text: Continental - Alluvial | |
| + Continental - Aeolian: | |
| + text: Continental - Aeolian | |
| + Continental - Fluvial: | |
| + text: Continental - Fluvial | |
| + Continental - Lacustrine: | |
| + text: Continental - Lacustrine | |
| + Transitional - Deltaic: | |
| + text: Transitional - Deltaic | |
| + Transitional - Tidal: | |
| + text: Transitional - Tidal | |
| + Transitional - Lagoonal: | |
| + text: Transitional - Lagoonal | |
| + Transitional - Beach: | |
| + text: Transitional - Beach | |
| + Transitional - Lake: | |
| + text: Transitional - Lake | |
| + Marine - Shallow: | |
| + text: Marine - Shallow | |
| + Marine - Deep: | |
| + text: Marine - Deep | |
| + Marine - Reef: | |
| + text: Marine - Reef | |
| + Other - Evaporite: | |
| + text: Other - Evaporite | |
| + Other - Glacial: | |
| + text: Other - Glacial | |
| + Other - Volcanic: | |
| + text: Other - Volcanic | |
| + other: | |
| + text: other | |
| + door_comp_type_enum: | |
| + name: door_comp_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + metal covered: | |
| + text: metal covered | |
| + revolving: | |
| + text: revolving | |
| + sliding: | |
| + text: sliding | |
| + telescopic: | |
| + text: telescopic | |
| + door_cond_enum: | |
| + name: door_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + damaged: | |
| + text: damaged | |
| + needs repair: | |
| + text: needs repair | |
| + new: | |
| + text: new | |
| + rupture: | |
| + text: rupture | |
| + visible wear: | |
| + text: visible wear | |
| + door_direct_enum: | |
| + name: door_direct_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + inward: | |
| + text: inward | |
| + outward: | |
| + text: outward | |
| + sideways: | |
| + text: sideways | |
| + door_loc_enum: | |
| + name: door_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + door_mat_enum: | |
| + name: door_mat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + aluminum: | |
| + text: aluminum | |
| + cellular PVC: | |
| + text: cellular PVC | |
| + engineered plastic: | |
| + text: engineered plastic | |
| + fiberboard: | |
| + text: fiberboard | |
| + fiberglass: | |
| + text: fiberglass | |
| + metal: | |
| + text: metal | |
| + thermoplastic alloy: | |
| + text: thermoplastic alloy | |
| + vinyl: | |
| + text: vinyl | |
| + wood: | |
| + text: wood | |
| + wood/plastic composite: | |
| + text: wood/plastic composite | |
| + door_move_enum: | |
| + name: door_move_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + collapsible: | |
| + text: collapsible | |
| + folding: | |
| + text: folding | |
| + revolving: | |
| + text: revolving | |
| + rolling shutter: | |
| + text: rolling shutter | |
| + sliding: | |
| + text: sliding | |
| + swinging: | |
| + text: swinging | |
| + door_type_enum: | |
| + name: door_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + composite: | |
| + text: composite | |
| + metal: | |
| + text: metal | |
| + wooden: | |
| + text: wooden | |
| + door_type_metal_enum: | |
| + name: door_type_metal_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + collapsible: | |
| + text: collapsible | |
| + corrugated steel: | |
| + text: corrugated steel | |
| + hollow: | |
| + text: hollow | |
| + rolling shutters: | |
| + text: rolling shutters | |
| + steel plate: | |
| + text: steel plate | |
| + door_type_wood_enum: | |
| + name: door_type_wood_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + bettened and ledged: | |
| + text: bettened and ledged | |
| + battened: | |
| + text: battened | |
| + ledged and braced: | |
| + text: ledged and braced | |
| + ledged and framed: | |
| + text: ledged and framed | |
| + ledged, braced and frame: | |
| + text: ledged, braced and frame | |
| + framed and paneled: | |
| + text: framed and paneled | |
| + glashed or sash: | |
| + text: glashed or sash | |
| + flush: | |
| + text: flush | |
| + louvered: | |
| + text: louvered | |
| + wire gauged: | |
| + text: wire gauged | |
| + drainage_class_enum: | |
| + name: drainage_class_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + very poorly: | |
| + text: very poorly | |
| + poorly: | |
| + text: poorly | |
| + somewhat poorly: | |
| + text: somewhat poorly | |
| + moderately well: | |
| + text: moderately well | |
| + well: | |
| + text: well | |
| + excessively drained: | |
| + text: excessively drained | |
| + drawings_enum: | |
| + name: drawings_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + operation: | |
| + text: operation | |
| + as built: | |
| + text: as built | |
| + construction: | |
| + text: construction | |
| + bid: | |
| + text: bid | |
| + design: | |
| + text: design | |
| + building navigation map: | |
| + text: building navigation map | |
| + diagram: | |
| + text: diagram | |
| + sketch: | |
| + text: sketch | |
| + ext_wall_orient_enum: | |
| + name: ext_wall_orient_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + northeast: | |
| + text: northeast | |
| + southeast: | |
| + text: southeast | |
| + southwest: | |
| + text: southwest | |
| + northwest: | |
| + text: northwest | |
| + ext_window_orient_enum: | |
| + name: ext_window_orient_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + northeast: | |
| + text: northeast | |
| + southeast: | |
| + text: southeast | |
| + southwest: | |
| + text: southwest | |
| + northwest: | |
| + text: northwest | |
| + fao_class_enum: | |
| + name: fao_class_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Acrisols: | |
| + text: Acrisols | |
| + Andosols: | |
| + text: Andosols | |
| + Arenosols: | |
| + text: Arenosols | |
| + Cambisols: | |
| + text: Cambisols | |
| + Chernozems: | |
| + text: Chernozems | |
| + Ferralsols: | |
| + text: Ferralsols | |
| + Fluvisols: | |
| + text: Fluvisols | |
| + Gleysols: | |
| + text: Gleysols | |
| + Greyzems: | |
| + text: Greyzems | |
| + Gypsisols: | |
| + text: Gypsisols | |
| + Histosols: | |
| + text: Histosols | |
| + Kastanozems: | |
| + text: Kastanozems | |
| + Lithosols: | |
| + text: Lithosols | |
| + Luvisols: | |
| + text: Luvisols | |
| + Nitosols: | |
| + text: Nitosols | |
| + Phaeozems: | |
| + text: Phaeozems | |
| + Planosols: | |
| + text: Planosols | |
| + Podzols: | |
| + text: Podzols | |
| + Podzoluvisols: | |
| + text: Podzoluvisols | |
| + Rankers: | |
| + text: Rankers | |
| + Regosols: | |
| + text: Regosols | |
| + Rendzinas: | |
| + text: Rendzinas | |
| + Solonchaks: | |
| + text: Solonchaks | |
| + Solonetz: | |
| + text: Solonetz | |
| + Vertisols: | |
| + text: Vertisols | |
| + Yermosols: | |
| + text: Yermosols | |
| + filter_type_enum: | |
| + name: filter_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + particulate air filter: | |
| + text: particulate air filter | |
| + chemical air filter: | |
| + text: chemical air filter | |
| + low-MERV pleated media: | |
| + text: low-MERV pleated media | |
| + HEPA: | |
| + text: HEPA | |
| + electrostatic: | |
| + text: electrostatic | |
| + gas-phase or ultraviolet air treatments: | |
| + text: gas-phase or ultraviolet air treatments | |
| + floor_cond_enum: | |
| + name: floor_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + new: | |
| + text: new | |
| + visible wear: | |
| + text: visible wear | |
| + needs repair: | |
| + text: needs repair | |
| + damaged: | |
| + text: damaged | |
| + rupture: | |
| + text: rupture | |
| + floor_finish_mat_enum: | |
| + name: floor_finish_mat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + tile: | |
| + text: tile | |
| + wood strip or parquet: | |
| + text: wood strip or parquet | |
| + carpet: | |
| + text: carpet | |
| + rug: | |
| + text: rug | |
| + laminate wood: | |
| + text: laminate wood | |
| + lineoleum: | |
| + text: lineoleum | |
| + vinyl composition tile: | |
| + text: vinyl composition tile | |
| + sheet vinyl: | |
| + text: sheet vinyl | |
| + stone: | |
| + text: stone | |
| + bamboo: | |
| + text: bamboo | |
| + cork: | |
| + text: cork | |
| + terrazo: | |
| + text: terrazo | |
| + concrete: | |
| + text: concrete | |
| + none: | |
| + text: none | |
| + sealed: | |
| + text: sealed | |
| + clear finish: | |
| + text: clear finish | |
| + paint: | |
| + text: paint | |
| + none or unfinished: | |
| + text: none or unfinished | |
| + floor_struc_enum: | |
| + name: floor_struc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + balcony: | |
| + text: balcony | |
| + floating floor: | |
| + text: floating floor | |
| + glass floor: | |
| + text: glass floor | |
| + raised floor: | |
| + text: raised floor | |
| + sprung floor: | |
| + text: sprung floor | |
| + wood-framed: | |
| + text: wood-framed | |
| + concrete: | |
| + text: concrete | |
| + floor_water_mold_enum: | |
| + name: floor_water_mold_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + mold odor: | |
| + text: mold odor | |
| + wet floor: | |
| + text: wet floor | |
| + water stains: | |
| + text: water stains | |
| + wall discoloration: | |
| + text: wall discoloration | |
| + floor discoloration: | |
| + text: floor discoloration | |
| + ceiling discoloration: | |
| + text: ceiling discoloration | |
| + peeling paint or wallpaper: | |
| + text: peeling paint or wallpaper | |
| + bulging walls: | |
| + text: bulging walls | |
| + condensation: | |
| + text: condensation | |
| + freq_clean_enum: | |
| + name: freq_clean_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Daily: | |
| + text: Daily | |
| + Weekly: | |
| + text: Weekly | |
| + Monthly: | |
| + text: Monthly | |
| + Quarterly: | |
| + text: Quarterly | |
| + Annually: | |
| + text: Annually | |
| + other: | |
| + text: other | |
| + furniture_enum: | |
| + name: furniture_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + cabinet: | |
| + text: cabinet | |
| + chair: | |
| + text: chair | |
| + desks: | |
| + text: desks | |
| + gender_restroom_enum: | |
| + name: gender_restroom_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + all gender: | |
| + text: all gender | |
| + female: | |
| + text: female | |
| + gender neurtral: | |
| + text: gender neurtral | |
| + male: | |
| + text: male | |
| + male and female: | |
| + text: male and female | |
| + unisex: | |
| + text: unisex | |
| + growth_habit_enum: | |
| + name: growth_habit_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + erect: | |
| + text: erect | |
| + semi-erect: | |
| + text: semi-erect | |
| + spreading: | |
| + text: spreading | |
| + prostrate: | |
| + text: prostrate | |
| + handidness_enum: | |
| + name: handidness_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + ambidexterity: | |
| + text: ambidexterity | |
| + left handedness: | |
| + text: left handedness | |
| + mixed-handedness: | |
| + text: mixed-handedness | |
| + right handedness: | |
| + text: right handedness | |
| + hc_produced_enum: | |
| + name: hc_produced_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Oil: | |
| + text: Oil | |
| + Gas-Condensate: | |
| + text: Gas-Condensate | |
| + Gas: | |
| + text: Gas | |
| + Bitumen: | |
| + text: Bitumen | |
| + Coalbed Methane: | |
| + text: Coalbed Methane | |
| + other: | |
| + text: other | |
| + hcr_enum: | |
| + name: hcr_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Oil Reservoir: | |
| + text: Oil Reservoir | |
| + Gas Reservoir: | |
| + text: Gas Reservoir | |
| + Oil Sand: | |
| + text: Oil Sand | |
| + Coalbed: | |
| + text: Coalbed | |
| + Shale: | |
| + text: Shale | |
| + Tight Oil Reservoir: | |
| + text: Tight Oil Reservoir | |
| + Tight Gas Reservoir: | |
| + text: Tight Gas Reservoir | |
| + other: | |
| + text: other | |
| + hcr_geol_age_enum: | |
| + name: hcr_geol_age_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Archean: | |
| + text: Archean | |
| + Cambrian: | |
| + text: Cambrian | |
| + Carboniferous: | |
| + text: Carboniferous | |
| + Cenozoic: | |
| + text: Cenozoic | |
| + Cretaceous: | |
| + text: Cretaceous | |
| + Devonian: | |
| + text: Devonian | |
| + Jurassic: | |
| + text: Jurassic | |
| + Mesozoic: | |
| + text: Mesozoic | |
| + Neogene: | |
| + text: Neogene | |
| + Ordovician: | |
| + text: Ordovician | |
| + Paleogene: | |
| + text: Paleogene | |
| + Paleozoic: | |
| + text: Paleozoic | |
| + Permian: | |
| + text: Permian | |
| + Precambrian: | |
| + text: Precambrian | |
| + Proterozoic: | |
| + text: Proterozoic | |
| + Silurian: | |
| + text: Silurian | |
| + Triassic: | |
| + text: Triassic | |
| + other: | |
| + text: other | |
| + heat_cool_type_enum: | |
| + name: heat_cool_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + radiant system: | |
| + text: radiant system | |
| + heat pump: | |
| + text: heat pump | |
| + forced air system: | |
| + text: forced air system | |
| + steam forced heat: | |
| + text: steam forced heat | |
| + wood stove: | |
| + text: wood stove | |
| + heat_deliv_loc_enum: | |
| + name: heat_deliv_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + horizon_enum: | |
| + name: horizon_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + O horizon: | |
| + text: O horizon | |
| + A horizon: | |
| + text: A horizon | |
| + E horizon: | |
| + text: E horizon | |
| + B horizon: | |
| + text: B horizon | |
| + C horizon: | |
| + text: C horizon | |
| + R layer: | |
| + text: R layer | |
| + Permafrost: | |
| + text: Permafrost | |
| + host_sex_enum: | |
| + name: host_sex_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + female: | |
| + text: female | |
| + hermaphrodite: | |
| + text: hermaphrodite | |
| + male: | |
| + text: male | |
| + neuter: | |
| + text: neuter | |
| + indoor_space_enum: | |
| + name: indoor_space_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + bedroom: | |
| + text: bedroom | |
| + office: | |
| + text: office | |
| + bathroom: | |
| + text: bathroom | |
| + foyer: | |
| + text: foyer | |
| + kitchen: | |
| + text: kitchen | |
| + locker room: | |
| + text: locker room | |
| + hallway: | |
| + text: hallway | |
| + elevator: | |
| + text: elevator | |
| + indoor_surf_enum: | |
| + name: indoor_surf_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + cabinet: | |
| + text: cabinet | |
| + ceiling: | |
| + text: ceiling | |
| + counter top: | |
| + text: counter top | |
| + door: | |
| + text: door | |
| + shelving: | |
| + text: shelving | |
| + vent cover: | |
| + text: vent cover | |
| + window: | |
| + text: window | |
| + wall: | |
| + text: wall | |
| + int_wall_cond_enum: | |
| + name: int_wall_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + new: | |
| + text: new | |
| + visible wear: | |
| + text: visible wear | |
| + needs repair: | |
| + text: needs repair | |
| + damaged: | |
| + text: damaged | |
| + rupture: | |
| + text: rupture | |
| + light_type_enum: | |
| + name: light_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + natural light: | |
| + text: natural light | |
| + electric light: | |
| + text: electric light | |
| + desk lamp: | |
| + text: desk lamp | |
| + flourescent lights: | |
| + text: flourescent lights | |
| + none: | |
| + text: none | |
| + lithology_enum: | |
| + name: lithology_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Basement: | |
| + text: Basement | |
| + Chalk: | |
| + text: Chalk | |
| + Chert: | |
| + text: Chert | |
| + Coal: | |
| + text: Coal | |
| + Conglomerate: | |
| + text: Conglomerate | |
| + Diatomite: | |
| + text: Diatomite | |
| + Dolomite: | |
| + text: Dolomite | |
| + Limestone: | |
| + text: Limestone | |
| + Sandstone: | |
| + text: Sandstone | |
| + Shale: | |
| + text: Shale | |
| + Siltstone: | |
| + text: Siltstone | |
| + Volcanic: | |
| + text: Volcanic | |
| + other: | |
| + text: other | |
| + mech_struc_enum: | |
| + name: mech_struc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + subway: | |
| + text: subway | |
| + coach: | |
| + text: coach | |
| + carriage: | |
| + text: carriage | |
| + elevator: | |
| + text: elevator | |
| + escalator: | |
| + text: escalator | |
| + boat: | |
| + text: boat | |
| + train: | |
| + text: train | |
| + car: | |
| + text: car | |
| + bus: | |
| + text: bus | |
| + occup_document_enum: | |
| + name: occup_document_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + automated count: | |
| + text: automated count | |
| + estimate: | |
| + text: estimate | |
| + manual count: | |
| + text: manual count | |
| + videos: | |
| + text: videos | |
| + organism_count_enum: | |
| + name: organism_count_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + ATP: | |
| + text: ATP | |
| + MPN: | |
| + text: MPN | |
| + other: | |
| + text: other | |
| + oxy_stat_samp_enum: | |
| + name: oxy_stat_samp_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + aerobic: | |
| + text: aerobic | |
| + anaerobic: | |
| + text: anaerobic | |
| + other: | |
| + text: other | |
| + plant_growth_med_enum: | |
| + name: plant_growth_med_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + other artificial liquid medium: | |
| + text: other artificial liquid medium | |
| + other artificial solid medium: | |
| + text: other artificial solid medium | |
| + peat moss: | |
| + text: peat moss | |
| + perlite: | |
| + text: perlite | |
| + pumice: | |
| + text: pumice | |
| + sand: | |
| + text: sand | |
| + soil: | |
| + text: soil | |
| + vermiculite: | |
| + text: vermiculite | |
| + water: | |
| + text: water | |
| + plant_sex_enum: | |
| + name: plant_sex_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Androdioecious: | |
| + text: Androdioecious | |
| + Androecious: | |
| + text: Androecious | |
| + Androgynous: | |
| + text: Androgynous | |
| + Androgynomonoecious: | |
| + text: Androgynomonoecious | |
| + Andromonoecious: | |
| + text: Andromonoecious | |
| + Bisexual: | |
| + text: Bisexual | |
| + Dichogamous: | |
| + text: Dichogamous | |
| + Diclinous: | |
| + text: Diclinous | |
| + Dioecious: | |
| + text: Dioecious | |
| + Gynodioecious: | |
| + text: Gynodioecious | |
| + Gynoecious: | |
| + text: Gynoecious | |
| + Gynomonoecious: | |
| + text: Gynomonoecious | |
| + Hermaphroditic: | |
| + text: Hermaphroditic | |
| + Imperfect: | |
| + text: Imperfect | |
| + Monoclinous: | |
| + text: Monoclinous | |
| + Monoecious: | |
| + text: Monoecious | |
| + Perfect: | |
| + text: Perfect | |
| + Polygamodioecious: | |
| + text: Polygamodioecious | |
| + Polygamomonoecious: | |
| + text: Polygamomonoecious | |
| + Polygamous: | |
| + text: Polygamous | |
| + Protandrous: | |
| + text: Protandrous | |
| + Protogynous: | |
| + text: Protogynous | |
| + Subandroecious: | |
| + text: Subandroecious | |
| + Subdioecious: | |
| + text: Subdioecious | |
| + Subgynoecious: | |
| + text: Subgynoecious | |
| + Synoecious: | |
| + text: Synoecious | |
| + Trimonoecious: | |
| + text: Trimonoecious | |
| + Trioecious: | |
| + text: Trioecious | |
| + Unisexual: | |
| + text: Unisexual | |
| + profile_position_enum: | |
| + name: profile_position_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + summit: | |
| + text: summit | |
| + shoulder: | |
| + text: shoulder | |
| + backslope: | |
| + text: backslope | |
| + footslope: | |
| + text: footslope | |
| + toeslope: | |
| + text: toeslope | |
| + quad_pos_enum: | |
| + name: quad_pos_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + North side: | |
| + text: North side | |
| + West side: | |
| + text: West side | |
| + South side: | |
| + text: South side | |
| + East side: | |
| + text: East side | |
| + rel_samp_loc_enum: | |
| + name: rel_samp_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + edge of car: | |
| + text: edge of car | |
| + center of car: | |
| + text: center of car | |
| + under a seat: | |
| + text: under a seat | |
| + rel_to_oxygen_enum: | |
| + name: rel_to_oxygen_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + aerobe: | |
| + text: aerobe | |
| + anaerobe: | |
| + text: anaerobe | |
| + facultative: | |
| + text: facultative | |
| + microaerophilic: | |
| + text: microaerophilic | |
| + microanaerobe: | |
| + text: microanaerobe | |
| + obligate aerobe: | |
| + text: obligate aerobe | |
| + obligate anaerobe: | |
| + text: obligate anaerobe | |
| + room_condt_enum: | |
| + name: room_condt_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + new: | |
| + text: new | |
| + visible wear: | |
| + text: visible wear | |
| + needs repair: | |
| + text: needs repair | |
| + damaged: | |
| + text: damaged | |
| + rupture: | |
| + text: rupture | |
| + visible signs of mold/mildew: | |
| + text: visible signs of mold/mildew | |
| + room_connected_enum: | |
| + name: room_connected_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + attic: | |
| + text: attic | |
| + bathroom: | |
| + text: bathroom | |
| + closet: | |
| + text: closet | |
| + conference room: | |
| + text: conference room | |
| + elevator: | |
| + text: elevator | |
| + examining room: | |
| + text: examining room | |
| + hallway: | |
| + text: hallway | |
| + kitchen: | |
| + text: kitchen | |
| + mail room: | |
| + text: mail room | |
| + office: | |
| + text: office | |
| + stairwell: | |
| + text: stairwell | |
| + room_loc_enum: | |
| + name: room_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + corner room: | |
| + text: corner room | |
| + interior room: | |
| + text: interior room | |
| + exterior wall: | |
| + text: exterior wall | |
| + room_samp_pos_enum: | |
| + name: room_samp_pos_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north corner: | |
| + text: north corner | |
| + south corner: | |
| + text: south corner | |
| + west corner: | |
| + text: west corner | |
| + east corner: | |
| + text: east corner | |
| + northeast corner: | |
| + text: northeast corner | |
| + northwest corner: | |
| + text: northwest corner | |
| + southeast corner: | |
| + text: southeast corner | |
| + southwest corner: | |
| + text: southwest corner | |
| + center: | |
| + text: center | |
| + room_type_enum: | |
| + name: room_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + attic: | |
| + text: attic | |
| + bathroom: | |
| + text: bathroom | |
| + closet: | |
| + text: closet | |
| + conference room: | |
| + text: conference room | |
| + elevator: | |
| + text: elevator | |
| + examining room: | |
| + text: examining room | |
| + hallway: | |
| + text: hallway | |
| + kitchen: | |
| + text: kitchen | |
| + mail room: | |
| + text: mail room | |
| + private office: | |
| + text: private office | |
| + open office: | |
| + text: open office | |
| + stairwell: | |
| + text: stairwell | |
| + ',restroom': | |
| + text: ',restroom' | |
| + lobby: | |
| + text: lobby | |
| + vestibule: | |
| + text: vestibule | |
| + mechanical or electrical room: | |
| + text: mechanical or electrical room | |
| + data center: | |
| + text: data center | |
| + laboratory_wet: | |
| + text: laboratory_wet | |
| + laboratory_dry: | |
| + text: laboratory_dry | |
| + gymnasium: | |
| + text: gymnasium | |
| + natatorium: | |
| + text: natatorium | |
| + auditorium: | |
| + text: auditorium | |
| + lockers: | |
| + text: lockers | |
| + cafe: | |
| + text: cafe | |
| + warehouse: | |
| + text: warehouse | |
| + samp_capt_status_enum: | |
| + name: samp_capt_status_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + active surveillance in response to an outbreak: | |
| + text: active surveillance in response to an outbreak | |
| + active surveillance not initiated by an outbreak: | |
| + text: active surveillance not initiated by an outbreak | |
| + farm sample: | |
| + text: farm sample | |
| + market sample: | |
| + text: market sample | |
| + other: | |
| + text: other | |
| + samp_collect_point_enum: | |
| + name: samp_collect_point_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + well: | |
| + text: well | |
| + test well: | |
| + text: test well | |
| + drilling rig: | |
| + text: drilling rig | |
| + wellhead: | |
| + text: wellhead | |
| + separator: | |
| + text: separator | |
| + storage tank: | |
| + text: storage tank | |
| + other: | |
| + text: other | |
| + samp_dis_stage_enum: | |
| + name: samp_dis_stage_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + dissemination: | |
| + text: dissemination | |
| + growth and reproduction: | |
| + text: growth and reproduction | |
| + infection: | |
| + text: infection | |
| + inoculation: | |
| + text: inoculation | |
| + penetration: | |
| + text: penetration | |
| + other: | |
| + text: other | |
| + samp_floor_enum: | |
| + name: samp_floor_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + 1st floor: | |
| + text: 1st floor | |
| + 2nd floor: | |
| + text: 2nd floor | |
| + basement: | |
| + text: basement | |
| + lobby: | |
| + text: lobby | |
| + samp_md_enum: | |
| + name: samp_md_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + DF: | |
| + text: DF | |
| + RT: | |
| + text: RT | |
| + KB: | |
| + text: KB | |
| + MSL: | |
| + text: MSL | |
| + other: | |
| + text: other | |
| + samp_subtype_enum: | |
| + name: samp_subtype_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + oil phase: | |
| + text: oil phase | |
| + water phase: | |
| + text: water phase | |
| + biofilm: | |
| + text: biofilm | |
| + not applicable: | |
| + text: not applicable | |
| + other: | |
| + text: other | |
| + samp_weather_enum: | |
| + name: samp_weather_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + clear sky: | |
| + text: clear sky | |
| + cloudy: | |
| + text: cloudy | |
| + foggy: | |
| + text: foggy | |
| + hail: | |
| + text: hail | |
| + rain: | |
| + text: rain | |
| + snow: | |
| + text: snow | |
| + sleet: | |
| + text: sleet | |
| + sunny: | |
| + text: sunny | |
| + windy: | |
| + text: windy | |
| + season_use_enum: | |
| + name: season_use_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Spring: | |
| + text: Spring | |
| + Summer: | |
| + text: Summer | |
| + Fall: | |
| + text: Fall | |
| + Winter: | |
| + text: Winter | |
| + sediment_type_enum: | |
| + name: sediment_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + biogenous: | |
| + text: biogenous | |
| + cosmogenous: | |
| + text: cosmogenous | |
| + hydrogenous: | |
| + text: hydrogenous | |
| + lithogenous: | |
| + text: lithogenous | |
| + shading_device_cond_enum: | |
| + name: shading_device_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + damaged: | |
| + text: damaged | |
| + needs repair: | |
| + text: needs repair | |
| + new: | |
| + text: new | |
| + rupture: | |
| + text: rupture | |
| + visible wear: | |
| + text: visible wear | |
| + shading_device_type_enum: | |
| + name: shading_device_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + bahama shutters: | |
| + text: bahama shutters | |
| + exterior roll blind: | |
| + text: exterior roll blind | |
| + gambrel awning: | |
| + text: gambrel awning | |
| + hood awning: | |
| + text: hood awning | |
| + porchroller awning: | |
| + text: porchroller awning | |
| + sarasota shutters: | |
| + text: sarasota shutters | |
| + slatted aluminum: | |
| + text: slatted aluminum | |
| + solid aluminum awning: | |
| + text: solid aluminum awning | |
| + sun screen: | |
| + text: sun screen | |
| + tree: | |
| + text: tree | |
| + trellis: | |
| + text: trellis | |
| + venetian awning: | |
| + text: venetian awning | |
| + soil_horizon_enum: | |
| + name: soil_horizon_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + O horizon: | |
| + text: O horizon | |
| + A horizon: | |
| + text: A horizon | |
| + E horizon: | |
| + text: E horizon | |
| + B horizon: | |
| + text: B horizon | |
| + C horizon: | |
| + text: C horizon | |
| + R layer: | |
| + text: R layer | |
| + Permafrost: | |
| + text: Permafrost | |
| + specific_enum: | |
| + name: specific_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + operation: | |
| + text: operation | |
| + as built: | |
| + text: as built | |
| + construction: | |
| + text: construction | |
| + bid: | |
| + text: bid | |
| + design: | |
| + text: design | |
| + photos: | |
| + text: photos | |
| + sr_dep_env_enum: | |
| + name: sr_dep_env_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Lacustine: | |
| + text: Lacustine | |
| + Fluvioldeltaic: | |
| + text: Fluvioldeltaic | |
| + Fluviomarine: | |
| + text: Fluviomarine | |
| + Marine: | |
| + text: Marine | |
| + other: | |
| + text: other | |
| + sr_geol_age_enum: | |
| + name: sr_geol_age_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Archean: | |
| + text: Archean | |
| + Cambrian: | |
| + text: Cambrian | |
| + Carboniferous: | |
| + text: Carboniferous | |
| + Cenozoic: | |
| + text: Cenozoic | |
| + Cretaceous: | |
| + text: Cretaceous | |
| + Devonian: | |
| + text: Devonian | |
| + Jurassic: | |
| + text: Jurassic | |
| + Mesozoic: | |
| + text: Mesozoic | |
| + Neogene: | |
| + text: Neogene | |
| + Ordovician: | |
| + text: Ordovician | |
| + Paleogene: | |
| + text: Paleogene | |
| + Paleozoic: | |
| + text: Paleozoic | |
| + Permian: | |
| + text: Permian | |
| + Precambrian: | |
| + text: Precambrian | |
| + Proterozoic: | |
| + text: Proterozoic | |
| + Silurian: | |
| + text: Silurian | |
| + Triassic: | |
| + text: Triassic | |
| + other: | |
| + text: other | |
| + sr_kerog_type_enum: | |
| + name: sr_kerog_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Type I: | |
| + text: Type I | |
| + Type II: | |
| + text: Type II | |
| + Type III: | |
| + text: Type III | |
| + Type IV: | |
| + text: Type IV | |
| + other: | |
| + text: other | |
| + sr_lithology_enum: | |
| + name: sr_lithology_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Clastic: | |
| + text: Clastic | |
| + Carbonate: | |
| + text: Carbonate | |
| + Coal: | |
| + text: Coal | |
| + Biosilicieous: | |
| + text: Biosilicieous | |
| + other: | |
| + text: other | |
| + substructure_type_enum: | |
| + name: substructure_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + crawlspace: | |
| + text: crawlspace | |
| + slab on grade: | |
| + text: slab on grade | |
| + basement: | |
| + text: basement | |
| + surf_air_cont_enum: | |
| + name: surf_air_cont_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + dust: | |
| + text: dust | |
| + organic matter: | |
| + text: organic matter | |
| + particulate matter: | |
| + text: particulate matter | |
| + volatile organic compounds: | |
| + text: volatile organic compounds | |
| + biological contaminants: | |
| + text: biological contaminants | |
| + radon: | |
| + text: radon | |
| + nutrients: | |
| + text: nutrients | |
| + biocides: | |
| + text: biocides | |
| + surf_material_enum: | |
| + name: surf_material_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + adobe: | |
| + text: adobe | |
| + carpet: | |
| + text: carpet | |
| + cinder blocks: | |
| + text: cinder blocks | |
| + concrete: | |
| + text: concrete | |
| + hay bales: | |
| + text: hay bales | |
| + glass: | |
| + text: glass | |
| + metal: | |
| + text: metal | |
| + paint: | |
| + text: paint | |
| + plastic: | |
| + text: plastic | |
| + stainless steel: | |
| + text: stainless steel | |
| + stone: | |
| + text: stone | |
| + stucco: | |
| + text: stucco | |
| + tile: | |
| + text: tile | |
| + vinyl: | |
| + text: vinyl | |
| + wood: | |
| + text: wood | |
| + tidal_stage_enum: | |
| + name: tidal_stage_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + low tide: | |
| + text: low tide | |
| + ebb tide: | |
| + text: ebb tide | |
| + flood tide: | |
| + text: flood tide | |
| + high tide: | |
| + text: high tide | |
| + tillage_enum: | |
| + name: tillage_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + drill: | |
| + text: drill | |
| + cutting disc: | |
| + text: cutting disc | |
| + ridge till: | |
| + text: ridge till | |
| + strip tillage: | |
| + text: strip tillage | |
| + zonal tillage: | |
| + text: zonal tillage | |
| + chisel: | |
| + text: chisel | |
| + tined: | |
| + text: tined | |
| + mouldboard: | |
| + text: mouldboard | |
| + disc plough: | |
| + text: disc plough | |
| + train_line_enum: | |
| + name: train_line_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + red: | |
| + text: red | |
| + green: | |
| + text: green | |
| + orange: | |
| + text: orange | |
| + train_stat_loc_enum: | |
| + name: train_stat_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + south station above ground: | |
| + text: south station above ground | |
| + south station underground: | |
| + text: south station underground | |
| + south station amtrak: | |
| + text: south station amtrak | |
| + forest hills: | |
| + text: forest hills | |
| + riverside: | |
| + text: riverside | |
| + train_stop_loc_enum: | |
| + name: train_stop_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + end: | |
| + text: end | |
| + mid: | |
| + text: mid | |
| + downtown: | |
| + text: downtown | |
| + vis_media_enum: | |
| + name: vis_media_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + photos: | |
| + text: photos | |
| + videos: | |
| + text: videos | |
| + commonly of the building: | |
| + text: commonly of the building | |
| + site context (adjacent buildings, vegetation, terrain, streets): | |
| + text: site context (adjacent buildings, vegetation, terrain, streets) | |
| + interiors: | |
| + text: interiors | |
| + equipment: | |
| + text: equipment | |
| + 3D scans: | |
| + text: 3D scans | |
| + wall_const_type_enum: | |
| + name: wall_const_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + frame construction: | |
| + text: frame construction | |
| + joisted masonry: | |
| + text: joisted masonry | |
| + light noncombustible: | |
| + text: light noncombustible | |
| + masonry noncombustible: | |
| + text: masonry noncombustible | |
| + modified fire resistive: | |
| + text: modified fire resistive | |
| + fire resistive: | |
| + text: fire resistive | |
| + wall_finish_mat_enum: | |
| + name: wall_finish_mat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + plaster: | |
| + text: plaster | |
| + gypsum plaster: | |
| + text: gypsum plaster | |
| + veneer plaster: | |
| + text: veneer plaster | |
| + gypsum board: | |
| + text: gypsum board | |
| + tile: | |
| + text: tile | |
| + terrazzo: | |
| + text: terrazzo | |
| + stone facing: | |
| + text: stone facing | |
| + acoustical treatment: | |
| + text: acoustical treatment | |
| + wood: | |
| + text: wood | |
| + metal: | |
| + text: metal | |
| + masonry: | |
| + text: masonry | |
| + wall_loc_enum: | |
| + name: wall_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + wall_surf_treatment_enum: | |
| + name: wall_surf_treatment_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + painted: | |
| + text: painted | |
| + wall paper: | |
| + text: wall paper | |
| + no treatment: | |
| + text: no treatment | |
| + paneling: | |
| + text: paneling | |
| + stucco: | |
| + text: stucco | |
| + fabric: | |
| + text: fabric | |
| + wall_texture_enum: | |
| + name: wall_texture_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + crows feet: | |
| + text: crows feet | |
| + crows-foot stomp: | |
| + text: crows-foot stomp | |
| + ? '' | |
| + : text: '' | |
| + double skip: | |
| + text: double skip | |
| + hawk and trowel: | |
| + text: hawk and trowel | |
| + knockdown: | |
| + text: knockdown | |
| + popcorn: | |
| + text: popcorn | |
| + orange peel: | |
| + text: orange peel | |
| + rosebud stomp: | |
| + text: rosebud stomp | |
| + Santa-Fe texture: | |
| + text: Santa-Fe texture | |
| + skip trowel: | |
| + text: skip trowel | |
| + smooth: | |
| + text: smooth | |
| + stomp knockdown: | |
| + text: stomp knockdown | |
| + swirl: | |
| + text: swirl | |
| + water_feat_type_enum: | |
| + name: water_feat_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + fountain: | |
| + text: fountain | |
| + pool: | |
| + text: pool | |
| + standing feature: | |
| + text: standing feature | |
| + stream: | |
| + text: stream | |
| + waterfall: | |
| + text: waterfall | |
| + weekday_enum: | |
| + name: weekday_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + Monday: | |
| + text: Monday | |
| + Tuesday: | |
| + text: Tuesday | |
| + Wednesday: | |
| + text: Wednesday | |
| + Thursday: | |
| + text: Thursday | |
| + Friday: | |
| + text: Friday | |
| + Saturday: | |
| + text: Saturday | |
| + Sunday: | |
| + text: Sunday | |
| + window_cond_enum: | |
| + name: window_cond_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + damaged: | |
| + text: damaged | |
| + needs repair: | |
| + text: needs repair | |
| + new: | |
| + text: new | |
| + rupture: | |
| + text: rupture | |
| + visible wear: | |
| + text: visible wear | |
| + window_cover_enum: | |
| + name: window_cover_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + blinds: | |
| + text: blinds | |
| + curtains: | |
| + text: curtains | |
| + none: | |
| + text: none | |
| + window_horiz_pos_enum: | |
| + name: window_horiz_pos_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + left: | |
| + text: left | |
| + middle: | |
| + text: middle | |
| + right: | |
| + text: right | |
| + window_loc_enum: | |
| + name: window_loc_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + north: | |
| + text: north | |
| + south: | |
| + text: south | |
| + east: | |
| + text: east | |
| + west: | |
| + text: west | |
| + window_mat_enum: | |
| + name: window_mat_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + clad: | |
| + text: clad | |
| + fiberglass: | |
| + text: fiberglass | |
| + metal: | |
| + text: metal | |
| + vinyl: | |
| + text: vinyl | |
| + wood: | |
| + text: wood | |
| + window_type_enum: | |
| + name: window_type_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + single-hung sash window: | |
| + text: single-hung sash window | |
| + horizontal sash window: | |
| + text: horizontal sash window | |
| + fixed window: | |
| + text: fixed window | |
| + window_vert_pos_enum: | |
| + name: window_vert_pos_enum | |
| + from_schema: http://w3id.org/mixs/terms | |
| + permissible_values: | |
| + bottom: | |
| + text: bottom | |
| + middle: | |
| + text: middle | |
| + top: | |
| + text: top | |
| + low: | |
| + text: low | |
| + high: | |
| + text: high | |
| slots: | |
| - submitted_to_insdc: | |
| - aliases: | |
| - - submitted to insdc | |
| - description: >- | |
| - Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:submitted_to_insdc | |
| - in_subset: | |
| - - investigation | |
| - | |
| - investigation_type: | |
| - aliases: | |
| - - investigation type | |
| - description: >- | |
| - Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig] | |
| - pattern: "[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks\\-survey|mimarks\\-specimen|misag|mimag|miuvig]" | |
| - mappings: | |
| - - mixs:investigation_type | |
| - in_subset: | |
| - - investigation | |
| - | |
| - project_name: | |
| - aliases: | |
| - - project name | |
| - description: >- | |
| - Name of the project within which the sequencing was organized | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:project_name | |
| - in_subset: | |
| - - investigation | |
| - | |
| - experimental_factor: | |
| - aliases: | |
| - - experimental factor | |
| - description: >- | |
| - Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]}|{text} | |
| - mappings: | |
| - - mixs:experimental_factor | |
| - in_subset: | |
| - - investigation | |
| - | |
| - lat_lon: | |
| - aliases: | |
| - - geographic location (latitude and longitude) | |
| - description: >- | |
| - The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: geolocation value ## syntax: {float} {float} | |
| - pattern: "\\d+[.\\d+] \\d+[.\\d+]" | |
| - string_serialization: "{float} {float}" | |
| - mappings: | |
| - - mixs:lat_lon | |
| - in_subset: | |
| - - environment | |
| - | |
| - depth: | |
| - aliases: | |
| - - geographic location (depth) | |
| - description: >- | |
| - Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: - | |
| - mappings: | |
| - - mixs:depth | |
| - in_subset: | |
| - - environment | |
| - | |
| + abs_air_humidity: | |
| + name: abs_air_humidity | |
| + aliases: | |
| + - absolute air humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per gram, kilogram per kilogram, kilogram, pound | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Actual mass of water vapor - mh20 - present in the air water vapor | |
| + mixture | |
| + title: absolute air humidity | |
| + examples: | |
| + - value: 9 gram per gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000122 | |
| + multivalued: false | |
| + range: quantity value | |
| + core field: | |
| + name: core field | |
| + description: basic fields | |
| + from_schema: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + abstract: true | |
| + add_recov_method: | |
| + name: add_recov_method | |
| + aliases: | |
| + - secondary and tertiary recovery methods and start date | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration;timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed | |
| + for increase of hydrocarbon recovery from resource and start date for each one | |
| + of them. If "other" is specified, please propose entry in "additional info" | |
| + field | |
| + title: secondary and tertiary recovery methods and start date | |
| + examples: | |
| + - value: Polymer Addition;2018-06-21T14:30Z | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001009 | |
| + multivalued: false | |
| + range: text value | |
| + additional_info: | |
| + name: additional_info | |
| + aliases: | |
| + - additional info | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Information that doesn't fit anywhere else. Can also be used to propose | |
| + new entries for fields with controlled vocabulary | |
| + title: additional info | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000300 | |
| + multivalued: false | |
| + range: text value | |
| + address: | |
| + name: address | |
| + aliases: | |
| + - address | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The street name and building number where the sampling occurred. | |
| + title: address | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer}{text}' | |
| + slot_uri: MIXS:0000218 | |
| + multivalued: false | |
| + range: text value | |
| + adj_room: | |
| + name: adj_room | |
| + aliases: | |
| + - adjacent rooms | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: room name;room number | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of rooms (room number, room name) immediately adjacent to the | |
| + sampling room | |
| + title: adjacent rooms | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{integer}' | |
| + slot_uri: MIXS:0000219 | |
| + multivalued: false | |
| + range: text value | |
| + aero_struc: | |
| + name: aero_struc | |
| + aliases: | |
| + - aerospace structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Aerospace structures typically consist of thin plates with stiffeners | |
| + for the external surfaces, bulkheads and frames to support the shape and fasteners | |
| + such as welds, rivets, screws and bolts to hold the components together | |
| + title: aerospace structure | |
| + examples: | |
| + - value: plane | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[plane|glider]' | |
| + slot_uri: MIXS:0000773 | |
| + multivalued: false | |
| + range: text value | |
| + agrochem_addition: | |
| + name: agrochem_addition | |
| + aliases: | |
| + - history/agrochemical additions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: agrochemical name;agrochemical amount;timestamp | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Addition of fertilizers, pesticides, etc. - amount and time of applications | |
| + title: history/agrochemical additions | |
| + examples: | |
| + - value: roundup;5 milligram per liter;2018-06-21 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{timestamp}' | |
| + slot_uri: MIXS:0000639 | |
| + multivalued: false | |
| + range: quantity value | |
| + air_temp: | |
| + name: air_temp | |
| + aliases: | |
| + - air temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Temperature of the air at the time of sampling | |
| + title: air temperature | |
| + examples: | |
| + - value: 20 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000124 | |
| + multivalued: false | |
| + range: quantity value | |
| + air_temp_regm: | |
| + name: air_temp_regm | |
| + aliases: | |
| + - air temperature regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: temperature value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving an exposure to varying temperatures; | |
| + should include the temperature, treatment regimen including how many times the | |
| + treatment was repeated, how long each treatment lasted, and the start and end | |
| + time of the entire treatment; can include different temperature regimens | |
| + title: air temperature regimen | |
| + examples: | |
| + - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000551 | |
| + multivalued: false | |
| + range: quantity value | |
| + al_sat: | |
| + name: al_sat | |
| + aliases: | |
| + - extreme_unusual_properties/Al saturation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Aluminum saturation (esp. For tropical soils) | |
| + title: extreme_unusual_properties/Al saturation | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000607 | |
| + multivalued: false | |
| + range: quantity value | |
| + al_sat_meth: | |
| + name: al_sat_meth | |
| + aliases: | |
| + - extreme_unusual_properties/Al saturation method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or URL | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining Al saturation | |
| + title: extreme_unusual_properties/Al saturation method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000324 | |
| + multivalued: false | |
| + range: text value | |
| + alkalinity: | |
| + name: alkalinity | |
| + aliases: | |
| + - alkalinity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milliequivalent per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Alkalinity, the ability of a solution to neutralize acids to the | |
| + equivalence point of carbonate or bicarbonate | |
| + title: alkalinity | |
| + examples: | |
| + - value: 50 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000421 | |
| + multivalued: false | |
| + range: quantity value | |
| + alkalinity_method: | |
| + name: alkalinity_method | |
| + aliases: | |
| + - alkalinity method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: description of method | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Method used for alkalinity measurement | |
| + title: alkalinity method | |
| + examples: | |
| + - value: titration | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000298 | |
| + multivalued: false | |
| + range: text value | |
| + alkyl_diethers: | |
| + name: alkyl_diethers | |
| + aliases: | |
| + - alkyl diethers | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of alkyl diethers | |
| + title: alkyl diethers | |
| + examples: | |
| + - value: 0.005 mole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000490 | |
| + multivalued: false | |
| + range: quantity value | |
| alt: | |
| - aliases: | |
| - - altitude | |
| - description: >- | |
| - Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earthbs surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:alt | |
| - in_subset: | |
| - - environment | |
| - | |
| - elev: | |
| - aliases: | |
| - - elevation | |
| - description: >- | |
| - Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:elev | |
| - in_subset: | |
| - - environment | |
| - | |
| - geo_loc_name: | |
| - aliases: | |
| - - "geographic location (country and/or sea,region)" | |
| - description: >- | |
| - The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {term};{term};{text} | |
| - mappings: | |
| - - mixs:geo_loc_name | |
| - in_subset: | |
| - - environment | |
| - | |
| + name: alt | |
| + aliases: | |
| + - altitude | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + description: Altitude is a term used to identify heights of objects such as airplanes, | |
| + space shuttles, rockets, atmospheric balloons and heights of places such as | |
| + atmospheric layers and clouds. It is used to measure the height of an object | |
| + which is above the earth's surface. In this context, the altitude measurement | |
| + is the vertical distance between the earth's surface above sea level and the | |
| + sampled position in the air | |
| + title: altitude | |
| + examples: | |
| + - value: 100 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000094 | |
| + multivalued: false | |
| + range: quantity value | |
| + environment field: | |
| + name: environment field | |
| + description: field describing environmental aspect of a sample | |
| + from_schema: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + abstract: true | |
| + aminopept_act: | |
| + name: aminopept_act | |
| + aliases: | |
| + - aminopeptidase activity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mole per liter per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of aminopeptidase activity | |
| + title: aminopeptidase activity | |
| + examples: | |
| + - value: 0.269 mole per liter per hour | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000172 | |
| + multivalued: false | |
| + range: quantity value | |
| + ammonium: | |
| + name: ammonium | |
| + aliases: | |
| + - ammonium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of ammonium in the sample | |
| + title: ammonium | |
| + examples: | |
| + - value: 1.5 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000427 | |
| + multivalued: false | |
| + range: quantity value | |
| + amount_light: | |
| + name: amount_light | |
| + aliases: | |
| + - amount of light | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: lux, lumens per square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The unit of illuminance and luminous emittance, measuring luminous | |
| + flux per unit area | |
| + title: amount of light | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000140 | |
| + multivalued: false | |
| + range: quantity value | |
| + ances_data: | |
| + name: ances_data | |
| + aliases: | |
| + - ancestral data | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Information about either pedigree or other ancestral information | |
| + description (e.g. parental variety in case of mutant or selection), e.g. A/3*B | |
| + (meaning [(A x B) x B] x B) | |
| + title: ancestral data | |
| + examples: | |
| + - value: A/3*B | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000247 | |
| + multivalued: false | |
| + range: text value | |
| + annual_precpt: | |
| + name: annual_precpt | |
| + aliases: | |
| + - mean annual precipitation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average of all annual precipitation values known, or an estimated | |
| + equivalent value derived by such methods as regional indexes or Isohyetal maps. | |
| + title: mean annual precipitation | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000644 | |
| + multivalued: false | |
| + range: quantity value | |
| + annual_temp: | |
| + name: annual_temp | |
| + aliases: | |
| + - mean annual temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Mean annual temperature | |
| + title: mean annual temperature | |
| + examples: | |
| + - value: 12.5 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000642 | |
| + multivalued: false | |
| + range: quantity value | |
| + antibiotic_regm: | |
| + name: antibiotic_regm | |
| + aliases: | |
| + - antibiotic regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: antibiotic name;antibiotic amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving antibiotic administration; | |
| + should include the name of antibiotic, amount administered, treatment regimen | |
| + including how many times the treatment was repeated, how long each treatment | |
| + lasted, and the start and end time of the entire treatment; can include multiple | |
| + antibiotic regimens | |
| + title: antibiotic regimen | |
| + examples: | |
| + - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000553 | |
| + multivalued: false | |
| + range: quantity value | |
| + api: | |
| + name: api | |
| + aliases: | |
| + - API gravity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degrees API | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'API gravity is a measure of how heavy or light a petroleum liquid | |
| + is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. | |
| + 31.1° API)' | |
| + title: API gravity | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000157 | |
| + multivalued: false | |
| + range: quantity value | |
| + arch_struc: | |
| + name: arch_struc | |
| + aliases: | |
| + - architectural structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: An architectural structure is a human-made, free-standing, immobile | |
| + outdoor construction | |
| + title: architectural structure | |
| + examples: | |
| + - value: shed | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000774 | |
| + multivalued: false | |
| + range: text value | |
| + aromatics_pc: | |
| + name: aromatics_pc | |
| + aliases: | |
| + - aromatics wt% | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis | |
| + method that divides crude oil components according to their polarizability | |
| + and polarity. There are three main methods to obtain SARA results. The most | |
| + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: | |
| + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' | |
| + title: aromatics wt% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000133 | |
| + multivalued: false | |
| + range: quantity value | |
| + asphaltenes_pc: | |
| + name: asphaltenes_pc | |
| + aliases: | |
| + - asphaltenes wt% | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis | |
| + method that divides crude oil components according to their polarizability | |
| + and polarity. There are three main methods to obtain SARA results. The most | |
| + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: | |
| + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' | |
| + title: asphaltenes wt% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000135 | |
| + multivalued: false | |
| + range: quantity value | |
| + atmospheric_data: | |
| + name: atmospheric_data | |
| + aliases: | |
| + - atmospheric data | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: atmospheric data name;measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Measurement of atmospheric data; can include multiple data | |
| + title: atmospheric data | |
| + examples: | |
| + - value: wind speed;9 knots | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0001097 | |
| + multivalued: false | |
| + range: quantity value | |
| + avg_dew_point: | |
| + name: avg_dew_point | |
| + aliases: | |
| + - average dew point | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average of dew point measures taken at the beginning of every | |
| + hour over a 24 hour period on the sampling day | |
| + title: average dew point | |
| + examples: | |
| + - value: 25.5 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000141 | |
| + multivalued: false | |
| + range: quantity value | |
| + avg_occup: | |
| + name: avg_occup | |
| + aliases: | |
| + - average daily occupancy | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Daily average occupancy of room. Indicate the number of person(s) | |
| + daily occupying the sampling room. | |
| + title: average daily occupancy | |
| + examples: | |
| + - value: '2' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000775 | |
| + multivalued: false | |
| + range: text value | |
| + avg_temp: | |
| + name: avg_temp | |
| + aliases: | |
| + - average temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average of temperatures taken at the beginning of every hour | |
| + over a 24 hour period on the sampling day | |
| + title: average temperature | |
| + examples: | |
| + - value: 12.5 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000142 | |
| + multivalued: false | |
| + range: quantity value | |
| + bac_prod: | |
| + name: bac_prod | |
| + aliases: | |
| + - bacterial production | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per cubic meter per day | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Bacterial production in the water column measured by isotope uptake | |
| + title: bacterial production | |
| + examples: | |
| + - value: 5 milligram per cubic meter per day | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000683 | |
| + multivalued: false | |
| + range: quantity value | |
| + bac_resp: | |
| + name: bac_resp | |
| + aliases: | |
| + - bacterial respiration | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per cubic meter per day, micromole oxygen per liter per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of bacterial respiration in the water column | |
| + title: bacterial respiration | |
| + examples: | |
| + - value: 300 micromole oxygen per liter per hour | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000684 | |
| + multivalued: false | |
| + range: quantity value | |
| + bacteria_carb_prod: | |
| + name: bacteria_carb_prod | |
| + aliases: | |
| + - bacterial carbon production | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: nanogram per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of bacterial carbon production | |
| + title: bacterial carbon production | |
| + examples: | |
| + - value: 2.53 microgram per liter per hour | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000173 | |
| + multivalued: false | |
| + range: quantity value | |
| + barometric_press: | |
| + name: barometric_press | |
| + aliases: | |
| + - barometric pressure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millibar | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Force per unit area exerted against a surface by the weight of air | |
| + above that surface | |
| + title: barometric pressure | |
| + examples: | |
| + - value: 5 millibar | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000096 | |
| + multivalued: false | |
| + range: quantity value | |
| + basin: | |
| + name: basin | |
| + aliases: | |
| + - basin name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of the basin (e.g. Campos) | |
| + title: basin name | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000290 | |
| + multivalued: false | |
| + range: text value | |
| + bathroom_count: | |
| + name: bathroom_count | |
| + aliases: | |
| + - bathroom count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of bathrooms in the building | |
| + title: bathroom count | |
| + examples: | |
| + - value: '1' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000776 | |
| + multivalued: false | |
| + range: text value | |
| + bedroom_count: | |
| + name: bedroom_count | |
| + aliases: | |
| + - bedroom count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of bedrooms in the building | |
| + title: bedroom count | |
| + examples: | |
| + - value: '2' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000777 | |
| + multivalued: false | |
| + range: text value | |
| + benzene: | |
| + name: benzene | |
| + aliases: | |
| + - benzene | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of benzene in the sample | |
| + title: benzene | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000153 | |
| + multivalued: false | |
| + range: quantity value | |
| + biochem_oxygen_dem: | |
| + name: biochem_oxygen_dem | |
| + aliases: | |
| + - biochemical oxygen demand | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Amount of dissolved oxygen needed by aerobic biological organisms | |
| + in a body of water to break down organic material present in a given water sample | |
| + at certain temperature over a specific time period | |
| + title: biochemical oxygen demand | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000653 | |
| + multivalued: false | |
| + range: quantity value | |
| + biocide: | |
| + name: biocide | |
| + aliases: | |
| + - biocide administration | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;name;timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of biocides (commercial name of product and supplier) and date | |
| + of administration | |
| + title: biocide administration | |
| + examples: | |
| + - value: ALPHA 1427;Baker Hughes;2008-01-23 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{text};{timestamp}' | |
| + slot_uri: MIXS:0001011 | |
| + multivalued: false | |
| + range: text value | |
| + biocide_admin_method: | |
| + name: biocide_admin_method | |
| + aliases: | |
| + - biocide administration method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;frequency;duration;duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Method of biocide administration (dose, frequency, duration, time | |
| + elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 | |
| + days) | |
| + title: biocide administration method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' | |
| + slot_uri: MIXS:0000456 | |
| + multivalued: false | |
| + range: quantity value | |
| + biol_stat: | |
| + name: biol_stat | |
| + aliases: | |
| + - biological status | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The level of genome modification. | |
| + title: biological status | |
| + examples: | |
| + - value: natural | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000858 | |
| + multivalued: false | |
| + range: text value | |
| + biomass: | |
| + name: biomass | |
| + aliases: | |
| + - biomass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: biomass type;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: ton, kilogram, gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Amount of biomass; should include the name for the part of biomass | |
| + measured, e.g. Microbial, total. Can include multiple measurements | |
| + title: biomass | |
| + examples: | |
| + - value: total;20 gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000174 | |
| + multivalued: false | |
| + range: quantity value | |
| + biotic_regm: | |
| + name: biotic_regm | |
| + aliases: | |
| + - biotic regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Information about treatment(s) involving use of biotic factors, such | |
| + as bacteria, viruses or fungi. | |
| + title: biotic regimen | |
| + examples: | |
| + - value: sample inoculated with Rhizobium spp. Culture | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0001038 | |
| + multivalued: false | |
| + range: text value | |
| + biotic_relationship: | |
| + name: biotic_relationship | |
| + aliases: | |
| + - observed biotic relationship | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + description: Description of relationship(s) between the subject organism and other | |
| + organism(s) it is associated with. E.g., parasite on species X; mutualist with | |
| + species Y. The target organism is the subject of the relationship, and the other | |
| + organism(s) is the object | |
| + title: observed biotic relationship | |
| + examples: | |
| + - value: free living | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000028 | |
| + multivalued: false | |
| + range: text value | |
| + nucleic acid sequence source field: | |
| + name: nucleic acid sequence source field | |
| + from_schema: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + abstract: true | |
| + bishomohopanol: | |
| + name: bishomohopanol | |
| + aliases: | |
| + - bishomohopanol | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, microgram per gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of bishomohopanol | |
| + title: bishomohopanol | |
| + examples: | |
| + - value: 14 microgram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000175 | |
| + multivalued: false | |
| + range: quantity value | |
| + blood_press_diast: | |
| + name: blood_press_diast | |
| + aliases: | |
| + - host blood pressure diastolic | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter mercury | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Resting diastolic blood pressure, measured as mm mercury | |
| + title: host blood pressure diastolic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000258 | |
| + multivalued: false | |
| + range: quantity value | |
| + blood_press_syst: | |
| + name: blood_press_syst | |
| + aliases: | |
| + - host blood pressure systolic | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter mercury | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Resting systolic blood pressure, measured as mm mercury | |
| + title: host blood pressure systolic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000259 | |
| + multivalued: false | |
| + range: quantity value | |
| + bromide: | |
| + name: bromide | |
| + aliases: | |
| + - bromide | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of bromide | |
| + title: bromide | |
| + examples: | |
| + - value: 0.05 parts per million | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000176 | |
| + multivalued: false | |
| + range: quantity value | |
| + build_docs: | |
| + name: build_docs | |
| + aliases: | |
| + - design, construction, and operation documents | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The building design, construction and operation documents | |
| + title: design, construction, and operation documents | |
| + examples: | |
| + - value: maintenance plans | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000787 | |
| + multivalued: false | |
| + range: text value | |
| + build_occup_type: | |
| + name: build_occup_type | |
| + aliases: | |
| + - building occupancy type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: The primary function for which a building or discrete part of a building | |
| + is intended to be used | |
| + title: building occupancy type | |
| + examples: | |
| + - value: market | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000761 | |
| + multivalued: false | |
| + range: text value | |
| + building_setting: | |
| + name: building_setting | |
| + aliases: | |
| + - building setting | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A location (geography) where a building is set | |
| + title: building setting | |
| + examples: | |
| + - value: rural | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000768 | |
| + multivalued: false | |
| + range: text value | |
| + built_struc_age: | |
| + name: built_struc_age | |
| + aliases: | |
| + - built structure age | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: year | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The age of the built structure since construction | |
| + title: built structure age | |
| + examples: | |
| + - value: '15' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000145 | |
| + multivalued: false | |
| + range: quantity value | |
| + built_struc_set: | |
| + name: built_struc_set | |
| + aliases: | |
| + - built structure setting | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The characterization of the location of the built structure as high | |
| + or low human density | |
| + title: built structure setting | |
| + examples: | |
| + - value: rural | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[urban|rural]' | |
| + slot_uri: MIXS:0000778 | |
| + multivalued: false | |
| + range: text value | |
| + built_struc_type: | |
| + name: built_struc_type | |
| + aliases: | |
| + - built structure type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A physical structure that is a body or assemblage of bodies in space | |
| + to form a system capable of supporting loads | |
| + title: built structure type | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000721 | |
| + multivalued: false | |
| + range: text value | |
| + calcium: | |
| + name: calcium | |
| + aliases: | |
| + - calcium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, micromole per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of calcium in the sample | |
| + title: calcium | |
| + examples: | |
| + - value: 0.2 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000432 | |
| + multivalued: false | |
| + range: quantity value | |
| + carb_dioxide: | |
| + name: carb_dioxide | |
| + aliases: | |
| + - carbon dioxide | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Carbon dioxide (gas) amount or concentration at the time of sampling | |
| + title: carbon dioxide | |
| + examples: | |
| + - value: 410 parts per million | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000097 | |
| + multivalued: false | |
| + range: quantity value | |
| + carb_monoxide: | |
| + name: carb_monoxide | |
| + aliases: | |
| + - carbon monoxide | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Carbon monoxide (gas) amount or concentration at the time of sampling | |
| + title: carbon monoxide | |
| + examples: | |
| + - value: 0.1 parts per million | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000098 | |
| + multivalued: false | |
| + range: quantity value | |
| + carb_nitro_ratio: | |
| + name: carb_nitro_ratio | |
| + aliases: | |
| + - carbon/nitrogen ratio | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Ratio of amount or concentrations of carbon to nitrogen | |
| + title: carbon/nitrogen ratio | |
| + examples: | |
| + - value: '0.417361111' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000310 | |
| + multivalued: false | |
| + range: quantity value | |
| + ceil_area: | |
| + name: ceil_area | |
| + aliases: | |
| + - ceiling area | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The area of the ceiling space within the room | |
| + title: ceiling area | |
| + examples: | |
| + - value: 25 square meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000148 | |
| + multivalued: false | |
| + range: quantity value | |
| + ceil_cond: | |
| + name: ceil_cond | |
| + aliases: | |
| + - ceiling condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The physical condition of the ceiling at the time of sampling; photos | |
| + or video preferred; use drawings to indicate location of damaged areas | |
| + title: ceiling condition | |
| + examples: | |
| + - value: damaged | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000779 | |
| + multivalued: false | |
| + range: text value | |
| + ceil_finish_mat: | |
| + name: ceil_finish_mat | |
| + aliases: | |
| + - ceiling finish material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of material used to finish a ceiling | |
| + title: ceiling finish material | |
| + examples: | |
| + - value: stucco | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000780 | |
| + multivalued: false | |
| + range: text value | |
| + ceil_struc: | |
| + name: ceil_struc | |
| + aliases: | |
| + - ceiling structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The construction format of the ceiling | |
| + title: ceiling structure | |
| + examples: | |
| + - value: concrete | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[wood frame|concrete]' | |
| + slot_uri: MIXS:0000782 | |
| + multivalued: false | |
| + range: text value | |
| + ceil_texture: | |
| + name: ceil_texture | |
| + aliases: | |
| + - ceiling texture | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The feel, appearance, or consistency of a ceiling surface | |
| + title: ceiling texture | |
| + examples: | |
| + - value: popcorn | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000783 | |
| + multivalued: false | |
| + range: text value | |
| + ceil_thermal_mass: | |
| + name: ceil_thermal_mass | |
| + aliases: | |
| + - ceiling thermal mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: joule per degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The ability of the ceiling to provide inertia against temperature | |
| + fluctuations. Generally this means concrete that is exposed. A metal deck that | |
| + supports a concrete slab will act thermally as long as it is exposed to room | |
| + air flow | |
| + title: ceiling thermal mass | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000143 | |
| + multivalued: false | |
| + range: quantity value | |
| + ceil_type: | |
| + name: ceil_type | |
| + aliases: | |
| + - ceiling type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of ceiling according to the ceiling's appearance or construction | |
| + title: ceiling type | |
| + examples: | |
| + - value: coffered | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000784 | |
| + multivalued: false | |
| + range: text value | |
| + ceil_water_mold: | |
| + name: ceil_water_mold | |
| + aliases: | |
| + - ceiling signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew on the ceiling | |
| + title: ceiling signs of water/mold | |
| + examples: | |
| + - value: presence of mold visible | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[presence of mold visible|no presence of mold visible]' | |
| + slot_uri: MIXS:0000781 | |
| + multivalued: false | |
| + range: text value | |
| + chem_administration: | |
| + name: chem_administration | |
| + aliases: | |
| + - chemical administration | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: CHEBI;timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: List of chemical compounds administered to the host or site where | |
| + sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can | |
| + include multiple compounds. For chemical entities of biological interest ontology | |
| + (chebi) (v 163), http://purl.bioontology.org/ontology/chebi | |
| + title: chemical administration | |
| + examples: | |
| + - value: agar [CHEBI:2509];2018-05-11T20:00Z | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]};{timestamp}' | |
| + slot_uri: MIXS:0000751 | |
| + multivalued: false | |
| + range: controlled term value | |
| + chem_mutagen: | |
| + name: chem_mutagen | |
| + aliases: | |
| + - chemical mutagen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: mutagen name;mutagen amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Treatment involving use of mutagens; should include the name of mutagen, | |
| + amount administered, treatment regimen including how many times the treatment | |
| + was repeated, how long each treatment lasted, and the start and end time of | |
| + the entire treatment; can include multiple mutagen regimens | |
| + title: chemical mutagen | |
| + examples: | |
| + - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000555 | |
| + multivalued: false | |
| + range: quantity value | |
| + chem_oxygen_dem: | |
| + name: chem_oxygen_dem | |
| + aliases: | |
| + - chemical oxygen demand | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A measure of the capacity of water to consume oxygen during the decomposition | |
| + of organic matter and the oxidation of inorganic chemicals such as ammonia and | |
| + nitrite | |
| + title: chemical oxygen demand | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000656 | |
| + multivalued: false | |
| + range: quantity value | |
| + chem_treat_method: | |
| + name: chem_treat_method | |
| + aliases: | |
| + - chemical treatment method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;frequency;duration;duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Method of chemical administration(dose, frequency, duration, time | |
| + elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 | |
| + hr; 0 days) | |
| + title: chemical treatment method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' | |
| + slot_uri: MIXS:0000457 | |
| + multivalued: false | |
| + range: string | |
| + chem_treatment: | |
| + name: chem_treatment | |
| + aliases: | |
| + - chemical treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;name;timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of chemical compounds administered upstream the sampling location | |
| + where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, | |
| + demulsifiers, and other production chemicals etc.). The commercial name of the | |
| + product and name of the supplier should be provided. The date of administration | |
| + should also be included | |
| + title: chemical treatment | |
| + examples: | |
| + - value: ACCENT 1125;DOW;2010-11-17 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{text};{timestamp}' | |
| + slot_uri: MIXS:0001012 | |
| + multivalued: false | |
| + range: text value | |
| + chimera_check: | |
| + name: chimera_check | |
| + aliases: | |
| + - chimera check software | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name and version of software, parameters used | |
| + description: Tool(s) used for chimera checking, including version number and parameters, | |
| + to discover and remove chimeric sequences. A chimeric sequence is comprised | |
| + of two or more phylogenetically distinct parent sequences. | |
| + title: chimera check software | |
| + examples: | |
| + - value: uchime;v4.1;default parameters | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{software};{version};{parameters}' | |
| + slot_uri: MIXS:0000052 | |
| + multivalued: false | |
| + range: text value | |
| + sequencing field: | |
| + name: sequencing field | |
| + from_schema: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + abstract: true | |
| + chloride: | |
| + name: chloride | |
| + aliases: | |
| + - chloride | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of chloride in the sample | |
| + title: chloride | |
| + examples: | |
| + - value: 5000 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000429 | |
| + multivalued: false | |
| + range: quantity value | |
| + chlorophyll: | |
| + name: chlorophyll | |
| + aliases: | |
| + - chlorophyll | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per cubic meter, microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of chlorophyll | |
| + title: chlorophyll | |
| + examples: | |
| + - value: 5 milligram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000177 | |
| + multivalued: false | |
| + range: quantity value | |
| + climate_environment: | |
| + name: climate_environment | |
| + aliases: | |
| + - climate environment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: climate name;treatment interval and duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Treatment involving an exposure to a particular climate; treatment | |
| + regimen including how many times the treatment was repeated, how long each treatment | |
| + lasted, and the start and end time of the entire treatment; can include multiple | |
| + climates | |
| + title: climate environment | |
| + examples: | |
| + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0001040 | |
| + multivalued: false | |
| + range: text value | |
| collection_date: | |
| - aliases: | |
| - - collection date | |
| - description: >- | |
| - The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:collection_date | |
| - in_subset: | |
| - - environment | |
| - | |
| + name: collection_date | |
| + aliases: | |
| + - collection date | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: date and time | |
| + description: 'The time of sampling, either as an instance (single point in time) | |
| + or interval. In case no exact time is available, the date/time can be right | |
| + truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; | |
| + 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' | |
| + title: collection date | |
| + examples: | |
| + - value: 2018-05-11T10:00:00+01:00; 2018-05-11 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000011 | |
| + multivalued: false | |
| + range: timestamp value | |
| + conduc: | |
| + name: conduc | |
| + aliases: | |
| + - conductivity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milliSiemens per centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Electrical conductivity of water | |
| + title: conductivity | |
| + examples: | |
| + - value: 10 milliSiemens per centimeter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000692 | |
| + multivalued: false | |
| + range: quantity value | |
| + cool_syst_id: | |
| + name: cool_syst_id | |
| + aliases: | |
| + - cooling system identifier | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: unique identifier | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The cooling system identifier | |
| + title: cooling system identifier | |
| + examples: | |
| + - value: '12345' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000785 | |
| + multivalued: false | |
| + range: text value | |
| + crop_rotation: | |
| + name: crop_rotation | |
| + aliases: | |
| + - history/crop rotation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: crop rotation status;schedule | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Whether or not crop is rotated, and if yes, rotation schedule | |
| + title: history/crop rotation | |
| + examples: | |
| + - value: yes;R2/2017-01-01/2018-12-31/P6M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{boolean};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000318 | |
| + multivalued: false | |
| + range: text value | |
| + cult_root_med: | |
| + name: cult_root_med | |
| + aliases: | |
| + - culture rooting medium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name, PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name or reference for the hydroponic or in vitro culture rooting | |
| + medium; can be the name of a commonly used medium or reference to a specific | |
| + medium, e.g. Murashige and Skoog medium. If the medium has not been formally | |
| + published, use the rooting medium descriptors. | |
| + title: culture rooting medium | |
| + examples: | |
| + - value: http://himedialabs.com/TD/PT158.pdf | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}|{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0001041 | |
| + multivalued: false | |
| + range: text value | |
| + cur_land_use: | |
| + name: cur_land_use | |
| + aliases: | |
| + - current land use | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Present state of sample site | |
| + title: current land use | |
| + examples: | |
| + - value: conifers | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001080 | |
| + multivalued: false | |
| + range: text value | |
| + cur_vegetation: | |
| + name: cur_vegetation | |
| + aliases: | |
| + - current vegetation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: current vegetation type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Vegetation classification from one or more standard classification | |
| + systems, or agricultural crop | |
| + title: current vegetation | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000312 | |
| + multivalued: false | |
| + range: text value | |
| + cur_vegetation_meth: | |
| + name: cur_vegetation_meth | |
| + aliases: | |
| + - current vegetation method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in vegetation classification | |
| + title: current vegetation method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000314 | |
| + multivalued: false | |
| + range: text value | |
| + date_last_rain: | |
| + name: date_last_rain | |
| + aliases: | |
| + - date last rain | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The date of the last time it rained | |
| + title: date last rain | |
| + examples: | |
| + - value: 2018-05-11:T14:30Z | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000786 | |
| + multivalued: false | |
| + range: timestamp value | |
| + density: | |
| + name: density | |
| + aliases: | |
| + - density | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per cubic meter, gram per cubic centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Density of the sample, which is its mass per unit volume (aka volumetric | |
| + mass density) | |
| + title: density | |
| + examples: | |
| + - value: 1000 kilogram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000435 | |
| + multivalued: false | |
| + range: quantity value | |
| + depos_env: | |
| + name: depos_env | |
| + aliases: | |
| + - depositional environment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). | |
| + If "other" is specified, please propose entry in "additional info" field | |
| + title: depositional environment | |
| + examples: | |
| + - value: Continental - Alluvial | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000992 | |
| + multivalued: false | |
| + range: text value | |
| + depth: | |
| + name: depth | |
| + aliases: | |
| + - depth | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + description: The vertical distance below local surface, e.g. for sediment or soil | |
| + samples depth is measured from sediment or soil surface, respectively. Depth | |
| + can be reported as an interval for subsurface samples. | |
| + title: depth | |
| + examples: | |
| + - value: 10 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000018 | |
| + multivalued: false | |
| + range: quantity value | |
| + dew_point: | |
| + name: dew_point | |
| + aliases: | |
| + - dew point | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The temperature to which a given parcel of humid air must be cooled, | |
| + at constant barometric pressure, for water vapor to condense into water. | |
| + title: dew point | |
| + examples: | |
| + - value: 22 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000129 | |
| + multivalued: false | |
| + range: quantity value | |
| + diether_lipids: | |
| + name: diether_lipids | |
| + aliases: | |
| + - diether lipids | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: diether lipid name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: nanogram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of diether lipids; can include multiple types of diether | |
| + lipids | |
| + title: diether lipids | |
| + examples: | |
| + - value: 0.2 nanogram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000178 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_carb_dioxide: | |
| + name: diss_carb_dioxide | |
| + aliases: | |
| + - dissolved carbon dioxide | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved carbon dioxide in the sample or liquid | |
| + portion of the sample | |
| + title: dissolved carbon dioxide | |
| + examples: | |
| + - value: 5 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000436 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_hydrogen: | |
| + name: diss_hydrogen | |
| + aliases: | |
| + - dissolved hydrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved hydrogen | |
| + title: dissolved hydrogen | |
| + examples: | |
| + - value: 0.3 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000179 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_inorg_carb: | |
| + name: diss_inorg_carb | |
| + aliases: | |
| + - dissolved inorganic carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Dissolved inorganic carbon concentration in the sample, typically | |
| + measured after filtering the sample using a 0.45 micrometer filter | |
| + title: dissolved inorganic carbon | |
| + examples: | |
| + - value: 2059 micromole per kilogram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000434 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_inorg_nitro: | |
| + name: diss_inorg_nitro | |
| + aliases: | |
| + - dissolved inorganic nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved inorganic nitrogen | |
| + title: dissolved inorganic nitrogen | |
| + examples: | |
| + - value: 761 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000698 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_inorg_phosp: | |
| + name: diss_inorg_phosp | |
| + aliases: | |
| + - dissolved inorganic phosphorus | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved inorganic phosphorus in the sample | |
| + title: dissolved inorganic phosphorus | |
| + examples: | |
| + - value: 56.5 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000106 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_iron: | |
| + name: diss_iron | |
| + aliases: | |
| + - dissolved iron | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved iron in the sample | |
| + title: dissolved iron | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000139 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_org_carb: | |
| + name: diss_org_carb | |
| + aliases: | |
| + - dissolved organic carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved organic carbon in the sample, liquid portion | |
| + of the sample, or aqueous phase of the fluid | |
| + title: dissolved organic carbon | |
| + examples: | |
| + - value: 197 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000433 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_org_nitro: | |
| + name: diss_org_nitro | |
| + aliases: | |
| + - dissolved organic nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Dissolved organic nitrogen concentration measured as; total dissolved | |
| + nitrogen - NH4 - NO3 - NO2 | |
| + title: dissolved organic nitrogen | |
| + examples: | |
| + - value: 0.05 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000162 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_oxygen: | |
| + name: diss_oxygen | |
| + aliases: | |
| + - dissolved oxygen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per kilogram, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved oxygen | |
| + title: dissolved oxygen | |
| + examples: | |
| + - value: 175 micromole per kilogram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000119 | |
| + multivalued: false | |
| + range: quantity value | |
| + diss_oxygen_fluid: | |
| + name: diss_oxygen_fluid | |
| + aliases: | |
| + - dissolved oxygen in fluids | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per kilogram, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of dissolved oxygen in the oil field produced fluids | |
| + as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). | |
| + title: dissolved oxygen in fluids | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000438 | |
| + multivalued: false | |
| + range: quantity value | |
| + door_comp_type: | |
| + name: door_comp_type | |
| + aliases: | |
| + - door type, composite | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The composite type of the door | |
| + title: door type, composite | |
| + examples: | |
| + - value: revolving | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000795 | |
| + multivalued: false | |
| + range: text value | |
| + door_cond: | |
| + name: door_cond | |
| + aliases: | |
| + - door condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The phsical condition of the door | |
| + title: door condition | |
| + examples: | |
| + - value: new | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000788 | |
| + multivalued: false | |
| + range: text value | |
| + door_direct: | |
| + name: door_direct | |
| + aliases: | |
| + - door direction of opening | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The direction the door opens | |
| + title: door direction of opening | |
| + examples: | |
| + - value: inward | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000789 | |
| + multivalued: false | |
| + range: text value | |
| + door_loc: | |
| + name: door_loc | |
| + aliases: | |
| + - door location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The relative location of the door in the room | |
| + title: door location | |
| + examples: | |
| + - value: north | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000790 | |
| + multivalued: false | |
| + range: text value | |
| + door_mat: | |
| + name: door_mat | |
| + aliases: | |
| + - door material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The material the door is composed of | |
| + title: door material | |
| + examples: | |
| + - value: wood | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000791 | |
| + multivalued: false | |
| + range: text value | |
| + door_move: | |
| + name: door_move | |
| + aliases: | |
| + - door movement | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of movement of the door | |
| + title: door movement | |
| + examples: | |
| + - value: swinging | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000792 | |
| + multivalued: false | |
| + range: text value | |
| + door_size: | |
| + name: door_size | |
| + aliases: | |
| + - door area or size | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The size of the door | |
| + title: door area or size | |
| + examples: | |
| + - value: 2.5 square meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000158 | |
| + multivalued: false | |
| + range: quantity value | |
| + door_type: | |
| + name: door_type | |
| + aliases: | |
| + - door type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of door material | |
| + title: door type | |
| + examples: | |
| + - value: wooden | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000794 | |
| + multivalued: false | |
| + range: text value | |
| + door_type_metal: | |
| + name: door_type_metal | |
| + aliases: | |
| + - door type, metal | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of metal door | |
| + title: door type, metal | |
| + examples: | |
| + - value: hollow | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000796 | |
| + multivalued: false | |
| + range: text value | |
| + door_type_wood: | |
| + name: door_type_wood | |
| + aliases: | |
| + - door type, wood | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of wood door | |
| + title: door type, wood | |
| + examples: | |
| + - value: battened | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000797 | |
| + multivalued: false | |
| + range: text value | |
| + door_water_mold: | |
| + name: door_water_mold | |
| + aliases: | |
| + - door signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew on a door | |
| + title: door signs of water/mold | |
| + examples: | |
| + - value: presence of mold visible | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[presence of mold visible|no presence of mold visible]' | |
| + slot_uri: MIXS:0000793 | |
| + multivalued: false | |
| + range: text value | |
| + down_par: | |
| + name: down_par | |
| + aliases: | |
| + - downward PAR | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microEinstein per square meter per second, microEinstein per square | |
| + centimeter per second | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Visible waveband radiance and irradiance measurements in the water | |
| + column | |
| + title: downward PAR | |
| + examples: | |
| + - value: 28.71 microEinstein per square meter per second | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000703 | |
| + multivalued: false | |
| + range: quantity value | |
| + drainage_class: | |
| + name: drainage_class | |
| + aliases: | |
| + - drainage classification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Drainage classification from a standard system such as the USDA system | |
| + title: drainage classification | |
| + examples: | |
| + - value: well | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001085 | |
| + multivalued: false | |
| + range: text value | |
| + drawings: | |
| + name: drawings | |
| + aliases: | |
| + - drawings | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The buildings architectural drawings; if design is chosen, indicate | |
| + phase-conceptual, schematic, design development, and construction documents | |
| + title: drawings | |
| + examples: | |
| + - value: sketch | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000798 | |
| + multivalued: false | |
| + range: text value | |
| + efficiency_percent: | |
| + name: efficiency_percent | |
| + aliases: | |
| + - efficiency percent | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Percentage of volatile solids removed from the anaerobic digestor | |
| + title: efficiency percent | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000657 | |
| + multivalued: false | |
| + range: quantity value | |
| + elev: | |
| + name: elev | |
| + aliases: | |
| + - elevation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + description: Elevation of the sampling site is its height above a fixed reference | |
| + point, most commonly the mean sea level. Elevation is mainly used when referring | |
| + to points on the earth's surface, while altitude is used for points above the | |
| + surface, such as an aircraft in flight or a spacecraft in orbit. | |
| + title: elevation | |
| + examples: | |
| + - value: 100 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000093 | |
| + multivalued: false | |
| + range: quantity value | |
| + elevator: | |
| + name: elevator | |
| + aliases: | |
| + - elevator count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of elevators within the built structure | |
| + title: elevator count | |
| + examples: | |
| + - value: '2' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000799 | |
| + multivalued: false | |
| + range: text value | |
| + emulsions: | |
| + name: emulsions | |
| + aliases: | |
| + - emulsions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: emulsion name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Amount or concentration of substances such as paints, adhesives, | |
| + mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion | |
| + types | |
| + title: emulsions | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000660 | |
| + multivalued: false | |
| + range: quantity value | |
| env_broad_scale: | |
| - aliases: | |
| - - broad-scale environmental context | |
| - description: >- | |
| - In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVOUs biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:env_broad_scale | |
| - in_subset: | |
| - - environment | |
| - | |
| + name: env_broad_scale | |
| + aliases: | |
| + - broad-scale environmental context | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: The major environment type(s) where the sample was collected. Recommend | |
| + subclasses of biome [ENVO:00000428]. Multiple terms can be separated by | |
| + one or more pipes. | |
| + description: 'Report the major environmental system the sample or specimen came | |
| + from. The system(s) identified should have a coarse spatial grain, to provide | |
| + the general environmental context of where the sampling was done (e.g. in the | |
| + desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. | |
| + EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' | |
| + title: broad-scale environmental context | |
| + examples: | |
| + - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water | |
| + sample from the photic zone in middle of the Atlantic Ocean | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000012 | |
| + multivalued: false | |
| + range: controlled term value | |
| env_local_scale: | |
| - aliases: | |
| - - local environmental context | |
| - description: >- | |
| - In this field, report the entity or entities which are in your sample or specimenUs local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:env_local_scale | |
| - in_subset: | |
| - - environment | |
| - | |
| + name: env_local_scale | |
| + aliases: | |
| + - local environmental context | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: Environmental entities having causal influences upon the entity at | |
| + time of sampling. | |
| + description: 'Report the entity or entities which are in the sample or specimen’s | |
| + local vicinity and which you believe have significant causal influences on your | |
| + sample or specimen. We recommend using EnvO terms which are of smaller spatial | |
| + grain than your entry for env_broad_scale. Terms, such as anatomical sites, | |
| + from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) | |
| + are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.' | |
| + title: local environmental context | |
| + examples: | |
| + - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from | |
| + various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb | |
| + and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub | |
| + layer [ENVO:01000336].' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000013 | |
| + multivalued: false | |
| + range: controlled term value | |
| env_medium: | |
| - aliases: | |
| - - environmental medium | |
| - description: >- | |
| - In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVOUs environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:env_medium | |
| - in_subset: | |
| - - environment | |
| - | |
| - env_package: | |
| - aliases: | |
| - - environmental package | |
| - description: >- | |
| - MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc environment|plant-associated|sediment|soil|wastewater/sludge|water] | |
| - pattern: "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]" | |
| - mappings: | |
| - - mixs:env_package | |
| - in_subset: | |
| - - mixs extension | |
| - | |
| - subspecf_gen_lin: | |
| - aliases: | |
| - - subspecific genetic lineage | |
| - description: >- | |
| - This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123 | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {rank name}:{text} | |
| - mappings: | |
| - - mixs:subspecf_gen_lin | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - ploidy: | |
| - aliases: | |
| - - ploidy | |
| - description: >- | |
| - The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:ploidy | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - num_replicons: | |
| - aliases: | |
| - - number of replicons | |
| - description: >- | |
| - Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:num_replicons | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - extrachrom_elements: | |
| - aliases: | |
| - - extrachromosomal elements | |
| - description: >- | |
| - Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:extrachrom_elements | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - estimated_size: | |
| - aliases: | |
| - - estimated size | |
| - description: >- | |
| - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} bp | |
| - mappings: | |
| - - mixs:estimated_size | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - ref_biomaterial: | |
| - aliases: | |
| - - reference for biomaterial | |
| - description: >- | |
| - Primary publication if isolated before genome publication; otherwise, primary genome report | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:ref_biomaterial | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - source_mat_id: | |
| - aliases: | |
| - - source material identifiers | |
| - description: >- | |
| - A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:source_mat_id | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - pathogenicity: | |
| - aliases: | |
| - - known pathogenicity | |
| - description: >- | |
| - To what is the entity pathogenic | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:pathogenicity | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - biotic_relationship: | |
| - aliases: | |
| - - observed biotic relationship | |
| - description: >- | |
| - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [free living|parasitism|commensalism|symbiotic|mutualism] | |
| - pattern: "[free living|parasitism|commensalism|symbiotic|mutualism]" | |
| - mappings: | |
| - - mixs:biotic_relationship | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - specific_host: | |
| - aliases: | |
| - - specific host | |
| - description: >- | |
| - If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {NCBI taxid}|{text} | |
| - mappings: | |
| - - mixs:specific_host | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - host_spec_range: | |
| - aliases: | |
| - - host specificity or range | |
| - description: >- | |
| - The NCBI taxonomy identifier of the specific host if it is known | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:host_spec_range | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - health_disease_stat: | |
| - aliases: | |
| - - health or disease status of specific host at time of collection | |
| - description: >- | |
| - Health or disease status of specific host at time of collection | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing condition|pathological|life threatening|congenital] | |
| - pattern: "[healthy|diseased|dead|disease\\-free|undetermined|recovering|resolving|pre\\-existing condition|pathological|life threatening|congenital]" | |
| - mappings: | |
| - - mixs:health_disease_stat | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - trophic_level: | |
| - aliases: | |
| - - trophic level | |
| - description: >- | |
| - Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph] | |
| - pattern: "[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]" | |
| - mappings: | |
| - - mixs:trophic_level | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - propagation: | |
| - aliases: | |
| - - propagation | |
| - description: >- | |
| - This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:propagation | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - encoded_traits: | |
| - aliases: | |
| - - encoded traits | |
| - description: >- | |
| - Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:encoded_traits | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - rel_to_oxygen: | |
| - aliases: | |
| - - relationship to oxygen | |
| - description: >- | |
| - Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe] | |
| - pattern: "[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]" | |
| - mappings: | |
| - - mixs:rel_to_oxygen | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - isol_growth_condt: | |
| - aliases: | |
| - - isolation and growth condition | |
| - description: >- | |
| - Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:isol_growth_condt | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - samp_collect_device: | |
| - aliases: | |
| - - sample collection device or method | |
| - description: >- | |
| - The method or device employed for collecting the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:samp_collect_device | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - samp_mat_process: | |
| - aliases: | |
| - - sample material processing | |
| - description: >- | |
| - Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {text}|{termLabel} {[termID]} | |
| - mappings: | |
| - - mixs:samp_mat_process | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - size_frac: | |
| - aliases: | |
| - - size fraction selected | |
| - description: >- | |
| - Filtering pore size used in sample preparation | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float}-{float} {unit} | |
| - pattern: "\\d+[.\\d+]\\-\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float}-{float} {unit}" | |
| - mappings: | |
| - - mixs:size_frac | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - samp_size: | |
| - aliases: | |
| - - amount or size of sample collected | |
| - description: >- | |
| - Amount or size of sample (volume, mass or area) that was collected | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_size | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - source_uvig: | |
| - aliases: | |
| - - source of UViGs | |
| - description: >- | |
| - Type of dataset from which the UViG was obtained | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other] | |
| - pattern: "[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence\\-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence\\-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]" | |
| - mappings: | |
| - - mixs:source_uvig | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - virus_enrich_appr: | |
| - aliases: | |
| - - virus enrichment approach | |
| - description: >- | |
| - List of approaches used to enrich the sample for viruses, if any | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none] | |
| - pattern: "[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]" | |
| - mappings: | |
| - - mixs:virus_enrich_appr | |
| - in_subset: | |
| - - nucleic acid sequence source | |
| - | |
| - nucl_acid_ext: | |
| - aliases: | |
| - - nucleic acid extraction | |
| - description: >- | |
| - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:nucl_acid_ext | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - nucl_acid_amp: | |
| - aliases: | |
| - - nucleic acid amplification | |
| - description: >- | |
| - A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:nucl_acid_amp | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - lib_size: | |
| - aliases: | |
| - - library size | |
| - description: >- | |
| - Total number of clones in the library prepared for the project | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:lib_size | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - lib_reads_seqd: | |
| - aliases: | |
| - - library reads sequenced | |
| - description: >- | |
| - Total number of clones sequenced from the library | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:lib_reads_seqd | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - lib_layout: | |
| - aliases: | |
| - - library layout | |
| - description: >- | |
| - Specify whether to expect single, paired, or other configuration of reads | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [paired|single|vector|other] | |
| - pattern: "[paired|single|vector|other]" | |
| - mappings: | |
| - - mixs:lib_layout | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - lib_vector: | |
| - aliases: | |
| - - library vector | |
| - description: >- | |
| - Cloning vector type(s) used in construction of libraries | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:lib_vector | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - lib_screen: | |
| - aliases: | |
| - - library screening strategy | |
| - description: >- | |
| - Specific enrichment or screening methods applied before and/or after creating libraries | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:lib_screen | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - target_gene: | |
| - aliases: | |
| - - target gene | |
| - description: >- | |
| - Targeted gene or locus name for marker gene studies | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:target_gene | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - target_subfragment: | |
| - aliases: | |
| - - target subfragment | |
| - description: >- | |
| - Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:target_subfragment | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - pcr_primers: | |
| - aliases: | |
| - - pcr primers | |
| - description: >- | |
| - PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: FWD:{dna};REV:{dna} | |
| - mappings: | |
| - - mixs:pcr_primers | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - mid: | |
| - aliases: | |
| - - multiplex identifiers | |
| - description: >- | |
| - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {dna} | |
| - mappings: | |
| - - mixs:mid | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - adapters: | |
| - aliases: | |
| - - adapters | |
| - description: >- | |
| - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {dna};{dna} | |
| - mappings: | |
| - - mixs:adapters | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - pcr_cond: | |
| - aliases: | |
| - - pcr conditions | |
| - description: >- | |
| - Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles | |
| - pattern: "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles" | |
| - mappings: | |
| - - mixs:pcr_cond | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - seq_meth: | |
| - aliases: | |
| - - sequencing method | |
| - description: >- | |
| - Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [MinION|GridION|PromethION|454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiSeq 4000|Illumina HiSeq 3000|Illumina HiSeq 2500|Illumina HiSeq 2000|Illumina HiSeq 1500|Illumina HiSeq 1000|Illumina HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD PI System|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB 5500xl-W Genetic Analysis System|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|PacBio RS|PacBio RS II|Sequel|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|BGISEQ-500] | |
| - pattern: "[MinION|GridION|PromethION|454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiSeq 4000|Illumina HiSeq 3000|Illumina HiSeq 2500|Illumina HiSeq 2000|Illumina HiSeq 1500|Illumina HiSeq 1000|Illumina HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD PI System|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB 5500xl\\-W Genetic Analysis System|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|PacBio RS|PacBio RS II|Sequel|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|BGISEQ\\-500]" | |
| - mappings: | |
| - - mixs:seq_meth | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - seq_quality_check: | |
| - aliases: | |
| - - sequence quality check | |
| - description: >- | |
| - Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [none|manually edited] | |
| - pattern: "[none|manually edited]" | |
| - mappings: | |
| - - mixs:seq_quality_check | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - chimera_check: | |
| - aliases: | |
| - - chimera check | |
| - description: >- | |
| - A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:chimera_check | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - tax_ident: | |
| - aliases: | |
| - - taxonomic identity marker | |
| - description: >- | |
| - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [16S rRNA gene|multi-marker approach|other] | |
| - pattern: "[16S rRNA gene|multi\\-marker approach|other]" | |
| - mappings: | |
| - - mixs:tax_ident | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - assembly_qual: | |
| - aliases: | |
| - - assembly quality | |
| - description: >- | |
| - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 3 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality draft genome|Genome fragment(s)] | |
| - pattern: "[Finished genome|High\\-quality draft genome|Medium\\-quality draft genome|Low\\-quality draft genome|Genome fragment(s)]" | |
| - mappings: | |
| - - mixs:assembly_qual | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - assembly_name: | |
| - aliases: | |
| - - assembly name | |
| - description: >- | |
| - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} {text} | |
| - mappings: | |
| - - mixs:assembly_name | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - assembly_software: | |
| - aliases: | |
| - - assembly software | |
| - description: >- | |
| - Tool(s) used for assembly, including version number and parameters | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:assembly_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - annot: | |
| - aliases: | |
| - - annotation | |
| - description: >- | |
| - Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:annot | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - number_contig: | |
| - aliases: | |
| - - number of contigs | |
| - description: >- | |
| - Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:number_contig | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - feat_pred: | |
| - aliases: | |
| - - feature prediction | |
| - description: >- | |
| - Method used to predict UViGs features such as ORFs, integration site, etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:feat_pred | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - ref_db: | |
| - aliases: | |
| - - reference database(s) | |
| - description: >- | |
| - List of database(s) used for ORF annotation, along with version number and reference to website or publication | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {database};{version};{reference} | |
| - mappings: | |
| - - mixs:ref_db | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - sim_search_meth: | |
| - aliases: | |
| - - similarity search method | |
| - description: >- | |
| - Tool used to compare ORFs with database, along with version and cutoffs used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:sim_search_meth | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - tax_class: | |
| - aliases: | |
| - - taxonomic classification | |
| - description: >- | |
| - Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:tax_class | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - _16s_recover: | |
| - aliases: | |
| - - 16S recovered | |
| - description: >- | |
| - Can a 16S gene be recovered from the submitted SAG or MAG? | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:_16s_recover | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - _16s_recover_software: | |
| - aliases: | |
| - - 16S recovery software | |
| - description: >- | |
| - Tools used for 16S rRNA gene extraction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:_16s_recover_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - trnas: | |
| - aliases: | |
| - - number of standard tRNAs extracted | |
| - description: >- | |
| - The total number of tRNAs identified from the SAG or MAG | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:trnas | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - trna_ext_software: | |
| - aliases: | |
| - - tRNA extraction software | |
| - description: >- | |
| - Tools used for tRNA identification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:trna_ext_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - compl_score: | |
| - aliases: | |
| - - completeness score | |
| - description: >- | |
| - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [high|med|low];{percentage} | |
| - mappings: | |
| - - mixs:compl_score | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - compl_software: | |
| - aliases: | |
| - - completeness software | |
| - description: >- | |
| - Tools used for completion estimate, i.e. checkm, anvi'o, busco | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version} | |
| - mappings: | |
| - - mixs:compl_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - compl_appr: | |
| - aliases: | |
| - - completeness approach | |
| - description: >- | |
| - The approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [marker gene|reference based|other] | |
| - pattern: "[marker gene|reference based|other]" | |
| - mappings: | |
| - - mixs:compl_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - contam_score: | |
| - aliases: | |
| - - contamination score | |
| - description: >- | |
| - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {float} percentage | |
| - pattern: "\\d+[.\\d+] percentage" | |
| - mappings: | |
| - - mixs:contam_score | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - contam_screen_input: | |
| - aliases: | |
| - - contamination screening input | |
| - description: >- | |
| - The type of sequence data used as input | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [reads| contigs] | |
| - pattern: "[reads| contigs]" | |
| - mappings: | |
| - - mixs:contam_screen_input | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - contam_screen_param: | |
| - aliases: | |
| - - contamination screening parameters | |
| - description: >- | |
| - Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [ref db|kmer|coverage|combination];{text|integer} | |
| - mappings: | |
| - - mixs:contam_screen_param | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - decontam_software: | |
| - aliases: | |
| - - decontamination software | |
| - description: >- | |
| - Tool(s) used in contamination screening | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [checkm/refinem|anvi'o|prodege|bbtools:decontaminate.sh|acdc|combination] | |
| - pattern: "[checkm\\/refinem|anvi\\'o|prodege|bbtools:decontaminate.sh|acdc|combination]" | |
| - mappings: | |
| - - mixs:decontam_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - sort_tech: | |
| - aliases: | |
| - - sorting technology | |
| - description: >- | |
| - Method used to sort/isolate cells or particles of interest | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other] | |
| - pattern: "[flow cytometric cell sorting|microfluidics|lazer\\-tweezing|optical manipulation|micromanipulation|other]" | |
| - mappings: | |
| - - mixs:sort_tech | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - single_cell_lysis_appr: | |
| - aliases: | |
| - - single cell or viral particle lysis approach | |
| - description: >- | |
| - Method used to free DNA from interior of the cell(s) or particle(s) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [chemical|enzymatic|physical|combination] | |
| - pattern: "[chemical|enzymatic|physical|combination]" | |
| - mappings: | |
| - - mixs:single_cell_lysis_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - single_cell_lysis_prot: | |
| - aliases: | |
| - - single cell or viral particle lysis kit protocol | |
| - description: >- | |
| - Name of the kit or standard protocol used for cell(s) or particle(s) lysis | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:single_cell_lysis_prot | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - wga_amp_appr: | |
| - aliases: | |
| - - WGA amplification approach | |
| - description: >- | |
| - Method used to amplify genomic DNA in preparation for sequencing | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [pcr based|mda based] | |
| - pattern: "[pcr based|mda based]" | |
| - mappings: | |
| - - mixs:wga_amp_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - wga_amp_kit: | |
| - aliases: | |
| - - WGA amplification kit | |
| - description: >- | |
| - Kit used to amplify genomic DNA in preparation for sequencing | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:wga_amp_kit | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - bin_param: | |
| - aliases: | |
| - - binning parameters | |
| - description: >- | |
| - The parameters that have been applied during the extraction of genomes from metagenomic datasets | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [homology search|kmer|coverage|codon usage|combination] | |
| - pattern: "[homology search|kmer|coverage|codon usage|combination]" | |
| - mappings: | |
| - - mixs:bin_param | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - bin_software: | |
| - aliases: | |
| - - binning software | |
| - description: >- | |
| - Tool(s) used for the extraction of genomes from metagenomic datasets | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [metabat|maxbin|concoct|groupm|esom|metawatt|combination|other] | |
| - pattern: "[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]" | |
| - mappings: | |
| - - mixs:bin_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - reassembly_bin: | |
| - aliases: | |
| - - reassembly post binning | |
| - description: >- | |
| - Has an assembly been performed on a genome bin extracted from a metagenomic assembly? | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:reassembly_bin | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - mag_cov_software: | |
| - aliases: | |
| - - MAG coverage software | |
| - description: >- | |
| - Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [bwa|bbmap|bowtie|other] | |
| - pattern: "[bwa|bbmap|bowtie|other]" | |
| - mappings: | |
| - - mixs:mag_cov_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - vir_ident_software: | |
| - aliases: | |
| - - viral identification software | |
| - description: >- | |
| - Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:vir_ident_software | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - pred_genome_type: | |
| - aliases: | |
| - - predicted genome type | |
| - description: >- | |
| - Type of genome predicted for the UViG | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized] | |
| - pattern: "[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (\\-)|mixed|uncharacterized]" | |
| - mappings: | |
| - - mixs:pred_genome_type | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - pred_genome_struc: | |
| - aliases: | |
| - - predicted genome structure | |
| - description: >- | |
| - Expected structure of the viral genome | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [segmented|non-segmented|undetermined] | |
| - pattern: "[segmented|non\\-segmented|undetermined]" | |
| - mappings: | |
| - - mixs:pred_genome_struc | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - detec_type: | |
| - aliases: | |
| - - detection type | |
| - description: >- | |
| - Type of UViG detection | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [independent sequence (UViG)|provirus (UpViG)] | |
| - pattern: "[independent sequence (UViG)|provirus (UpViG)]" | |
| - mappings: | |
| - - mixs:detec_type | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - votu_class_appr: | |
| - aliases: | |
| - - vOTU classification approach | |
| - description: >- | |
| - Cutoffs and approach used when clustering new UViGs in Rspecies-levelS vOTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside vOTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {ANI cutoff};{AF cutoff};{clustering method} | |
| - mappings: | |
| - - mixs:votu_class_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - votu_seq_comp_appr: | |
| - aliases: | |
| - - vOTU sequence comparison approach | |
| - description: >- | |
| - Tool and thresholds used to compare sequences when computing 'species-level' vOTUs | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {software};{version};{parameters} | |
| - mappings: | |
| - - mixs:votu_seq_comp_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - votu_db: | |
| - aliases: | |
| - - vOTU database | |
| - description: >- | |
| - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in 'species-level' vOTUs, if any | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {database};{version} | |
| - mappings: | |
| - - mixs:votu_db | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - host_pred_appr: | |
| - aliases: | |
| - - host prediction approach | |
| - description: >- | |
| - Tool or approach used for host prediction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co-occurrence|combination|other] | |
| - pattern: "[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co\\-occurrence|combination|other]" | |
| - mappings: | |
| - - mixs:host_pred_appr | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - host_pred_est_acc: | |
| - aliases: | |
| - - host prediction estimated accuracy | |
| - description: >- | |
| - For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_pred_est_acc | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - mixs_url: | |
| - aliases: | |
| - - relevant electronic resources | |
| - description: >- | |
| - | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {URL} | |
| - mappings: | |
| - - mixs:mixs_url | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - sop: | |
| - aliases: | |
| - - relevant standard operating procedures | |
| - description: >- | |
| - Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:sop | |
| - in_subset: | |
| - - sequencing | |
| - | |
| - barometric_press: | |
| - aliases: | |
| - - barometric pressure | |
| - description: >- | |
| - Force per unit area exerted against a surface by the weight of air above that surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:barometric_press | |
| - | |
| - carb_dioxide: | |
| - aliases: | |
| - - carbon dioxide | |
| - description: >- | |
| - Carbon dioxide (gas) amount or concentration at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:carb_dioxide | |
| - | |
| - carb_monoxide: | |
| - aliases: | |
| - - carbon monoxide | |
| - description: >- | |
| - Carbon monoxide (gas) amount or concentration at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:carb_monoxide | |
| - | |
| - chem_administration: | |
| - aliases: | |
| - - chemical administration | |
| - description: >- | |
| - List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]};{timestamp} | |
| - mappings: | |
| - - mixs:chem_administration | |
| - | |
| - humidity: | |
| - aliases: | |
| - - humidity | |
| - description: >- | |
| - Amount of water vapour in the air, at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:humidity | |
| - | |
| - methane: | |
| - aliases: | |
| - - methane | |
| - description: >- | |
| - Methane (gas) amount or concentration at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:methane | |
| - | |
| - misc_param: | |
| - aliases: | |
| - - miscellaneous parameter | |
| - description: >- | |
| - Any other measurement performed or parameter collected, that is not listed here | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:misc_param | |
| - | |
| - organism_count: | |
| - aliases: | |
| - - organism count | |
| - description: >- | |
| - Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};[qPCR|ATP|MPN|other] | |
| - string_serialization: "{text};{float} {unit};[qPCR|ATP|MPN|other]" | |
| - mappings: | |
| - - mixs:organism_count | |
| - | |
| - oxygen: | |
| - aliases: | |
| - - oxygen | |
| - description: >- | |
| - Oxygen (gas) amount or concentration at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:oxygen | |
| - | |
| - oxy_stat_samp: | |
| - aliases: | |
| - - oxygenation status of sample | |
| - description: >- | |
| - Oxygenation status of sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [aerobic|anaerobic|other] | |
| - pattern: "[aerobic|anaerobic|other]" | |
| - mappings: | |
| - - mixs:oxy_stat_samp | |
| - | |
| - perturbation: | |
| - aliases: | |
| - - perturbation | |
| - description: >- | |
| - Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:perturbation | |
| - | |
| - pollutants: | |
| - aliases: | |
| - - pollutants | |
| - description: >- | |
| - Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:pollutants | |
| - | |
| - resp_part_matter: | |
| - aliases: | |
| - - respirable particulate matter | |
| - description: >- | |
| - Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:resp_part_matter | |
| - | |
| - samp_salinity: | |
| - aliases: | |
| - - sample salinity | |
| - description: >- | |
| - Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_salinity | |
| - | |
| - samp_store_dur: | |
| - aliases: | |
| - - sample storage duration | |
| - description: >- | |
| - Duration for which the sample was stored | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {duration} | |
| - mappings: | |
| - - mixs:samp_store_dur | |
| - | |
| - samp_store_loc: | |
| - aliases: | |
| - - sample storage location | |
| - description: >- | |
| - Location at which sample was stored, usually name of a specific freezer/room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:samp_store_loc | |
| - | |
| - samp_store_temp: | |
| - aliases: | |
| - - sample storage temperature | |
| - description: >- | |
| - Temperature at which sample was stored, e.g. -80 degree Celsius | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_store_temp | |
| - | |
| - samp_vol_we_dna_ext: | |
| - aliases: | |
| - - sample volume or weight for DNA extraction | |
| - description: >- | |
| - Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_vol_we_dna_ext | |
| - | |
| - solar_irradiance: | |
| - aliases: | |
| - - solar irradiance | |
| - description: >- | |
| - The amount of solar energy that arrives at a specific area of a surface during a specific time interval | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:solar_irradiance | |
| - | |
| - temp: | |
| - aliases: | |
| - - temperature | |
| - description: >- | |
| - Temperature of the sample at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:temp | |
| - | |
| - ventilation_rate: | |
| - aliases: | |
| - - ventilation rate | |
| - description: >- | |
| - Ventilation rate of the system in the sampled premises | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:ventilation_rate | |
| - | |
| - ventilation_type: | |
| - aliases: | |
| - - ventilation type | |
| - description: >- | |
| - Ventilation system used in the sampled premises | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:ventilation_type | |
| - | |
| - volatile_org_comp: | |
| - aliases: | |
| - - volatile organic compounds | |
| - description: >- | |
| - Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:volatile_org_comp | |
| - | |
| - wind_direction: | |
| - aliases: | |
| - - wind direction | |
| - description: >- | |
| - Wind direction is the direction from which a wind originates | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:wind_direction | |
| - | |
| - wind_speed: | |
| - aliases: | |
| - - wind speed | |
| - description: >- | |
| - Speed of wind measured at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:wind_speed | |
| - | |
| - surf_material: | |
| - aliases: | |
| - - surface material | |
| - description: >- | |
| - Surface materials at the point of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [concrete|wood|stone|tile|plastic|glass|vinyl|metal|carpet|stainless steel|paint|cinder blocks|hay bales|stucco|adobe] | |
| - pattern: "[concrete|wood|stone|tile|plastic|glass|vinyl|metal|carpet|stainless steel|paint|cinder blocks|hay bales|stucco|adobe]" | |
| - mappings: | |
| - - mixs:surf_material | |
| - | |
| - surf_air_cont: | |
| - aliases: | |
| - - surface-air contaminant | |
| - description: >- | |
| - Contaminant identified on surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [dust|organic matter|particulate matter|volatile organic compounds|biological contaminants|radon|nutrients|biocides] | |
| - pattern: "[dust|organic matter|particulate matter|volatile organic compounds|biological contaminants|radon|nutrients|biocides]" | |
| - mappings: | |
| - - mixs:surf_air_cont | |
| - | |
| - rel_air_humidity: | |
| - aliases: | |
| - - relative air humidity | |
| - description: >- | |
| - Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:rel_air_humidity | |
| - | |
| - abs_air_humidity: | |
| - aliases: | |
| - - absolute air humidity | |
| - description: >- | |
| - Actual mass of water vapor - mh20 - present in the air water vapor mixture | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:abs_air_humidity | |
| - | |
| - surf_humidity: | |
| - aliases: | |
| - - surface humidity | |
| - description: >- | |
| - Surfaces: water activity as a function of air and material moisture | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:surf_humidity | |
| - | |
| - air_temp: | |
| - aliases: | |
| - - air temperature | |
| - description: >- | |
| - Temperature of the air at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:air_temp | |
| - | |
| - surf_temp: | |
| - aliases: | |
| - - surface temperature | |
| - description: >- | |
| - Temperature of the surface at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:surf_temp | |
| - | |
| - surf_moisture_ph: | |
| - aliases: | |
| - - surface moisture pH | |
| - description: >- | |
| - ph measurement of surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:surf_moisture_ph | |
| - | |
| - build_occup_type: | |
| - aliases: | |
| - - building occupancy type | |
| - description: >- | |
| - The primary function for which a building or discrete part of a building is intended to be used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [office|market|restaurant|residence|school|residential|commercial|low rise|high rise|wood framed|office|health care|school|airport|sports complex] | |
| - pattern: "[office|market|restaurant|residence|school|residential|commercial|low rise|high rise|wood framed|office|health care|school|airport|sports complex]" | |
| - mappings: | |
| - - mixs:build_occup_type | |
| - | |
| - surf_moisture: | |
| - aliases: | |
| - - surface moisture | |
| - description: >- | |
| - Water held on a surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:surf_moisture | |
| - | |
| - dew_point: | |
| - aliases: | |
| - - dew point | |
| - description: >- | |
| - The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:dew_point | |
| - | |
| - indoor_space: | |
| - aliases: | |
| - - indoor space | |
| - description: >- | |
| - A distinguishable space within a structure, the purpose for which discrete areas of a building is used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator] | |
| - pattern: "[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]" | |
| - mappings: | |
| - - mixs:indoor_space | |
| - | |
| - indoor_surf: | |
| - aliases: | |
| - - indoor surface | |
| - description: >- | |
| - Type of indoor surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [counter top|window|wall|cabinet|ceiling|door|shelving|vent cover] | |
| - pattern: "[counter top|window|wall|cabinet|ceiling|door|shelving|vent cover]" | |
| - mappings: | |
| - - mixs:indoor_surf | |
| - | |
| - filter_type: | |
| - aliases: | |
| - - filter type | |
| - description: >- | |
| - A device which removes solid particulates or airborne molecular contaminants | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [particulate air filter|chemical air filter|low-MERV pleated media|HEPA|electrostatic|gas-phase or ultraviolet air treatments] | |
| - pattern: "[particulate air filter|chemical air filter|low\\-MERV pleated media|HEPA|electrostatic|gas\\-phase or ultraviolet air treatments]" | |
| - mappings: | |
| - - mixs:filter_type | |
| - | |
| - heat_cool_type: | |
| - aliases: | |
| - - heating and cooling system type | |
| - description: >- | |
| - Methods of conditioning or heating a room or building | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [radiant system|heat pump|forced air system|steam forced heat|wood stove] | |
| - pattern: "[radiant system|heat pump|forced air system|steam forced heat|wood stove]" | |
| - mappings: | |
| - - mixs:heat_cool_type | |
| - | |
| - substructure_type: | |
| - aliases: | |
| - - substructure type | |
| - description: >- | |
| - The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [crawlspace|slab on grade|basement] | |
| - pattern: "[crawlspace|slab on grade|basement]" | |
| - mappings: | |
| - - mixs:substructure_type | |
| - | |
| - building_setting: | |
| - aliases: | |
| - - building setting | |
| - description: >- | |
| - A location (geography) where a building is set | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [urban|suburban|exurban|rural] | |
| - pattern: "[urban|suburban|exurban|rural]" | |
| - mappings: | |
| - - mixs:building_setting | |
| - | |
| - light_type: | |
| - aliases: | |
| - - light type | |
| - description: >- | |
| - Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [natural light|electric light|desk lamp|flourescent lights|natural light|none] | |
| - pattern: "[natural light|electric light|desk lamp|flourescent lights|natural light|none]" | |
| - mappings: | |
| - - mixs:light_type | |
| - | |
| - samp_sort_meth: | |
| - aliases: | |
| - - sample size sorting method | |
| - description: >- | |
| - Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:samp_sort_meth | |
| - | |
| - space_typ_state: | |
| - aliases: | |
| - - space typical state | |
| - description: >- | |
| - Customary or normal state of the space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [typically occupied|typically unoccupied] | |
| - pattern: "[typically occupied|typically unoccupied]" | |
| - mappings: | |
| - - mixs:space_typ_state | |
| - | |
| - typ_occup_density: | |
| - aliases: | |
| - - typical occupant density | |
| - description: >- | |
| - Customary or normal density of occupants | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:typ_occup_density | |
| - | |
| - occup_samp: | |
| - aliases: | |
| - - occupancy at sampling | |
| - description: >- | |
| - Number of occupants present at time of sample within the given space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:occup_samp | |
| - | |
| - occup_density_samp: | |
| - aliases: | |
| - - occupant density at sampling | |
| - description: >- | |
| - Average number of occupants at time of sampling per square footage | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:occup_density_samp | |
| - | |
| - address: | |
| - aliases: | |
| - - address | |
| - description: >- | |
| - The street name and building number where the sampling occurred. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer}{text} | |
| - mappings: | |
| - - mixs:address | |
| - | |
| - adj_room: | |
| - aliases: | |
| - - adjacent rooms | |
| - description: >- | |
| - List of rooms (room number, room name) immediately adjacent to the sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{integer} | |
| - mappings: | |
| - - mixs:adj_room | |
| - | |
| - aero_struc: | |
| - aliases: | |
| - - aerospace structure | |
| - description: >- | |
| - Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [plane|glider] | |
| - pattern: "[plane|glider]" | |
| - mappings: | |
| - - mixs:aero_struc | |
| - | |
| - amount_light: | |
| - aliases: | |
| - - amount of light | |
| - description: >- | |
| - The unit of illuminance and luminous emittance, measuring luminous flux per unit area | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:amount_light | |
| - | |
| - arch_struc: | |
| - aliases: | |
| - - architectural structure | |
| - description: >- | |
| - An architectural structure is a human-made, free-standing, immobile outdoor construction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [building|shed|home] | |
| - pattern: "[building|shed|home]" | |
| - mappings: | |
| - - mixs:arch_struc | |
| - | |
| - avg_occup: | |
| - aliases: | |
| - - average daily occupancy | |
| - description: >- | |
| - Daily average occupancy of room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:avg_occup | |
| - | |
| - avg_dew_point: | |
| - aliases: | |
| - - average dew point | |
| - description: >- | |
| - The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:avg_dew_point | |
| - | |
| - avg_temp: | |
| - aliases: | |
| - - average temperature | |
| - description: >- | |
| - The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:avg_temp | |
| - | |
| - bathroom_count: | |
| - aliases: | |
| - - bathroom count | |
| - description: >- | |
| - The number of bathrooms in the building | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:bathroom_count | |
| - | |
| - bedroom_count: | |
| - aliases: | |
| - - bedroom count | |
| - description: >- | |
| - The number of bedrooms in the building | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:bedroom_count | |
| - | |
| - built_struc_age: | |
| - aliases: | |
| - - built structure age | |
| - description: >- | |
| - The age of the built structure since construction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:built_struc_age | |
| - | |
| - built_struc_set: | |
| - aliases: | |
| - - built structure setting | |
| - description: >- | |
| - The characterization of the location of the built structure as high or low human density | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [urban|rural] | |
| - pattern: "[urban|rural]" | |
| - mappings: | |
| - - mixs:built_struc_set | |
| - | |
| - built_struc_type: | |
| - aliases: | |
| - - built structure type | |
| - description: >- | |
| - A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:built_struc_type | |
| - | |
| - ceil_area: | |
| - aliases: | |
| - - ceiling area | |
| - description: >- | |
| - The area of the ceiling space within the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:ceil_area | |
| - | |
| - ceil_cond: | |
| - aliases: | |
| - - ceiling condition | |
| - description: >- | |
| - The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [new|visible wear|needs repair|damaged|rupture] | |
| - pattern: "[new|visible wear|needs repair|damaged|rupture]" | |
| - mappings: | |
| - - mixs:ceil_cond | |
| - | |
| - ceil_finish_mat: | |
| - aliases: | |
| - - ceiling finish material | |
| - description: >- | |
| - The type of material used to finish a ceiling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral wool/calcium silicate|wood] | |
| - pattern: "[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral wool\\/calcium silicate|wood]" | |
| - mappings: | |
| - - mixs:ceil_finish_mat | |
| - | |
| - ceil_water_mold: | |
| - aliases: | |
| - - ceiling signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew on the ceiling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [presence of mold visible|no presence of mold visible] | |
| - pattern: "[presence of mold visible|no presence of mold visible]" | |
| - mappings: | |
| - - mixs:ceil_water_mold | |
| - | |
| - ceil_struc: | |
| - aliases: | |
| - - ceiling structure | |
| - description: >- | |
| - The construction format of the ceiling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [wood frame|concrete] | |
| - pattern: "[wood frame|concrete]" | |
| - mappings: | |
| - - mixs:ceil_struc | |
| - | |
| - ceil_texture: | |
| - aliases: | |
| - - ceiling texture | |
| - description: >- | |
| - The feel, appearance, or consistency of a ceiling surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl] | |
| - pattern: "[crows feet|crows\\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]" | |
| - mappings: | |
| - - mixs:ceil_texture | |
| - | |
| - ceil_thermal_mass: | |
| - aliases: | |
| - - ceiling thermal mass | |
| - description: >- | |
| - The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:ceil_thermal_mass | |
| - | |
| - ceil_type: | |
| - aliases: | |
| - - ceiling type | |
| - description: >- | |
| - The type of ceiling according to the ceiling's appearance or construction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched] | |
| - pattern: "[cathedral|dropped|concave|barrel\\-shaped|coffered|cove|stretched]" | |
| - mappings: | |
| - - mixs:ceil_type | |
| - | |
| - cool_syst_id: | |
| - aliases: | |
| - - cooling system identifier | |
| - description: >- | |
| - The cooling system identifier | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:cool_syst_id | |
| - | |
| - date_last_rain: | |
| - aliases: | |
| - - date last rain | |
| - description: >- | |
| - The date of the last time it rained | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:date_last_rain | |
| - | |
| - build_docs: | |
| - aliases: | |
| - - "design, construction, and operation documents" | |
| - description: >- | |
| - The building design, construction and operation documents | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [building information model|commissioning report|complaint logs|contract administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop drawings|submittals|ventilation system|windows] | |
| - pattern: "[building information model|commissioning report|complaint logs|contract administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop drawings|submittals|ventilation system|windows] " | |
| - mappings: | |
| - - mixs:build_docs | |
| - | |
| - door_size: | |
| - aliases: | |
| - - door area or size | |
| - description: >- | |
| - The size of the door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:door_size | |
| - | |
| - door_cond: | |
| - aliases: | |
| - - door condition | |
| - description: >- | |
| - The phsical condition of the door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [damaged|needs repair|new|rupture|visible wear] | |
| - pattern: "[damaged|needs repair|new|rupture|visible wear]" | |
| - mappings: | |
| - - mixs:door_cond | |
| - | |
| - door_direct: | |
| - aliases: | |
| - - door direction of opening | |
| - description: >- | |
| - The direction the door opens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [inward|outward|sideways] | |
| - pattern: "[inward|outward|sideways]" | |
| - mappings: | |
| - - mixs:door_direct | |
| - | |
| - door_loc: | |
| - aliases: | |
| - - door location | |
| - description: >- | |
| - The relative location of the door in the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west] | |
| - pattern: "[north|south|east|west]" | |
| - mappings: | |
| - - mixs:door_loc | |
| - | |
| - door_mat: | |
| - aliases: | |
| - - door material | |
| - description: >- | |
| - The material the door is composed of | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic alloy|vinyl|wood|wood/plastic composite] | |
| - pattern: "[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic alloy|vinyl|wood|wood\\/plastic composite]" | |
| - mappings: | |
| - - mixs:door_mat | |
| - | |
| - door_move: | |
| - aliases: | |
| - - door movement | |
| - description: >- | |
| - The type of movement of the door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [collapsible|folding|revolving|rolling shutter|sliding|swinging] | |
| - pattern: "[collapsible|folding|revolving|rolling shutter|sliding|swinging] " | |
| - mappings: | |
| - - mixs:door_move | |
| - | |
| - door_water_mold: | |
| - aliases: | |
| - - door signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew on a door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [presence of mold visible|no presence of mold visible] | |
| - pattern: "[presence of mold visible|no presence of mold visible]" | |
| - mappings: | |
| - - mixs:door_water_mold | |
| - | |
| - door_type: | |
| - aliases: | |
| - - door type | |
| - description: >- | |
| - The type of door material | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [composite|metal|wooden] | |
| - pattern: "[composite|metal|wooden]" | |
| - mappings: | |
| - - mixs:door_type | |
| - | |
| - door_comp_type: | |
| - aliases: | |
| - - "door type, composite" | |
| - description: >- | |
| - The composite type of the door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [metal covered|revolving|sliding|telescopic] | |
| - pattern: "[metal covered|revolving|sliding|telescopic]" | |
| - mappings: | |
| - - mixs:door_comp_type | |
| - | |
| - door_type_metal: | |
| - aliases: | |
| - - "door type, metal" | |
| - description: >- | |
| - The type of metal door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [collapsible|corrugated steel|hollow|rolling shutters|steel plate] | |
| - pattern: "[collapsible|corrugated steel|hollow|rolling shutters|steel plate]" | |
| - mappings: | |
| - - mixs:door_type_metal | |
| - | |
| - door_type_wood: | |
| - aliases: | |
| - - "door type, wood" | |
| - description: >- | |
| - The type of wood door | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: "[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]" | |
| - pattern: "[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]" | |
| - mappings: | |
| - - mixs:door_type_wood | |
| - | |
| - drawings: | |
| - aliases: | |
| - - drawings | |
| - description: >- | |
| - The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [operation|as built|construction|bid|design|building navigation map|diagram|sketch] | |
| - pattern: "[operation|as built|construction|bid|design|building navigation map|diagram|sketch]" | |
| - mappings: | |
| - - mixs:drawings | |
| - | |
| - elevator: | |
| - aliases: | |
| - - elevator count | |
| - description: >- | |
| - The number of elevators within the built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:elevator | |
| - | |
| - escalator: | |
| - aliases: | |
| - - escalator count | |
| - description: >- | |
| - The number of escalators within the built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:escalator | |
| - | |
| - exp_duct: | |
| - aliases: | |
| - - exposed ductwork | |
| - description: >- | |
| - The amount of exposed ductwork in the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:exp_duct | |
| - | |
| - exp_pipe: | |
| - aliases: | |
| - - exposed pipes | |
| - description: >- | |
| - The number of exposed pipes in the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:exp_pipe | |
| - | |
| - ext_door: | |
| - aliases: | |
| - - exterior door count | |
| - description: >- | |
| - The number of exterior doors in the built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:ext_door | |
| - | |
| - fireplace_type: | |
| - aliases: | |
| - - fireplace type | |
| - description: >- | |
| - A firebox with chimney | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [gas burning|wood burning] | |
| - pattern: "[gas burning|wood burning]" | |
| - mappings: | |
| - - mixs:fireplace_type | |
| - | |
| - floor_age: | |
| - aliases: | |
| - - floor age | |
| - description: >- | |
| - The time period since installment of the carpet or flooring | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:floor_age | |
| - | |
| - floor_area: | |
| - aliases: | |
| - - floor area | |
| - description: >- | |
| - The area of the floor space within the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:floor_area | |
| - | |
| - floor_cond: | |
| - aliases: | |
| - - floor condition | |
| - description: >- | |
| - The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [new|visible wear|needs repair|damaged|rupture] | |
| - pattern: "[new|visible wear|needs repair|damaged|rupture]" | |
| - mappings: | |
| - - mixs:floor_cond | |
| - | |
| - floor_count: | |
| - aliases: | |
| - - floor count | |
| - description: >- | |
| - The number of floors in the building, including basements and mechanical penthouse | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:floor_count | |
| - | |
| - floor_finish_mat: | |
| - aliases: | |
| - - floor finish material | |
| - description: >- | |
| - The floor covering type; the finished surface that is walked on | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint] | |
| - pattern: "[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint]" | |
| - mappings: | |
| - - mixs:floor_finish_mat | |
| - | |
| - floor_water_mold: | |
| - aliases: | |
| - - floor signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew in a room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling discoloration|peeling paint or wallpaper|bulging walls|condensation] | |
| - pattern: "[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling discoloration|peeling paint or wallpaper|bulging walls|condensation]" | |
| - mappings: | |
| - - mixs:floor_water_mold | |
| - | |
| - floor_struc: | |
| - aliases: | |
| - - floor structure | |
| - description: >- | |
| - Refers to the structural elements and subfloor upon which the finish flooring is installed | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete] | |
| - pattern: "[balcony|floating floor|glass floor|raised floor|sprung floor|wood\\-framed|concrete]" | |
| - mappings: | |
| - - mixs:floor_struc | |
| - | |
| - floor_thermal_mass: | |
| - aliases: | |
| - - floor thermal mass | |
| - description: >- | |
| - The ability of the floor to provide inertia against temperature fluctuations | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:floor_thermal_mass | |
| - | |
| - freq_clean: | |
| - aliases: | |
| - - frequency of cleaning | |
| - description: >- | |
| - The number of times the building is cleaned per week | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:freq_clean | |
| - | |
| - freq_cook: | |
| - aliases: | |
| - - frequency of cooking | |
| - description: >- | |
| - The number of times a meal is cooked per week | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:freq_cook | |
| - | |
| - furniture: | |
| - aliases: | |
| - - furniture | |
| - description: >- | |
| - The types of furniture present in the sampled room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [cabinet|chair|desks] | |
| - pattern: "[cabinet|chair|desks]" | |
| - mappings: | |
| - - mixs:furniture | |
| - | |
| - gender_restroom: | |
| - aliases: | |
| - - gender of restroom | |
| - description: >- | |
| - The gender type of the restroom | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [male|female] | |
| - pattern: "[male|female]" | |
| - mappings: | |
| - - mixs:gender_restroom | |
| - | |
| - hall_count: | |
| - aliases: | |
| - - hallway/corridor count | |
| - description: >- | |
| - The total count of hallways and cooridors in the built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:hall_count | |
| - | |
| - handidness: | |
| - aliases: | |
| - - handidness | |
| - description: >- | |
| - The handidness of the individual sampled | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [ambidexterity|left handedness|mixed-handedness|right handedness] | |
| - pattern: "[ambidexterity|left handedness|mixed\\-handedness|right handedness]" | |
| - mappings: | |
| - - mixs:handidness | |
| - | |
| - heat_deliv_loc: | |
| - aliases: | |
| - - heating delivery locations | |
| - description: >- | |
| - The location of heat delivery within the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west] | |
| - pattern: "[north|south|east|west]" | |
| - mappings: | |
| - - mixs:heat_deliv_loc | |
| - | |
| - heat_system_deliv_meth: | |
| - aliases: | |
| - - heating system delivery method | |
| - description: >- | |
| - The method by which the heat is delivered through the system | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [conductive|radiant] | |
| - pattern: "[conductive|radiant]" | |
| - mappings: | |
| - - mixs:heat_system_deliv_meth | |
| - | |
| - heat_system_id: | |
| - aliases: | |
| - - heating system identifier | |
| - description: >- | |
| - The heating system identifier | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:heat_system_id | |
| - | |
| - height_carper_fiber: | |
| - aliases: | |
| - - height carpet fiber mat | |
| - description: >- | |
| - The average carpet fiber height in the indoor environment | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:height_carper_fiber | |
| - | |
| - inside_lux: | |
| - aliases: | |
| - - inside lux light | |
| - description: >- | |
| - The recorded value at sampling time (power density) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:inside_lux | |
| - | |
| - int_wall_cond: | |
| - aliases: | |
| - - interior wall condition | |
| - description: >- | |
| - The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [new|visible wear|needs repair|damaged|rupture] | |
| - pattern: "[new|visible wear|needs repair|damaged|rupture]" | |
| - mappings: | |
| - - mixs:int_wall_cond | |
| - | |
| - last_clean: | |
| - aliases: | |
| - - last time swept/mopped/vacuumed | |
| - description: >- | |
| - The last time the floor was cleaned (swept, mopped, vacuumed) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:last_clean | |
| - | |
| - max_occup: | |
| - aliases: | |
| - - maximum occupancy | |
| - description: >- | |
| - The maximum amount of people allowed in the indoor environment | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:max_occup | |
| - | |
| - mech_struc: | |
| - aliases: | |
| - - mechanical structure | |
| - description: >- | |
| - mechanical structure: a moving structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [subway|coach|carriage|elevator|escalator|boat|train|car|bus] | |
| - pattern: "[subway|coach|carriage|elevator|escalator|boat|train|car|bus]" | |
| - mappings: | |
| - - mixs:mech_struc | |
| - | |
| - number_plants: | |
| - aliases: | |
| - - number of houseplants | |
| - description: >- | |
| - The number of plant(s) in the sampling space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:number_plants | |
| - | |
| - number_pets: | |
| - aliases: | |
| - - number of pets | |
| - description: >- | |
| - The number of pets residing in the sampled space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:number_pets | |
| - | |
| - number_resident: | |
| - aliases: | |
| - - number of residents | |
| - description: >- | |
| - The number of individuals currently occupying in the sampling location | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:number_resident | |
| - | |
| - occup_document: | |
| - aliases: | |
| - - occupancy documentation | |
| - description: >- | |
| - The type of documentation of occupancy | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [automated count|estimate|manual count|videos] | |
| - pattern: "[automated count|estimate|manual count|videos]" | |
| - mappings: | |
| - - mixs:occup_document | |
| - | |
| - ext_wall_orient: | |
| - aliases: | |
| - - orientations of exterior wall | |
| - description: >- | |
| - The orientation of the exterior wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west|northeast|southeast|southwest|northwest] | |
| - pattern: "[north|south|east|west|northeast|southeast|southwest|northwest]" | |
| - mappings: | |
| - - mixs:ext_wall_orient | |
| - | |
| - ext_window_orient: | |
| - aliases: | |
| - - orientations of exterior window | |
| - description: >- | |
| - The compass direction the exterior window of the room is facing | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west|northeast|southeast|southwest|northwest] | |
| - pattern: "[north|south|east|west|northeast|southeast|southwest|northwest]" | |
| - mappings: | |
| - - mixs:ext_window_orient | |
| - | |
| - rel_humidity_out: | |
| - aliases: | |
| - - outside relative humidity | |
| - description: >- | |
| - The recorded outside relative humidity value at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:rel_humidity_out | |
| - | |
| - pres_animal: | |
| - aliases: | |
| - - "presence of pets, animals, or insects" | |
| - description: >- | |
| - The number and type of animals present in the sampling space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [cat|dog|rodent|snake|other];{integer} | |
| - mappings: | |
| - - mixs:pres_animal | |
| - | |
| - quad_pos: | |
| - aliases: | |
| - - quadrant position | |
| - description: >- | |
| - The quadrant position of the sampling room within the building | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [North side|West side|South side|East side] | |
| - pattern: "[North side|West side|South side|East side]" | |
| - mappings: | |
| - - mixs:quad_pos | |
| - | |
| - rel_samp_loc: | |
| - aliases: | |
| - - relative sampling location | |
| - description: >- | |
| - The sampling location within the train car | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [edge of car|center of car|under a seat] | |
| - pattern: "[edge of car|center of car|under a seat]" | |
| - mappings: | |
| - - mixs:rel_samp_loc | |
| - | |
| - room_air_exch_rate: | |
| - aliases: | |
| - - room air exchange rate | |
| - description: >- | |
| - The rate at which outside air replaces indoor air in a given space | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:room_air_exch_rate | |
| - | |
| - room_architec_element: | |
| - aliases: | |
| - - room architectural elements | |
| - description: >- | |
| - The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:room_architec_element | |
| - | |
| - room_condt: | |
| - aliases: | |
| - - room condition | |
| - description: >- | |
| - The condition of the room at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew] | |
| - pattern: "[new|visible wear|needs repair|damaged|rupture|visible signs of mold\\/mildew]" | |
| - mappings: | |
| - - mixs:room_condt | |
| - | |
| - room_count: | |
| - aliases: | |
| - - room count | |
| - description: >- | |
| - The total count of rooms in the built structure including all room types | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:room_count | |
| - | |
| - room_dim: | |
| - aliases: | |
| - - room dimensions | |
| - description: >- | |
| - The length, width and height of sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} {unit} x {integer} {unit} x {integer} {unit} | |
| - string_serialization: "{integer} {unit} x {integer} {unit} x {integer} {unit}" | |
| - mappings: | |
| - - mixs:room_dim | |
| - | |
| - room_door_dist: | |
| - aliases: | |
| - - room door distance | |
| - description: >- | |
| - Distance between doors (meters) in the hallway between the sampling room and adjacent rooms | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} {unit} | |
| - string_serialization: "{integer} {unit}" | |
| - mappings: | |
| - - mixs:room_door_dist | |
| - | |
| - room_loc: | |
| - aliases: | |
| - - room location in building | |
| - description: >- | |
| - The position of the room within the building | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [corner room|interior room|exterior wall] | |
| - pattern: "[corner room|interior room|exterior wall]" | |
| - mappings: | |
| - - mixs:room_loc | |
| - | |
| - room_moist_damage_hist: | |
| - aliases: | |
| - - room moisture damage or mold history | |
| - description: >- | |
| - The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:room_moist_damage_hist | |
| - | |
| - room_net_area: | |
| - aliases: | |
| - - room net area | |
| - description: >- | |
| - The net floor area of sampling room. Net area excludes wall thicknesses | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} {unit} | |
| - string_serialization: "{integer} {unit}" | |
| - mappings: | |
| - - mixs:room_net_area | |
| - | |
| - room_occup: | |
| - aliases: | |
| - - room occupancy | |
| - description: >- | |
| - Count of room occupancy at time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:room_occup | |
| - | |
| - room_samp_pos: | |
| - aliases: | |
| - - room sampling position | |
| - description: >- | |
| - The horizontal sampling position in the room relative to architectural elements | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north corner|south corner|west corner|east corner|northeast corner|northwest corner|southeast corner|southwest corner|center] | |
| - pattern: "[north corner|south corner|west corner|east corner|northeast corner|northwest corner|southeast corner|southwest corner|center]" | |
| - mappings: | |
| - - mixs:room_samp_pos | |
| - | |
| - room_type: | |
| - aliases: | |
| - - room type | |
| - description: >- | |
| - The main purpose or activity of the sampling room. A room is any distinguishable space within a structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: "[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse] " | |
| - pattern: "[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]" | |
| - mappings: | |
| - - mixs:room_type | |
| - | |
| - room_vol: | |
| - aliases: | |
| - - room volume | |
| - description: >- | |
| - Volume of sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} {unit} | |
| - string_serialization: "{integer} {unit}" | |
| - mappings: | |
| - - mixs:room_vol | |
| - | |
| - room_window_count: | |
| - aliases: | |
| - - room window count | |
| - description: >- | |
| - Number of windows in the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:room_window_count | |
| - | |
| - room_connected: | |
| - aliases: | |
| - - rooms connected by a doorway | |
| - description: >- | |
| - List of rooms connected to the sampling room by a doorway | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|office|stairwell] | |
| - pattern: "[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|office|stairwell]" | |
| - mappings: | |
| - - mixs:room_connected | |
| - | |
| - room_hallway: | |
| - aliases: | |
| - - rooms that are on the same hallway | |
| - description: >- | |
| - List of room(s) (room number, room name) located in the same hallway as sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{integer} | |
| - mappings: | |
| - - mixs:room_hallway | |
| - | |
| - room_door_share: | |
| - aliases: | |
| - - rooms that share a door with sampling room | |
| - description: >- | |
| - List of room(s) (room number, room name) sharing a door with the sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{integer} | |
| - mappings: | |
| - - mixs:room_door_share | |
| - | |
| - room_wall_share: | |
| - aliases: | |
| - - rooms that share a wall with sampling room | |
| - description: >- | |
| - List of room(s) (room number, room name) sharing a wall with the sampling room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{integer} | |
| - mappings: | |
| - - mixs:room_wall_share | |
| - | |
| - samp_weather: | |
| - aliases: | |
| - - sampling day weather | |
| - description: >- | |
| - The weather on the sampling day | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy] | |
| - pattern: "[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]" | |
| - mappings: | |
| - - mixs:samp_weather | |
| - | |
| - samp_floor: | |
| - aliases: | |
| - - sampling floor | |
| - description: >- | |
| - The floor of the building, where the sampling room is located | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [lobby|basement|1st floor|2nd floor|{integer} floor] | |
| - mappings: | |
| - - mixs:samp_floor | |
| - | |
| - samp_room_id: | |
| - aliases: | |
| - - sampling room ID or name | |
| - description: >- | |
| - Sampling room number. This ID should be consistent with the designations on the building floor plans | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:samp_room_id | |
| - | |
| - samp_time_out: | |
| - aliases: | |
| - - sampling time outside | |
| - description: >- | |
| - The recent and long term history of outside sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:samp_time_out | |
| - | |
| - season: | |
| - aliases: | |
| - - season | |
| - description: >- | |
| - The season when sampling occurred | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Spring|Summer|Fall|Winter] | |
| - pattern: "[Spring|Summer|Fall|Winter]" | |
| - mappings: | |
| - - mixs:season | |
| - | |
| - season_use: | |
| - aliases: | |
| - - seasonal use | |
| - description: >- | |
| - The seasons the space is occupied | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Spring|Summer|Fall|Winter] | |
| - pattern: "[Spring|Summer|Fall|Winter]" | |
| - mappings: | |
| - - mixs:season_use | |
| - | |
| - shading_device_cond: | |
| - aliases: | |
| - - shading device condition | |
| - description: >- | |
| - The physical condition of the shading device at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [damaged|needs repair|new|rupture|visible wear] | |
| - pattern: "[damaged|needs repair|new|rupture|visible wear]" | |
| - mappings: | |
| - - mixs:shading_device_cond | |
| - | |
| - shading_device_loc: | |
| - aliases: | |
| - - shading device location | |
| - description: >- | |
| - The location of the shading device in relation to the built structure | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [exterior|interior] | |
| - pattern: "[exterior|interior]" | |
| - mappings: | |
| - - mixs:shading_device_loc | |
| - | |
| - shading_device_mat: | |
| - aliases: | |
| - - shading device material | |
| - description: >- | |
| - The material the shading device is composed of | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:shading_device_mat | |
| - | |
| - shading_device_water_mold: | |
| - aliases: | |
| - - shading device signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew on the shading device | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [presence of mold visible|no presence of mold visible] | |
| - pattern: "[presence of mold visible|no presence of mold visible]" | |
| - mappings: | |
| - - mixs:shading_device_water_mold | |
| - | |
| - shading_device_type: | |
| - aliases: | |
| - - shading device type | |
| - description: >- | |
| - The type of shading device | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian awning] | |
| - pattern: "[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian awning]" | |
| - mappings: | |
| - - mixs:shading_device_type | |
| - | |
| - specific_humidity: | |
| - aliases: | |
| - - specific humidity | |
| - description: >- | |
| - The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:specific_humidity | |
| - | |
| - specific: | |
| - aliases: | |
| - - specifications | |
| - description: >- | |
| - The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [operation|as built|construction|bid|design|photos] | |
| - pattern: "[operation|as built|construction|bid|design|photos]" | |
| - mappings: | |
| - - mixs:specific | |
| - | |
| - temp_out: | |
| - aliases: | |
| - - temperature outside house | |
| - description: >- | |
| - The recorded temperature value at sampling time outside | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:temp_out | |
| - | |
| - train_line: | |
| - aliases: | |
| - - train line | |
| - description: >- | |
| - The subway line name | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [red|green|orange] | |
| - pattern: "[red|green|orange]" | |
| - mappings: | |
| - - mixs:train_line | |
| - | |
| - train_stat_loc: | |
| - aliases: | |
| - - train station collection location | |
| - description: >- | |
| - The train station collection location | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [south station above ground|south station underground|south station amtrak|forest hills|riverside] | |
| - pattern: "[south station above ground|south station underground|south station amtrak|forest hills|riverside]" | |
| - mappings: | |
| - - mixs:train_stat_loc | |
| - | |
| - train_stop_loc: | |
| - aliases: | |
| - - train stop collection location | |
| - description: >- | |
| - The train stop collection location | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [end|mid|downtown] | |
| - pattern: "[end|mid|downtown]" | |
| - mappings: | |
| - - mixs:train_stop_loc | |
| - | |
| - vis_media: | |
| - aliases: | |
| - - visual media | |
| - description: >- | |
| - The building visual media | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: "[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]" | |
| - pattern: "[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]" | |
| - mappings: | |
| - - mixs:vis_media | |
| - | |
| - wall_area: | |
| - aliases: | |
| - - wall area | |
| - description: >- | |
| - The total area of the sampled room's walls | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:wall_area | |
| - | |
| - wall_const_type: | |
| - aliases: | |
| - - wall construction type | |
| - description: >- | |
| - The building class of the wall defined by the composition of the building elements and fire-resistance rating. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified fire resistive|fire resistive] | |
| - pattern: "[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified fire resistive|fire resistive]" | |
| - mappings: | |
| - - mixs:wall_const_type | |
| - | |
| - wall_finish_mat: | |
| - aliases: | |
| - - wall finish material | |
| - description: >- | |
| - The material utilized to finish the outer most layer of the wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone facing|acoustical treatment|wood|metal|masonry] | |
| - pattern: "[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone facing|acoustical treatment|wood|metal|masonry]" | |
| - mappings: | |
| - - mixs:wall_finish_mat | |
| - | |
| - wall_height: | |
| - aliases: | |
| - - wall height | |
| - description: >- | |
| - The average height of the walls in the sampled room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:wall_height | |
| - | |
| - wall_loc: | |
| - aliases: | |
| - - wall location | |
| - description: >- | |
| - The relative location of the wall within the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west] | |
| - pattern: "[north|south|east|west]" | |
| - mappings: | |
| - - mixs:wall_loc | |
| - | |
| - wall_water_mold: | |
| - aliases: | |
| - - wall signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew on a wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [presence of mold visible|no presence of mold visible] | |
| - pattern: "[presence of mold visible|no presence of mold visible]" | |
| - mappings: | |
| - - mixs:wall_water_mold | |
| - | |
| - wall_surf_treatment: | |
| - aliases: | |
| - - wall surface treatment | |
| - description: >- | |
| - The surface treatment of interior wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [painted|wall paper|no treatment|paneling|stucco|fabric] | |
| - pattern: "[painted|wall paper|no treatment|paneling|stucco|fabric]" | |
| - mappings: | |
| - - mixs:wall_surf_treatment | |
| - | |
| - wall_texture: | |
| - aliases: | |
| - - wall texture | |
| - description: >- | |
| - The feel, appearance, or consistency of a wall surface | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl] | |
| - pattern: "[crows feet|crows\\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]" | |
| - mappings: | |
| - - mixs:wall_texture | |
| - | |
| - wall_thermal_mass: | |
| - aliases: | |
| - - wall thermal mass | |
| - description: >- | |
| - The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:wall_thermal_mass | |
| - | |
| - water_feat_size: | |
| - aliases: | |
| - - water feature size | |
| - description: >- | |
| - The size of the water feature | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:water_feat_size | |
| - | |
| - water_feat_type: | |
| - aliases: | |
| - - water feature type | |
| - description: >- | |
| - The type of water feature present within the building being sampled | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [fountain|pool|standing feature|stream|waterfall] | |
| - pattern: "[fountain|pool|standing feature|stream|waterfall]" | |
| - mappings: | |
| - - mixs:water_feat_type | |
| - | |
| - weekday: | |
| - aliases: | |
| - - weekday | |
| - description: >- | |
| - The day of the week when sampling occurred | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday] | |
| - pattern: "[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]" | |
| - mappings: | |
| - - mixs:weekday | |
| - | |
| - window_size: | |
| - aliases: | |
| - - window area/size | |
| - description: >- | |
| - The window's length and width | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} x {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+ x \\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit} x {float} {unit}" | |
| - mappings: | |
| - - mixs:window_size | |
| - | |
| - window_cond: | |
| - aliases: | |
| - - window condition | |
| - description: >- | |
| - The physical condition of the window at the time of sampling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [damaged|needs repair|new|rupture|visible wear] | |
| - pattern: "[damaged|needs repair|new|rupture|visible wear]" | |
| - mappings: | |
| - - mixs:window_cond | |
| - | |
| - window_cover: | |
| - aliases: | |
| - - window covering | |
| - description: >- | |
| - The type of window covering | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [blinds|curtains|none] | |
| - pattern: "[blinds|curtains|none]" | |
| - mappings: | |
| - - mixs:window_cover | |
| - | |
| - window_horiz_pos: | |
| - aliases: | |
| - - window horizontal position | |
| - description: >- | |
| - The horizontal position of the window on the wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [left|middle|right] | |
| - pattern: "[left|middle|right]" | |
| - mappings: | |
| - - mixs:window_horiz_pos | |
| - | |
| - window_loc: | |
| - aliases: | |
| - - window location | |
| - description: >- | |
| - The relative location of the window within the room | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [north|south|east|west] | |
| - pattern: "[north|south|east|west]" | |
| - mappings: | |
| - - mixs:window_loc | |
| - | |
| - window_mat: | |
| - aliases: | |
| - - window material | |
| - description: >- | |
| - The type of material used to finish a window | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [clad|fiberglass|metal|vinyl|wood] | |
| - pattern: "[clad|fiberglass|metal|vinyl|wood]" | |
| - mappings: | |
| - - mixs:window_mat | |
| - | |
| - window_open_freq: | |
| - aliases: | |
| - - window open frequency | |
| - description: >- | |
| - The number of times windows are opened per week | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:window_open_freq | |
| - | |
| - window_water_mold: | |
| - aliases: | |
| - - window signs of water/mold | |
| - description: >- | |
| - Signs of the presence of mold or mildew on the window. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [presence of mold visible|no presence of mold visible] | |
| - pattern: "[presence of mold visible|no presence of mold visible]" | |
| - mappings: | |
| - - mixs:window_water_mold | |
| - | |
| - window_status: | |
| - aliases: | |
| - - window status | |
| - description: >- | |
| - Defines whether the windows were open or closed during environmental testing | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [closed|open] | |
| - pattern: "[closed|open]" | |
| - mappings: | |
| - - mixs:window_status | |
| - | |
| - window_type: | |
| - aliases: | |
| - - window type | |
| - description: >- | |
| - The type of windows | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [single-hung sash window|horizontal sash window|fixed window] | |
| - pattern: "[single\\-hung sash window|horizontal sash window|fixed window] " | |
| - mappings: | |
| - - mixs:window_type | |
| - | |
| - window_vert_pos: | |
| - aliases: | |
| - - window vertical position | |
| - description: >- | |
| - The vertical position of the window on the wall | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [bottom|middle|top|low|middle|high] | |
| - pattern: "[bottom|middle|top|low|middle|high]" | |
| - mappings: | |
| - - mixs:window_vert_pos | |
| - | |
| - ances_data: | |
| - aliases: | |
| - - ancestral data | |
| - description: >- | |
| - Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:ances_data | |
| - | |
| - biol_stat: | |
| - aliases: | |
| - - biological status | |
| - description: >- | |
| - The level of genome modification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [wild|natural|semi-natural|inbred line|breeder's line|hybrid|clonal selection|mutant] | |
| - pattern: "[wild|natural|semi\\-natural|inbred line|breeder\\'s line|hybrid|clonal selection|mutant]" | |
| - mappings: | |
| - - mixs:biol_stat | |
| - | |
| - genetic_mod: | |
| - aliases: | |
| - - genetic modification | |
| - description: >- | |
| - Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL}|{text} | |
| - mappings: | |
| - - mixs:genetic_mod | |
| - | |
| - host_common_name: | |
| - aliases: | |
| - - host common name | |
| - description: >- | |
| - Common name of the host, e.g. Human | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_common_name | |
| - | |
| - samp_capt_status: | |
| - aliases: | |
| - - sample capture status | |
| - description: >- | |
| - Reason for the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|farm sample|market sample|other] | |
| - pattern: "[active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|farm sample|market sample|other]" | |
| - mappings: | |
| - - mixs:samp_capt_status | |
| - | |
| - samp_dis_stage: | |
| - aliases: | |
| - - sample disease stage | |
| - description: >- | |
| - Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:samp_dis_stage | |
| - | |
| - host_taxid: | |
| - aliases: | |
| - - host taxid | |
| - description: >- | |
| - NCBI taxon id of the host, e.g. 9606 | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {NCBI taxid} | |
| - mappings: | |
| - - mixs:host_taxid | |
| - | |
| - host_subject_id: | |
| - aliases: | |
| - - host subject id | |
| - description: >- | |
| - A unique identifier by which each subject can be referred to, de-identified, e.g. #131 | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_subject_id | |
| - | |
| - host_age: | |
| - aliases: | |
| - - host age | |
| - description: >- | |
| - Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_age | |
| - | |
| - host_life_stage: | |
| - aliases: | |
| - - host life stage | |
| - description: >- | |
| - Description of life stage of host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_life_stage | |
| - | |
| - host_sex: | |
| - aliases: | |
| - - host sex | |
| - description: >- | |
| - Physical sex of the host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [male|female|neuter|hermaphrodite|not determined] | |
| - pattern: "[male|female|neuter|hermaphrodite|not determined]" | |
| - mappings: | |
| - - mixs:host_sex | |
| - | |
| - host_disease_stat: | |
| - aliases: | |
| - - host disease status | |
| - description: >- | |
| - List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from do (disease ontology) at http://www.disease-ontology.org, other hosts are free text | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]}|{text} | |
| - mappings: | |
| - - mixs:host_disease_stat | |
| - | |
| - host_body_habitat: | |
| - aliases: | |
| - - host body habitat | |
| - description: >- | |
| - Original body habitat where the sample was obtained from | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_body_habitat | |
| - | |
| - host_body_site: | |
| - aliases: | |
| - - host body site | |
| - description: >- | |
| - Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:host_body_site | |
| - | |
| - host_body_product: | |
| - aliases: | |
| - - host body product | |
| - description: >- | |
| - Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:host_body_product | |
| - | |
| - host_tot_mass: | |
| - aliases: | |
| - - host total mass | |
| - description: >- | |
| - Total mass of the host at collection, the unit depends on host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_tot_mass | |
| - | |
| - host_height: | |
| - aliases: | |
| - - host height | |
| - description: >- | |
| - The height of subject | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_height | |
| - | |
| - host_length: | |
| - aliases: | |
| - - host length | |
| - description: >- | |
| - The length of subject | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_length | |
| - | |
| - host_diet: | |
| - aliases: | |
| - - host diet | |
| - description: >- | |
| - Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_diet | |
| - | |
| - host_last_meal: | |
| - aliases: | |
| - - host last meal | |
| - description: >- | |
| - Content of last meal and time since feeding; can include multiple values | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{duration} | |
| - mappings: | |
| - - mixs:host_last_meal | |
| - | |
| - host_growth_cond: | |
| - aliases: | |
| - - host growth conditions | |
| - description: >- | |
| - Literature reference giving growth conditions of the host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL}|{text} | |
| - mappings: | |
| - - mixs:host_growth_cond | |
| - | |
| - host_substrate: | |
| - aliases: | |
| - - host substrate | |
| - description: >- | |
| - The growth substrate of the host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_substrate | |
| - | |
| - host_family_relationship: | |
| - aliases: | |
| - - host family relationship | |
| - description: >- | |
| - Relationships to other hosts in the same study; can include multiple relationships | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{text} | |
| - mappings: | |
| - - mixs:host_family_relationship | |
| - | |
| - host_infra_specific_name: | |
| - aliases: | |
| - - host infra-specific name | |
| - description: >- | |
| - Taxonomic information about the host below subspecies level | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_infra_specific_name | |
| - | |
| - host_infra_specific_rank: | |
| - aliases: | |
| - - host infra-specific rank | |
| - description: >- | |
| - Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_infra_specific_rank | |
| - | |
| - host_genotype: | |
| - aliases: | |
| - - host genotype | |
| - description: >- | |
| - Observed genotype | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_genotype | |
| - | |
| - host_phenotype: | |
| - aliases: | |
| - - host phenotype | |
| - description: >- | |
| - Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:host_phenotype | |
| - | |
| - host_body_temp: | |
| - aliases: | |
| - - host body temperature | |
| - description: >- | |
| - Core body temperature of the host when sample was collected | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_body_temp | |
| - | |
| - host_dry_mass: | |
| - aliases: | |
| - - host dry mass | |
| - description: >- | |
| - Measurement of dry mass | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_dry_mass | |
| - | |
| - host_blood_press_diast: | |
| - aliases: | |
| - - host blood pressure diastolic | |
| - description: >- | |
| - Resting diastolic blood pressure, measured as mm mercury | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_blood_press_diast | |
| - | |
| - host_blood_press_syst: | |
| - aliases: | |
| - - host blood pressure systolic | |
| - description: >- | |
| - Resting systolic blood pressure, measured as mm mercury | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_blood_press_syst | |
| - | |
| - host_color: | |
| - aliases: | |
| - - host color | |
| - description: >- | |
| - The color of host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_color | |
| - | |
| - host_shape: | |
| - aliases: | |
| - - host shape | |
| - description: >- | |
| - Morphological shape of host | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:host_shape | |
| - | |
| - gravidity: | |
| - aliases: | |
| - - gravidity | |
| - description: >- | |
| - Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{timestamp} | |
| - mappings: | |
| - - mixs:gravidity | |
| - | |
| - ihmc_medication_code: | |
| - aliases: | |
| - - IHMC medication code | |
| - description: >- | |
| - Can include multiple medication codes | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:ihmc_medication_code | |
| - | |
| - smoker: | |
| - aliases: | |
| - - smoker | |
| - description: >- | |
| - Specification of smoking status | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:smoker | |
| - | |
| - host_hiv_stat: | |
| - aliases: | |
| - - host HIV status | |
| - description: >- | |
| - HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{boolean} | |
| - pattern: "[true|false];[true|false]" | |
| - mappings: | |
| - - mixs:host_hiv_stat | |
| - | |
| - drug_usage: | |
| - aliases: | |
| - - drug usage | |
| - description: >- | |
| - Any drug used by subject and the frequency of usage; can include multiple drugs used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{integer}/[year|month|week|day|hour] | |
| - mappings: | |
| - - mixs:drug_usage | |
| - | |
| - host_body_mass_index: | |
| - aliases: | |
| - - host body-mass index | |
| - description: >- | |
| - Body mass index, calculated as weight/(height)squared | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_body_mass_index | |
| - | |
| - diet_last_six_month: | |
| - aliases: | |
| - - major diet change in last six months | |
| - description: >- | |
| - Specification of major diet changes in the last six months, if yes the change should be specified | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{text} | |
| - mappings: | |
| - - mixs:diet_last_six_month | |
| - | |
| - weight_loss_3_month: | |
| - aliases: | |
| - - weight loss in last three months | |
| - description: >- | |
| - Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {boolean};{float} {unit} | |
| - pattern: "[true|false];\\d+[.\\d+] \\S+" | |
| - string_serialization: "{boolean};{float} {unit}" | |
| - mappings: | |
| - - mixs:weight_loss_3_month | |
| - | |
| - ihmc_ethnicity: | |
| - aliases: | |
| - - IHMC ethnicity | |
| - description: >- | |
| - Ethnicity of the subject | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer}|{text} | |
| - mappings: | |
| - - mixs:ihmc_ethnicity | |
| - | |
| - host_occupation: | |
| - aliases: | |
| - - host occupation | |
| - description: >- | |
| - Most frequent job performed by subject | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {integer} | |
| - mappings: | |
| - - mixs:host_occupation | |
| - | |
| - pet_farm_animal: | |
| - aliases: | |
| - - presence of pets or farm animals | |
| - description: >- | |
| - Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{text} | |
| - mappings: | |
| - - mixs:pet_farm_animal | |
| - | |
| - travel_out_six_month: | |
| - aliases: | |
| - - travel outside the country in last six months | |
| - description: >- | |
| - Specification of the countries travelled in the last six months; can include multiple travels | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:travel_out_six_month | |
| - | |
| - twin_sibling: | |
| - aliases: | |
| - - twin sibling presence | |
| - description: >- | |
| - Specification of twin sibling presence | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:twin_sibling | |
| - | |
| - medic_hist_perform: | |
| - aliases: | |
| - - medical history performed | |
| - description: >- | |
| - Whether full medical history was collected | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:medic_hist_perform | |
| - | |
| - study_complt_stat: | |
| - aliases: | |
| - - study completion status | |
| - description: >- | |
| - Specification of study completion status, if no the reason should be specified | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};[adverse event|non-compliance|lost to follow up|other-specify] | |
| - pattern: "[true|false];[adverse event|non\\-compliance|lost to follow up|other\\-specify]" | |
| - mappings: | |
| - - mixs:study_complt_stat | |
| - | |
| - pulmonary_disord: | |
| - aliases: | |
| - - lung/pulmonary disorder | |
| - description: >- | |
| - History of pulmonary disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:pulmonary_disord | |
| - | |
| - nose_throat_disord: | |
| - aliases: | |
| - - lung/nose-throat disorder | |
| - description: >- | |
| - History of nose-throat disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:nose_throat_disord | |
| - | |
| - blood_blood_disord: | |
| - aliases: | |
| - - blood/blood disorder | |
| - description: >- | |
| - History of blood disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:blood_blood_disord | |
| - | |
| - host_pulse: | |
| - aliases: | |
| - - host pulse | |
| - description: >- | |
| - Resting pulse, measured as beats per minute | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_pulse | |
| - | |
| - gestation_state: | |
| - aliases: | |
| - - amniotic fluid/gestation state | |
| - description: >- | |
| - Specification of the gestation state | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:gestation_state | |
| - | |
| - maternal_health_stat: | |
| - aliases: | |
| - - amniotic fluid/maternal health status | |
| - description: >- | |
| - Specification of the maternal health status | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:maternal_health_stat | |
| - | |
| - foetal_health_stat: | |
| - aliases: | |
| - - amniotic fluid/foetal health status | |
| - description: >- | |
| - Specification of foetal health status, should also include abortion | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:foetal_health_stat | |
| - | |
| - amniotic_fluid_color: | |
| - aliases: | |
| - - amniotic fluid/color | |
| - description: >- | |
| - Specification of the color of the amniotic fluid sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:amniotic_fluid_color | |
| - | |
| - kidney_disord: | |
| - aliases: | |
| - - urine/kidney disorder | |
| - description: >- | |
| - History of kidney disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:kidney_disord | |
| - | |
| - urogenit_tract_disor: | |
| - aliases: | |
| - - urine/urogenital tract disorder | |
| - description: >- | |
| - History of urogenitaltract disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:urogenit_tract_disor | |
| - | |
| - urine_collect_meth: | |
| - aliases: | |
| - - urine/collection method | |
| - description: >- | |
| - Specification of urine collection method | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [clean catch|catheter] | |
| - pattern: "[clean catch|catheter]" | |
| - mappings: | |
| - - mixs:urine_collect_meth | |
| - | |
| - gastrointest_disord: | |
| - aliases: | |
| - - gastrointestinal tract disorder | |
| - description: >- | |
| - History of gastrointestinal tract disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:gastrointest_disord | |
| - | |
| - liver_disord: | |
| - aliases: | |
| - - liver disorder | |
| - description: >- | |
| - History of liver disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:liver_disord | |
| - | |
| - special_diet: | |
| - aliases: | |
| - - special diet | |
| - description: >- | |
| - Specification of special diet; can include multiple special diets | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [low carb|reduced calorie|vegetarian|other(to be specified)] | |
| - pattern: "[low carb|reduced calorie|vegetarian|other(to be specified)]" | |
| - mappings: | |
| - - mixs:special_diet | |
| - | |
| - nose_mouth_teeth_throat_disord: | |
| - aliases: | |
| - - nose/mouth/teeth/throat disorder | |
| - description: >- | |
| - History of nose/mouth/teeth/throat disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:nose_mouth_teeth_throat_disord | |
| - | |
| - time_last_toothbrush: | |
| - aliases: | |
| - - time since last toothbrushing | |
| - description: >- | |
| - Specification of the time since last toothbrushing | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {duration} | |
| - mappings: | |
| - - mixs:time_last_toothbrush | |
| - | |
| - dermatology_disord: | |
| - aliases: | |
| - - dermatology disorder | |
| - description: >- | |
| - History of dermatology disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:dermatology_disord | |
| - | |
| - time_since_last_wash: | |
| - aliases: | |
| - - time since last wash | |
| - description: >- | |
| - Specification of the time since last wash | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {duration} | |
| - mappings: | |
| - - mixs:time_since_last_wash | |
| - | |
| - dominant_hand: | |
| - aliases: | |
| - - dominant hand | |
| - description: >- | |
| - Dominant hand of the subject | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [left|right|ambidextrous] | |
| - pattern: "[left|right|ambidextrous]" | |
| - mappings: | |
| - - mixs:dominant_hand | |
| - | |
| - menarche: | |
| - aliases: | |
| - - menarche | |
| - description: >- | |
| - Date of most recent menstruation | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:menarche | |
| - | |
| - sexual_act: | |
| - aliases: | |
| - - sexual activity | |
| - description: >- | |
| - Current sexual partner and frequency of sex | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:sexual_act | |
| - | |
| - pregnancy: | |
| - aliases: | |
| - - pregnancy | |
| - description: >- | |
| - Date due of pregnancy | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:pregnancy | |
| - | |
| - douche: | |
| - aliases: | |
| - - douche | |
| - description: >- | |
| - Date of most recent douche | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:douche | |
| - | |
| - birth_control: | |
| - aliases: | |
| - - birth control | |
| - description: >- | |
| - Specification of birth control medication used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:birth_control | |
| - | |
| - menopause: | |
| - aliases: | |
| - - menopause | |
| - description: >- | |
| - Date of onset of menopause | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:menopause | |
| - | |
| - hrt: | |
| - aliases: | |
| - - HRT | |
| - description: >- | |
| - Whether subject had hormone replacement theraphy, and if yes start date | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:hrt | |
| - | |
| - hysterectomy: | |
| - aliases: | |
| - - hysterectomy | |
| - description: >- | |
| - Specification of whether hysterectomy was performed | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: boolean value ## syntax: {boolean} | |
| - pattern: "[true|false]" | |
| - mappings: | |
| - - mixs:hysterectomy | |
| - | |
| - gynecologic_disord: | |
| - aliases: | |
| - - gynecological disorder | |
| - description: >- | |
| - History of gynecological disorders; can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:gynecologic_disord | |
| - | |
| - urogenit_disord: | |
| - aliases: | |
| - - urogenital disorder | |
| - description: >- | |
| - History of urogenital disorders, can include multiple disorders | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:urogenit_disord | |
| - | |
| - hcr: | |
| - aliases: | |
| - - hydrocarbon resource type | |
| - description: >- | |
| - Main Hydrocarbon Resource type. The term 'Hydrocarbon Resource' HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight Gas Reservoir|other] | |
| - pattern: "[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight Gas Reservoir|other]" | |
| - mappings: | |
| - - mixs:hcr | |
| - | |
| - hc_produced: | |
| - aliases: | |
| - - hydrocarbon type produced | |
| - description: >- | |
| - Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other] | |
| - pattern: "[Oil|Gas\\-Condensate|Gas|Bitumen|Coalbed Methane|other]" | |
| - mappings: | |
| - - mixs:hc_produced | |
| - | |
| - basin: | |
| - aliases: | |
| - - basin name | |
| - description: >- | |
| - Name of the basin (e.g. Campos) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:basin | |
| - | |
| - field: | |
| - aliases: | |
| - - field name | |
| - description: >- | |
| - Name of the hydrocarbon field (e.g. Albacora) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:field | |
| - | |
| - reservoir: | |
| - aliases: | |
| - - reservoir name | |
| - description: >- | |
| - Name of the reservoir (e.g. Carapebus) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:reservoir | |
| - | |
| - hcr_temp: | |
| - aliases: | |
| - - hydrocarbon resource original temperature | |
| - description: >- | |
| - Original temperature of the hydrocarbon resource | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} - {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\- \\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} - {float} {unit}" | |
| - mappings: | |
| - - mixs:hcr_temp | |
| - | |
| - tvdss_of_hcr_temp: | |
| - aliases: | |
| - - depth (TVDSS) of hydrocarbon resource temperature | |
| - description: >- | |
| - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tvdss_of_hcr_temp | |
| - | |
| - hcr_pressure: | |
| - aliases: | |
| - - hydrocarbon resource original pressure | |
| - description: >- | |
| - Original pressure of the hydrocarbon resource | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} - {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\- \\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} - {float} {unit}" | |
| - mappings: | |
| - - mixs:hcr_pressure | |
| - | |
| - tvdss_of_hcr_pressure: | |
| - aliases: | |
| - - depth (TVDSS) of hydrocarbon resource pressure | |
| - description: >- | |
| - True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m ) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tvdss_of_hcr_pressure | |
| - | |
| - permeability: | |
| - aliases: | |
| - - permeability | |
| - description: >- | |
| - Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {integer} - {integer} {unit} | |
| - string_serialization: "{integer} - {integer} {unit}" | |
| - mappings: | |
| - - mixs:permeability | |
| - | |
| - porosity: | |
| - aliases: | |
| - - porosity | |
| - description: >- | |
| - Porosity of deposited sediment is volume of voids divided by the total volume of sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} - {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\- \\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} - {float} {unit}" | |
| - mappings: | |
| - - mixs:porosity | |
| - | |
| - lithology: | |
| - aliases: | |
| - - lithology | |
| - description: >- | |
| - Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other] | |
| - pattern: "[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]" | |
| - mappings: | |
| - - mixs:lithology | |
| - | |
| - depos_env: | |
| - aliases: | |
| - - depositional environment | |
| - description: >- | |
| - Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|Continental - Lacustrine|Transitional - Deltaic|Transitional - Tidal|Transitional - Lagoonal|Transitional - Beach|Transitional - Lake|Marine - Shallow|Marine - Deep|Marine - Reef|Other - Evaporite|Other - Glacial|Other - Volcanic|other] | |
| - pattern: "[Continental \\- Alluvial|Continental \\- Aeolian|Continental \\- Fluvial|Continental \\- Lacustrine|Transitional \\- Deltaic|Transitional \\- Tidal|Transitional \\- Lagoonal|Transitional \\- Beach|Transitional \\- Lake|Marine \\- Shallow|Marine \\- Deep|Marine \\- Reef|Other \\- Evaporite|Other \\- Glacial|Other \\- Volcanic|other]" | |
| - mappings: | |
| - - mixs:depos_env | |
| - | |
| - hcr_geol_age: | |
| - aliases: | |
| - - hydrocarbon resource geological age | |
| - description: >- | |
| - Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other] | |
| - pattern: "[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]" | |
| - mappings: | |
| - - mixs:hcr_geol_age | |
| - | |
| - owc_tvdss: | |
| - aliases: | |
| - - oil water contact depth | |
| - description: >- | |
| - Depth of the original oil water contact (OWC) zone (average) (m TVDSS) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:owc_tvdss | |
| - | |
| - hcr_fw_salinity: | |
| - aliases: | |
| - - formation water salinity | |
| - description: >- | |
| - Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:hcr_fw_salinity | |
| - | |
| - sulfate_fw: | |
| - aliases: | |
| - - sulfate in formation water | |
| - description: >- | |
| - Original sulfate concentration in the hydrocarbon resource | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:sulfate_fw | |
| - | |
| - vfa_fw: | |
| - aliases: | |
| - - vfa in formation water | |
| - description: >- | |
| - Original volatile fatty acid concentration in the hydrocarbon resource | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:vfa_fw | |
| - | |
| - sr_kerog_type: | |
| - aliases: | |
| - - source rock kerogen type | |
| - description: >- | |
| - Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Type I|Type II|Type III|Type IV|other] | |
| - pattern: "[Type I|Type II|Type III|Type IV|other]" | |
| - mappings: | |
| - - mixs:sr_kerog_type | |
| - | |
| - sr_lithology: | |
| - aliases: | |
| - - source rock lithology | |
| - description: >- | |
| - Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Clastic|Carbonate|Coal|Biosilicieous|other] | |
| - pattern: "[Clastic|Carbonate|Coal|Biosilicieous|other]" | |
| - mappings: | |
| - - mixs:sr_lithology | |
| - | |
| - sr_dep_env: | |
| - aliases: | |
| - - source rock depositional environment | |
| - description: >- | |
| - Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other] | |
| - pattern: "[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]" | |
| - mappings: | |
| - - mixs:sr_dep_env | |
| - | |
| - sr_geol_age: | |
| - aliases: | |
| - - source rock geological age | |
| - description: >- | |
| - Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other] | |
| - pattern: "[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]" | |
| - mappings: | |
| - - mixs:sr_geol_age | |
| - | |
| - samp_well_name: | |
| - aliases: | |
| - - sample well name | |
| - description: >- | |
| - Name of the well (e.g. BXA1123) where sample was taken | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:samp_well_name | |
| - | |
| - win: | |
| - aliases: | |
| - - well identification number | |
| - description: >- | |
| - A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:win | |
| - | |
| - samp_type: | |
| - aliases: | |
| - - sample type | |
| - description: >- | |
| - Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|produced fluid|produced water|injected water|water from treatment plant|fresh water|sea water|drilling fluid|procedural blank|positive control|negative control|other] | |
| - pattern: "[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|produced fluid|produced water|injected water|water from treatment plant|fresh water|sea water|drilling fluid|procedural blank|positive control|negative control|other]" | |
| - mappings: | |
| - - mixs:samp_type | |
| - | |
| - samp_subtype: | |
| - aliases: | |
| - - sample subtype | |
| - description: >- | |
| - Name of sample sub-type. For example if 'sample type' is 'Produced Water' then subtype could be 'Oil Phase' or 'Water Phase'. If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [oil phase|water phase|biofilm|not applicable|other] | |
| - pattern: "[oil phase|water phase|biofilm|not applicable|other]" | |
| - mappings: | |
| - - mixs:samp_subtype | |
| - | |
| - pressure: | |
| - aliases: | |
| - - pressure | |
| - description: >- | |
| - Pressure to which the sample is subject to, in atmospheres | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:pressure | |
| - | |
| - samp_tvdss: | |
| - aliases: | |
| - - sample true vertical depth subsea | |
| - description: >- | |
| - Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float}-{float} {unit} | |
| - pattern: "\\d+[.\\d+]\\-\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float}-{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_tvdss | |
| - | |
| - samp_md: | |
| - aliases: | |
| - - sample measured depth | |
| - description: >- | |
| - In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};[GL|DF|RT|KB|MSL|other] | |
| - pattern: "\\d+[.\\d+] \\S+;[GL|DF|RT|KB|MSL|other]" | |
| - string_serialization: "{float} {unit};[GL|DF|RT|KB|MSL|other]" | |
| - mappings: | |
| - - mixs:samp_md | |
| - | |
| - samp_transport_cond: | |
| - aliases: | |
| - - sample transport conditions | |
| - description: >- | |
| - Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 B0C) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+;\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit};{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_transport_cond | |
| - | |
| - organism_count_qpcr_info: | |
| - aliases: | |
| - - organism count qPCR information | |
| - description: >- | |
| - If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles | |
| - mappings: | |
| - - mixs:organism_count_qpcr_info | |
| - | |
| - ph: | |
| - aliases: | |
| - - pH | |
| - description: >- | |
| - Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:ph | |
| - | |
| - alkalinity: | |
| - aliases: | |
| - - alkalinity | |
| - description: >- | |
| - Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:alkalinity | |
| - | |
| - alkalinity_method: | |
| - aliases: | |
| - - alkalinity method | |
| - description: >- | |
| - Method used for alkalinity measurement | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:alkalinity_method | |
| - | |
| - sulfate: | |
| - aliases: | |
| - - sulfate | |
| - description: >- | |
| - Concentration of sulfate in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:sulfate | |
| - | |
| - sulfide: | |
| - aliases: | |
| - - sulfide | |
| - description: >- | |
| - Concentration of sulfide in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:sulfide | |
| - | |
| - tot_sulfur: | |
| - aliases: | |
| - - total sulfur | |
| - description: >- | |
| - Concentration of total sulfur in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_sulfur | |
| - | |
| - nitrate: | |
| - aliases: | |
| - - nitrate | |
| - description: >- | |
| - Concentration of nitrate in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:nitrate | |
| - | |
| - nitrite: | |
| - aliases: | |
| - - nitrite | |
| - description: >- | |
| - Concentration of nitrite in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:nitrite | |
| - | |
| - ammonium: | |
| - aliases: | |
| - - ammonium | |
| - description: >- | |
| - Concentration of ammonium in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:ammonium | |
| - | |
| - tot_nitro: | |
| - aliases: | |
| - - total nitrogen concentration | |
| - description: >- | |
| - Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_nitro | |
| - | |
| - diss_iron: | |
| - aliases: | |
| - - dissolved iron | |
| - description: >- | |
| - Concentration of dissolved iron in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_iron | |
| - | |
| - sodium: | |
| - aliases: | |
| - - sodium | |
| - description: >- | |
| - Sodium concentration in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:sodium | |
| - | |
| - chloride: | |
| - aliases: | |
| - - chloride | |
| - description: >- | |
| - Concentration of chloride in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:chloride | |
| - | |
| - potassium: | |
| - aliases: | |
| - - potassium | |
| - description: >- | |
| - Concentration of potassium in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:potassium | |
| - | |
| - magnesium: | |
| - aliases: | |
| - - magnesium | |
| - description: >- | |
| - Concentration of magnesium in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:magnesium | |
| - | |
| - calcium: | |
| - aliases: | |
| - - calcium | |
| - description: >- | |
| - Concentration of calcium in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:calcium | |
| - | |
| - tot_iron: | |
| - aliases: | |
| - - total iron | |
| - description: >- | |
| - Concentration of total iron in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_iron | |
| - | |
| - diss_org_carb: | |
| - aliases: | |
| - - dissolved organic carbon | |
| - description: >- | |
| - Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_org_carb | |
| - | |
| - diss_inorg_carb: | |
| - aliases: | |
| - - dissolved inorganic carbon | |
| - description: >- | |
| - Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_inorg_carb | |
| - | |
| - diss_inorg_phosp: | |
| - aliases: | |
| - - dissolved inorganic phosphorus | |
| - description: >- | |
| - Concentration of dissolved inorganic phosphorus in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_inorg_phosp | |
| - | |
| - tot_phosp: | |
| - aliases: | |
| - - total phosphorus | |
| - description: >- | |
| - Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_phosp | |
| - | |
| - suspend_solids: | |
| - aliases: | |
| - - suspended solids | |
| - description: >- | |
| - Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:suspend_solids | |
| - | |
| - density: | |
| - aliases: | |
| - - density | |
| - description: >- | |
| - Density of the sample, which is its mass per unit volume (aka volumetric mass density) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:density | |
| - | |
| - diss_carb_dioxide: | |
| - aliases: | |
| - - dissolved carbon dioxide | |
| - description: >- | |
| - Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_carb_dioxide | |
| - | |
| - diss_oxygen_fluid: | |
| - aliases: | |
| - - dissolved oxygen in fluids | |
| - description: >- | |
| - Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_oxygen_fluid | |
| - | |
| - vfa: | |
| - aliases: | |
| - - volatile fatty acids | |
| - description: >- | |
| - Concentration of Volatile Fatty Acids in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:vfa | |
| - | |
| - benzene: | |
| - aliases: | |
| - - benzene | |
| - description: >- | |
| - Concentration of benzene in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:benzene | |
| - | |
| - toluene: | |
| - aliases: | |
| - - toluene | |
| - description: >- | |
| - Concentration of toluene in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:toluene | |
| - | |
| - ethylbenzene: | |
| - aliases: | |
| - - ethylbenzene | |
| - description: >- | |
| - Concentration of ethylbenzene in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:ethylbenzene | |
| - | |
| - xylene: | |
| - aliases: | |
| - - xylene | |
| - description: >- | |
| - Concentration of xylene in the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:xylene | |
| - | |
| - api: | |
| - aliases: | |
| - - API gravity | |
| - description: >- | |
| - API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1B0 API) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:api | |
| - | |
| - tan: | |
| - aliases: | |
| - - total acid number | |
| - description: >- | |
| - Total Acid NumberB (TAN) is a measurement of acidity that is determined by the amount ofB potassium hydroxideB in milligrams that is needed to neutralize the acids in one gram of oil.B It is an important quality measurement ofB crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tan | |
| - | |
| - viscosity: | |
| - aliases: | |
| - - viscosity | |
| - description: >- | |
| - A measure of oil's resistanceB to gradual deformation byB shear stressB orB tensile stress (e.g. 3.5 cp; 100 B0C) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+;\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit};{float} {unit}" | |
| - mappings: | |
| - - mixs:viscosity | |
| - | |
| - pour_point : | |
| - aliases: | |
| - - pour point | |
| - description: >- | |
| - Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a highB pour pointB is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:pour_point | |
| - | |
| - saturates_pc: | |
| - aliases: | |
| - - saturates wt% | |
| - description: >- | |
| - Saturate, Aromatic, Resin and AsphalteneB (SARA) is an analysis method that dividesB crude oilB components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:saturates_pc | |
| - | |
| - aromatics_pc: | |
| - aliases: | |
| - - aromatics wt% | |
| - description: >- | |
| - Saturate, Aromatic, Resin and AsphalteneB (SARA) is an analysis method that dividesB crude oilB components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:aromatics_pc | |
| - | |
| - resins_pc: | |
| - aliases: | |
| - - resins wt% | |
| - description: >- | |
| - Saturate, Aromatic, Resin and AsphalteneB (SARA) is an analysis method that dividesB crude oilB components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:resins_pc | |
| - | |
| - asphaltenes_pc: | |
| - aliases: | |
| - - asphaltenes wt% | |
| - description: >- | |
| - Saturate, Aromatic, Resin and AsphalteneB (SARA) is an analysis method that dividesB crude oilB components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:asphaltenes_pc | |
| - | |
| - additional_info: | |
| - aliases: | |
| - - additional info | |
| - description: >- | |
| - Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:additional_info | |
| - | |
| - prod_start_date: | |
| - aliases: | |
| - - production start date | |
| - description: >- | |
| - Date of field's first production | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:prod_start_date | |
| - | |
| - prod_rate: | |
| - aliases: | |
| - - production rate | |
| - description: >- | |
| - Oil and/or gas production rates per well (e.g. 524 m3 / day) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:prod_rate | |
| - | |
| - water_production_rate: | |
| - aliases: | |
| - - water production rate | |
| - description: >- | |
| - Water production rates per well (e.g. 987 m3 / day) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:water_production_rate | |
| - | |
| - water_cut: | |
| - aliases: | |
| - - water cut | |
| - description: >- | |
| - Current amount of water (%) in a produced fluid stream; or the average of the combined streams | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:water_cut | |
| - | |
| - iwf: | |
| - aliases: | |
| - - injection water fraction | |
| - description: >- | |
| - Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:iwf | |
| - | |
| - add_recov_method: | |
| - aliases: | |
| - - secondary and tertiary recovery methods and start date | |
| - description: >- | |
| - Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other];{timestamp} | |
| - mappings: | |
| - - mixs:add_recov_method | |
| - | |
| - iw_bt_date_well: | |
| - aliases: | |
| - - injection water breakthrough date of specific well | |
| - description: >- | |
| - Injection water breakthrough date per well following a secondary and/or tertiary recovery | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:iw_bt_date_well | |
| - | |
| - biocide: | |
| - aliases: | |
| - - biocide administration | |
| - description: >- | |
| - List of biocides (commercial name of product and supplier) and date of administration | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{text};{timestamp} | |
| - mappings: | |
| - - mixs:biocide | |
| - | |
| - biocide_admin_method: | |
| - aliases: | |
| - - biocide administration method | |
| - description: >- | |
| - Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration};{duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration};{duration}" | |
| - mappings: | |
| - - mixs:biocide_admin_method | |
| - | |
| - chem_treatment: | |
| - aliases: | |
| - - chemical treatment | |
| - description: >- | |
| - List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{text};{timestamp} | |
| - mappings: | |
| - - mixs:chem_treatment | |
| - | |
| - chem_treatment_method: | |
| - aliases: | |
| - - chemical treatment method | |
| - description: >- | |
| - Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration};{duration};{duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}" | |
| - mappings: | |
| - - mixs:chem_treatment_method | |
| - | |
| - samp_loc_corr_rate: | |
| - aliases: | |
| - - corrosion rate at sample location | |
| - description: >- | |
| - Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} - {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\- \\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} - {float} {unit}" | |
| - mappings: | |
| - - mixs:samp_loc_corr_rate | |
| - | |
| - samp_collection_point: | |
| - aliases: | |
| - - sample collection point | |
| - description: >- | |
| - Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If 'other' is specified, please propose entry in 'additional info' field | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [well|test well|drilling rig|wellhead|separator|storage tank|other] | |
| - pattern: "[well|test well|drilling rig|wellhead|separator|storage tank|other]" | |
| - mappings: | |
| - - mixs:samp_collection_point | |
| - | |
| - samp_preserv: | |
| - aliases: | |
| - - preservative added to sample | |
| - description: >- | |
| - Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:samp_preserv | |
| - | |
| - alkyl_diethers: | |
| - aliases: | |
| - - alkyl diethers | |
| - description: >- | |
| - Concentration of alkyl diethers | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:alkyl_diethers | |
| - | |
| - aminopept_act: | |
| - aliases: | |
| - - aminopeptidase activity | |
| - description: >- | |
| - Measurement of aminopeptidase activity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:aminopept_act | |
| - | |
| - bacteria_carb_prod: | |
| - aliases: | |
| - - bacterial carbon production | |
| - description: >- | |
| - Measurement of bacterial carbon production | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:bacteria_carb_prod | |
| - | |
| - biomass: | |
| - aliases: | |
| - - biomass | |
| - description: >- | |
| - Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:biomass | |
| - | |
| - bishomohopanol: | |
| - aliases: | |
| - - bishomohopanol | |
| - description: >- | |
| - Concentration of bishomohopanol | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:bishomohopanol | |
| - | |
| - bromide: | |
| - aliases: | |
| - - bromide | |
| - description: >- | |
| - Concentration of bromide | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:bromide | |
| - | |
| - carb_nitro_ratio: | |
| - aliases: | |
| - - carbon/nitrogen ratio | |
| - description: >- | |
| - Ratio of amount or concentrations of carbon to nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:carb_nitro_ratio | |
| - | |
| - chlorophyll: | |
| - aliases: | |
| - - chlorophyll | |
| - description: >- | |
| - Concentration of chlorophyll | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:chlorophyll | |
| - | |
| - diether_lipids: | |
| - aliases: | |
| - - diether lipids | |
| - description: >- | |
| - Concentration of diether lipids; can include multiple types of diether lipids | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:diether_lipids | |
| - | |
| - diss_hydrogen: | |
| - aliases: | |
| - - dissolved hydrogen | |
| - description: >- | |
| - Concentration of dissolved hydrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_hydrogen | |
| - | |
| - diss_org_nitro: | |
| - aliases: | |
| - - dissolved organic nitrogen | |
| - description: >- | |
| - Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_org_nitro | |
| - | |
| - diss_oxygen: | |
| - aliases: | |
| - - dissolved oxygen | |
| - description: >- | |
| - Concentration of dissolved oxygen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_oxygen | |
| - | |
| - glucosidase_act: | |
| - aliases: | |
| - - glucosidase activity | |
| - description: >- | |
| - Measurement of glucosidase activity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:glucosidase_act | |
| - | |
| - mean_frict_vel: | |
| - aliases: | |
| - - mean friction velocity | |
| - description: >- | |
| - Measurement of mean friction velocity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:mean_frict_vel | |
| - | |
| - mean_peak_frict_vel: | |
| - aliases: | |
| - - mean peak friction velocity | |
| - description: >- | |
| - Measurement of mean peak friction velocity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:mean_peak_frict_vel | |
| - | |
| - n_alkanes: | |
| - aliases: | |
| - - n-alkanes | |
| - description: >- | |
| - Concentration of n-alkanes; can include multiple n-alkanes | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:n_alkanes | |
| - | |
| - nitro: | |
| - aliases: | |
| - - nitrogen | |
| - description: >- | |
| - Concentration of nitrogen (total) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:nitro | |
| - | |
| - org_carb: | |
| - aliases: | |
| - - organic carbon | |
| - description: >- | |
| - Concentration of organic carbon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:org_carb | |
| - | |
| - org_matter: | |
| - aliases: | |
| - - organic matter | |
| - description: >- | |
| - Concentration of organic matter | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:org_matter | |
| - | |
| - org_nitro: | |
| - aliases: | |
| - - organic nitrogen | |
| - description: >- | |
| - Concentration of organic nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:org_nitro | |
| - | |
| - part_org_carb: | |
| - aliases: | |
| - - particulate organic carbon | |
| - description: >- | |
| - Concentration of particulate organic carbon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:part_org_carb | |
| - | |
| - petroleum_hydrocarb: | |
| - aliases: | |
| - - petroleum hydrocarbon | |
| - description: >- | |
| - Concentration of petroleum hydrocarbon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:petroleum_hydrocarb | |
| - | |
| - phaeopigments: | |
| - aliases: | |
| - - phaeopigments | |
| - description: >- | |
| - Concentration of phaeopigments; can include multiple phaeopigments | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:phaeopigments | |
| - | |
| - phosphate: | |
| - aliases: | |
| - - phosphate | |
| - description: >- | |
| - Concentration of phosphate | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:phosphate | |
| - | |
| - phosplipid_fatt_acid: | |
| - aliases: | |
| - - phospholipid fatty acid | |
| - description: >- | |
| - Concentration of phospholipid fatty acids; can include multiple values | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:phosplipid_fatt_acid | |
| - | |
| - redox_potential: | |
| - aliases: | |
| - - redox potential | |
| - description: >- | |
| - Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:redox_potential | |
| - | |
| - salinity: | |
| - aliases: | |
| - - salinity | |
| - description: >- | |
| - Salinity is the total concentration of all dissolved salts in a water sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:salinity | |
| - | |
| - silicate: | |
| - aliases: | |
| - - silicate | |
| - description: >- | |
| - Concentration of silicate | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:silicate | |
| - | |
| - tot_carb: | |
| - aliases: | |
| - - total carbon | |
| - description: >- | |
| - Total carbon content | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_carb | |
| - | |
| - tot_nitro_content: | |
| - aliases: | |
| - - total nitrogen content | |
| - description: >- | |
| - Total nitrogen content of the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_nitro_content | |
| - | |
| - tot_org_carb: | |
| - aliases: | |
| - - total organic carbon | |
| - description: >- | |
| - Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_org_carb | |
| - | |
| - turbidity: | |
| - aliases: | |
| - - turbidity | |
| - description: >- | |
| - Measure of the amount of cloudiness or haziness in water caused by individual particles | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:turbidity | |
| - | |
| - water_content: | |
| - aliases: | |
| - - water content | |
| - description: >- | |
| - Water content measurement | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:water_content | |
| - | |
| - water_current: | |
| - aliases: | |
| - - water current | |
| - description: >- | |
| - Measurement of magnitude and direction of flow within a fluid | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:water_current | |
| - | |
| - air_temp_regm: | |
| - aliases: | |
| - - air temperature regimen | |
| - description: >- | |
| - Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:air_temp_regm | |
| - | |
| - antibiotic_regm: | |
| - aliases: | |
| - - antibiotic regimen | |
| - description: >- | |
| - Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:antibiotic_regm | |
| - | |
| - biotic_regm: | |
| - aliases: | |
| - - biotic regimen | |
| - description: >- | |
| - Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:biotic_regm | |
| - | |
| - chem_mutagen: | |
| - aliases: | |
| - - chemical mutagen | |
| - description: >- | |
| - Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:chem_mutagen | |
| - | |
| - climate_environment: | |
| - aliases: | |
| - - climate environment | |
| - description: >- | |
| - Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:climate_environment | |
| - | |
| - cult_root_med: | |
| - aliases: | |
| - - culture rooting medium | |
| - description: >- | |
| - Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text}|{PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:cult_root_med | |
| - | |
| - fertilizer_regm: | |
| - aliases: | |
| - - fertilizer regimen | |
| - description: >- | |
| - Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:fertilizer_regm | |
| - | |
| - fungicide_regm: | |
| - aliases: | |
| - - fungicide regimen | |
| - description: >- | |
| - Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:fungicide_regm | |
| - | |
| - gaseous_environment: | |
| - aliases: | |
| - - gaseous environment | |
| - description: >- | |
| - Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:gaseous_environment | |
| - | |
| - gravity: | |
| - aliases: | |
| - - gravity | |
| - description: >- | |
| - Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:gravity | |
| - | |
| - growth_facil: | |
| - aliases: | |
| - - growth facility | |
| - description: >- | |
| - Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {text}|{termLabel} {[termID]} | |
| - mappings: | |
| - - mixs:growth_facil | |
| - | |
| - growth_habit: | |
| - aliases: | |
| - - growth habit | |
| - description: >- | |
| - Characteristic shape, appearance or growth form of a plant species | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [erect|semi-erect|spreading|prostrate] | |
| - pattern: "[erect|semi\\-erect|spreading|prostrate] " | |
| - mappings: | |
| - - mixs:growth_habit | |
| - | |
| - growth_hormone_regm: | |
| - aliases: | |
| - - growth hormone regimen | |
| - description: >- | |
| - Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:growth_hormone_regm | |
| - | |
| - herbicide_regm: | |
| - aliases: | |
| - - herbicide regimen | |
| - description: >- | |
| - Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:herbicide_regm | |
| - | |
| - host_wet_mass: | |
| - aliases: | |
| - - host wet mass | |
| - description: >- | |
| - Measurement of wet mass | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:host_wet_mass | |
| - | |
| - humidity_regm: | |
| - aliases: | |
| - - humidity regimen | |
| - description: >- | |
| - Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:humidity_regm | |
| - | |
| - light_regm: | |
| - aliases: | |
| - - light regimen | |
| - description: >- | |
| - Information about treatment(s) involving exposure to light, including both light intensity and quality. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{float} {unit} | |
| - string_serialization: "{text};{float} {unit};{float} {unit}" | |
| - mappings: | |
| - - mixs:light_regm | |
| - | |
| - mechanical_damage: | |
| - aliases: | |
| - - mechanical damage | |
| - description: >- | |
| - Information about any mechanical damage exerted on the plant; can include multiple damages and sites | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{text} | |
| - mappings: | |
| - - mixs:mechanical_damage | |
| - | |
| - mineral_nutr_regm: | |
| - aliases: | |
| - - mineral nutrient regimen | |
| - description: >- | |
| - Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:mineral_nutr_regm | |
| - | |
| - non_mineral_nutr_regm: | |
| - aliases: | |
| - - non-mineral nutrient regimen | |
| - description: >- | |
| - Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:non_mineral_nutr_regm | |
| - | |
| - ph_regm: | |
| - aliases: | |
| - - pH regimen | |
| - description: >- | |
| - Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {float};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:ph_regm | |
| - | |
| - pesticide_regm: | |
| - aliases: | |
| - - pesticide regimen | |
| - description: >- | |
| - Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:pesticide_regm | |
| - | |
| - plant_growth_med: | |
| - aliases: | |
| - - plant growth medium | |
| - description: >- | |
| - Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:plant_growth_med | |
| - | |
| - plant_product: | |
| - aliases: | |
| - - plant product | |
| - description: >- | |
| - Substance produced by the plant, where the sample was obtained from | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:plant_product | |
| - | |
| - plant_sex: | |
| - aliases: | |
| - - plant sex | |
| - description: >- | |
| - Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual] | |
| - pattern: "[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]" | |
| - mappings: | |
| - - mixs:plant_sex | |
| - | |
| - plant_struc: | |
| - aliases: | |
| - - plant structure | |
| - description: >- | |
| - Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: controlled term value ## syntax: {termLabel} {[termID]} | |
| - pattern: ".* \\S+:\\S+" | |
| - mappings: | |
| - - mixs:plant_struc | |
| - | |
| - radiation_regm: | |
| - aliases: | |
| - - radiation regimen | |
| - description: >- | |
| - Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:radiation_regm | |
| - | |
| - rainfall_regm: | |
| - aliases: | |
| - - rainfall regimen | |
| - description: >- | |
| - Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:rainfall_regm | |
| - | |
| - root_cond: | |
| - aliases: | |
| - - rooting conditions | |
| - description: >- | |
| - Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL}|{text} | |
| - mappings: | |
| - - mixs:root_cond | |
| - | |
| - root_med_carbon: | |
| - aliases: | |
| - - rooting medium carbon | |
| - description: >- | |
| - Source of organic carbon in the culture rooting medium; e.g. sucrose. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:root_med_carbon | |
| - | |
| - root_med_macronutr: | |
| - aliases: | |
| - - rooting medium macronutrients | |
| - description: >- | |
| - Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170B mg/L). | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:root_med_macronutr | |
| - | |
| - root_med_micronutr: | |
| - aliases: | |
| - - rooting medium micronutrients | |
| - description: >- | |
| - Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2B mg/L). | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:root_med_micronutr | |
| - | |
| - root_med_suppl: | |
| - aliases: | |
| - - rooting medium organic supplements | |
| - description: >- | |
| - Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5B mg/L). | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:root_med_suppl | |
| - | |
| - root_med_ph: | |
| - aliases: | |
| - - rooting medium pH | |
| - description: >- | |
| - pH measurement of the culture rooting medium; e.g. 5.5. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} | |
| - pattern: "\\d+[.\\d+]" | |
| - mappings: | |
| - - mixs:root_med_ph | |
| - | |
| - root_med_regl: | |
| - aliases: | |
| - - rooting medium regulators | |
| - description: >- | |
| - Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5B mg/L NAA. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:root_med_regl | |
| - | |
| - root_med_solid: | |
| - aliases: | |
| - - rooting medium solidifier | |
| - description: >- | |
| - Specification of the solidifying agent in the culture rooting medium; e.g. agar. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:root_med_solid | |
| - | |
| - salt_regm: | |
| - aliases: | |
| - - salt regimen | |
| - description: >- | |
| - Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{text};{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:salt_regm | |
| - | |
| - season_environment: | |
| - aliases: | |
| - - seasonal environment | |
| - description: >- | |
| - Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:season_environment | |
| - | |
| - standing_water_regm: | |
| - aliases: | |
| - - standing water regimen | |
| - description: >- | |
| - Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:standing_water_regm | |
| - | |
| - tiss_cult_growth_med: | |
| - aliases: | |
| - - tissue culture growth media | |
| - description: >- | |
| - Description of plant tissue culture growth media used | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL}|{text} | |
| - mappings: | |
| - - mixs:tiss_cult_growth_med | |
| - | |
| - water_temp_regm: | |
| - aliases: | |
| - - water temperature regimen | |
| - description: >- | |
| - Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:water_temp_regm | |
| - | |
| - watering_regm: | |
| - aliases: | |
| - - watering regimen | |
| - description: >- | |
| - Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit};{Rn/start_time/end_time/duration} | |
| - string_serialization: "{float} {unit};{Rn/start_time/end_time/duration}" | |
| - mappings: | |
| - - mixs:watering_regm | |
| - | |
| - particle_class: | |
| - aliases: | |
| - - particle classification | |
| - description: >- | |
| - Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:particle_class | |
| - | |
| - sediment_type: | |
| - aliases: | |
| - - sediment type | |
| - description: >- | |
| - Information about the sediment type based on major constituents | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [biogenous|cosmogenous|hydrogenous|lithogenous] | |
| - pattern: "[biogenous|cosmogenous|hydrogenous|lithogenous]" | |
| - mappings: | |
| - - mixs:sediment_type | |
| - | |
| - tidal_stage: | |
| - aliases: | |
| - - tidal stage | |
| - description: >- | |
| - Stage of tide | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [low tide|ebb tide|flood tide|high tide] | |
| - pattern: "[low tide|ebb tide|flood tide|high tide]" | |
| - mappings: | |
| - - mixs:tidal_stage | |
| - | |
| - tot_depth_water_col: | |
| - aliases: | |
| - - total depth of water column | |
| - description: >- | |
| - Measurement of total depth of water column | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_depth_water_col | |
| - | |
| - cur_land_use: | |
| - aliases: | |
| - - current land use | |
| - description: >- | |
| - Present state of sample site | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: "[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]" | |
| - pattern: "[cities|farmstead|industrial areas|roads\\/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines\\/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage\\-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi\\-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]" | |
| - mappings: | |
| - - mixs:cur_land_use | |
| - | |
| - cur_vegetation: | |
| - aliases: | |
| - - current vegetation | |
| - description: >- | |
| - Vegetation classification from one or more standard classification systems, or agricultural crop | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:cur_vegetation | |
| - | |
| - cur_vegetation_meth: | |
| - aliases: | |
| - - current vegetation method | |
| - description: >- | |
| - Reference or method used in vegetation classification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:cur_vegetation_meth | |
| - | |
| - previous_land_use: | |
| - aliases: | |
| - - history/previous land use | |
| - description: >- | |
| - Previous land use and dates | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{timestamp} | |
| - mappings: | |
| - - mixs:previous_land_use | |
| - | |
| - previous_land_use_meth: | |
| - aliases: | |
| - - history/previous land use method | |
| - description: >- | |
| - Reference or method used in determining previous land use and dates | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:previous_land_use_meth | |
| - | |
| - crop_rotation: | |
| - aliases: | |
| - - history/crop rotation | |
| - description: >- | |
| - Whether or not crop is rotated, and if yes, rotation schedule | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{Rn/start_time/end_time/duration} | |
| - mappings: | |
| - - mixs:crop_rotation | |
| - | |
| - agrochem_addition: | |
| - aliases: | |
| - - history/agrochemical additions | |
| - description: >- | |
| - Addition of fertilizers, pesticides, etc. - amount and time of applications | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit};{timestamp} | |
| - string_serialization: "{text};{float} {unit};{timestamp}" | |
| - mappings: | |
| - - mixs:agrochem_addition | |
| - | |
| - tillage: | |
| - aliases: | |
| - - history/tillage | |
| - description: >- | |
| - Note method(s) used for tilling | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc plough] | |
| - pattern: "[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc plough]" | |
| - mappings: | |
| - - mixs:tillage | |
| - | |
| - fire: | |
| - aliases: | |
| - - history/fire | |
| - description: >- | |
| - Historical and/or physical evidence of fire | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:fire | |
| - | |
| - flooding: | |
| - aliases: | |
| - - history/flooding | |
| - description: >- | |
| - Historical and/or physical evidence of flooding | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:flooding | |
| - | |
| + name: env_medium | |
| + aliases: | |
| + - environmental medium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: The material displaced by the entity at time of sampling. Recommend | |
| + subclasses of environmental material [ENVO:00010483]. | |
| + description: 'Report the environmental material(s) immediately surrounding the | |
| + sample or specimen at the time of sampling. We recommend using subclasses of | |
| + ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO | |
| + documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS | |
| + . Terms from other OBO ontologies are permissible as long as they reference | |
| + mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities | |
| + (e.g. a tree, a leaf, a table top).' | |
| + title: environmental medium | |
| + examples: | |
| + - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m | |
| + of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating | |
| + a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000014 | |
| + multivalued: false | |
| + range: controlled term value | |
| + escalator: | |
| + name: escalator | |
| + aliases: | |
| + - escalator count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of escalators within the built structure | |
| + title: escalator count | |
| + examples: | |
| + - value: '4' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000800 | |
| + multivalued: false | |
| + range: text value | |
| + ethylbenzene: | |
| + name: ethylbenzene | |
| + aliases: | |
| + - ethylbenzene | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of ethylbenzene in the sample | |
| + title: ethylbenzene | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000155 | |
| + multivalued: false | |
| + range: quantity value | |
| + exp_duct: | |
| + name: exp_duct | |
| + aliases: | |
| + - exposed ductwork | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The amount of exposed ductwork in the room | |
| + title: exposed ductwork | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000144 | |
| + multivalued: false | |
| + range: quantity value | |
| + exp_pipe: | |
| + name: exp_pipe | |
| + aliases: | |
| + - exposed pipes | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of exposed pipes in the room | |
| + title: exposed pipes | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000220 | |
| + multivalued: false | |
| + range: quantity value | |
| + experimental_factor: | |
| + name: experimental_factor | |
| + aliases: | |
| + - experimental factor | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: text or EFO and/or OBI | |
| + description: Experimental factors are essentially the variable aspects of an experiment | |
| + design which can be used to describe an experiment, or set of experiments, in | |
| + an increasingly detailed manner. This field accepts ontology terms from Experimental | |
| + Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For | |
| + a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; | |
| + for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI | |
| + title: experimental factor | |
| + examples: | |
| + - value: time series design [EFO:EFO_0001779] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}|{text}' | |
| + slot_uri: MIXS:0000008 | |
| + multivalued: false | |
| + range: controlled term value | |
| + investigation field: | |
| + name: investigation field | |
| + description: field describing aspect of the investigation/study to which the sample | |
| + belongs | |
| + from_schema: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + abstract: true | |
| + ext_door: | |
| + name: ext_door | |
| + aliases: | |
| + - exterior door count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of exterior doors in the built structure | |
| + title: exterior door count | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000170 | |
| + multivalued: false | |
| + range: text value | |
| + ext_wall_orient: | |
| + name: ext_wall_orient | |
| + aliases: | |
| + - orientations of exterior wall | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The orientation of the exterior wall | |
| + title: orientations of exterior wall | |
| + examples: | |
| + - value: northwest | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000817 | |
| + multivalued: false | |
| + range: text value | |
| + ext_window_orient: | |
| + name: ext_window_orient | |
| + aliases: | |
| + - orientations of exterior window | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The compass direction the exterior window of the room is facing | |
| + title: orientations of exterior window | |
| + examples: | |
| + - value: southwest | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000818 | |
| + multivalued: false | |
| + range: text value | |
| extreme_event: | |
| - aliases: | |
| - - history/extreme events | |
| - description: >- | |
| - Unusual physical events that may have affected microbial populations | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: timestamp value ## syntax: {timestamp} | |
| - mappings: | |
| - - mixs:extreme_event | |
| - | |
| - horizon: | |
| - aliases: | |
| - - horizon | |
| - description: >- | |
| - Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost] | |
| - pattern: "[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]" | |
| - mappings: | |
| - - mixs:horizon | |
| - | |
| - horizon_meth: | |
| - aliases: | |
| - - horizon method | |
| - description: >- | |
| - Reference or method used in determining the horizon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:horizon_meth | |
| - | |
| - sieving: | |
| - aliases: | |
| - - composite design/sieving (if any) | |
| - description: >- | |
| - Collection design of pooled samples and/or sieve size and amount of sample sieved | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {{text}|{float} {unit}};{float} {unit} | |
| - string_serialization: "{{text}|{float} {unit}};{float} {unit}" | |
| - mappings: | |
| - - mixs:sieving | |
| - | |
| - water_content_soil_meth: | |
| - aliases: | |
| - - water content method | |
| - description: >- | |
| - Reference or method used in determining the water content of soil | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:water_content_soil_meth | |
| - | |
| - pool_dna_extracts: | |
| - aliases: | |
| - - pooling of DNA extracts (if done) | |
| - description: >- | |
| - Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {boolean};{integer} | |
| - mappings: | |
| - - mixs:pool_dna_extracts | |
| - | |
| - store_cond: | |
| - aliases: | |
| - - storage conditions (fresh/frozen/other) | |
| - description: >- | |
| - Explain how and for how long the soil sample was stored before DNA extraction | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text};{duration} | |
| - mappings: | |
| - - mixs:store_cond | |
| - | |
| - link_climate_info: | |
| - aliases: | |
| - - link to climate information | |
| - description: >- | |
| - Link to climate resource | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:link_climate_info | |
| - | |
| - annual_temp: | |
| - aliases: | |
| - - mean annual temperature | |
| - description: >- | |
| - Mean annual temperature | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:annual_temp | |
| - | |
| - season_temp: | |
| - aliases: | |
| - - mean seasonal temperature | |
| - description: >- | |
| - Mean seasonal temperature | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:season_temp | |
| - | |
| - annual_precpt: | |
| - aliases: | |
| - - mean annual precipitation | |
| - description: >- | |
| - The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:annual_precpt | |
| - | |
| - season_precpt: | |
| - aliases: | |
| - - mean seasonal precipitation | |
| - description: >- | |
| - The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:season_precpt | |
| - | |
| - link_class_info: | |
| - aliases: | |
| - - link to classification information | |
| - description: >- | |
| - Link to digitized soil maps or other soil classification information | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:link_class_info | |
| - | |
| + name: extreme_event | |
| + aliases: | |
| + - history/extreme events | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: date | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Unusual physical events that may have affected microbial populations | |
| + title: history/extreme events | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000320 | |
| + multivalued: false | |
| + range: timestamp value | |
| fao_class: | |
| - aliases: | |
| - - soil_taxonomic/FAO classification | |
| - description: >- | |
| - Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols] | |
| - pattern: "[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]" | |
| - mappings: | |
| - - mixs:fao_class | |
| - | |
| - local_class: | |
| - aliases: | |
| - - soil_taxonomic/local classification | |
| - description: >- | |
| - Soil classification based on local soil classification system | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:local_class | |
| - | |
| - local_class_meth: | |
| - aliases: | |
| - - soil_taxonomic/local classification method | |
| - description: >- | |
| - Reference or method used in determining the local soil classification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:local_class_meth | |
| - | |
| - soil_type: | |
| - aliases: | |
| - - soil type | |
| - description: >- | |
| - Soil series name or other lower-level classification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:soil_type | |
| - | |
| - soil_type_meth: | |
| - aliases: | |
| - - soil type method | |
| - description: >- | |
| - Reference or method used in determining soil series name or other lower-level classification | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:soil_type_meth | |
| - | |
| - slope_gradient: | |
| - aliases: | |
| - - slope gradient | |
| - description: >- | |
| - Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:slope_gradient | |
| - | |
| - slope_aspect: | |
| - aliases: | |
| - - slope aspect | |
| - description: >- | |
| - The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:slope_aspect | |
| - | |
| - profile_position: | |
| - aliases: | |
| - - profile position | |
| - description: >- | |
| - Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [summit|shoulder|backslope|footslope|toeslope] | |
| - pattern: "[summit|shoulder|backslope|footslope|toeslope]" | |
| - mappings: | |
| - - mixs:profile_position | |
| - | |
| - drainage_class: | |
| - aliases: | |
| - - drainage classification | |
| - description: >- | |
| - Drainage classification from a standard system such as the USDA system | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: [very poorly|poorly|somewhat poorly|moderately well|well|excessively drained] | |
| - pattern: "[very poorly|poorly|somewhat poorly|moderately well|well|excessively drained]" | |
| - mappings: | |
| - - mixs:drainage_class | |
| - | |
| - texture: | |
| - aliases: | |
| - - texture | |
| - description: >- | |
| - The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:texture | |
| - | |
| - texture_meth: | |
| - aliases: | |
| - - texture method | |
| - description: >- | |
| - Reference or method used in determining soil texture | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:texture_meth | |
| - | |
| - ph_meth: | |
| - aliases: | |
| - - pH method | |
| - description: >- | |
| - Reference or method used in determining ph | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:ph_meth | |
| - | |
| - tot_org_c_meth: | |
| - aliases: | |
| - - total organic carbon method | |
| - description: >- | |
| - Reference or method used in determining total organic carbon | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:tot_org_c_meth | |
| - | |
| - tot_nitro_content_meth: | |
| - aliases: | |
| - - total nitrogen content method | |
| - description: >- | |
| - Reference or method used in determining the total nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:tot_nitro_content_meth | |
| - | |
| - microbial_biomass: | |
| - aliases: | |
| - - microbial biomass | |
| - description: >- | |
| - The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:microbial_biomass | |
| - | |
| - microbial_biomass_meth: | |
| - aliases: | |
| - - microbial biomass method | |
| - description: >- | |
| - Reference or method used in determining microbial biomass | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:microbial_biomass_meth | |
| - | |
| - link_addit_analys: | |
| - aliases: | |
| - - links to additional analysis | |
| - description: >- | |
| - Link to additional analysis results performed on the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:link_addit_analys | |
| - | |
| - extreme_salinity: | |
| - aliases: | |
| - - extreme_unusual_properties/salinity | |
| - description: >- | |
| - Measured salinity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:extreme_salinity | |
| - | |
| - salinity_meth: | |
| - aliases: | |
| - - extreme_unusual_properties/salinity method | |
| - description: >- | |
| - Reference or method used in determining salinity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:salinity_meth | |
| - | |
| + name: fao_class | |
| + aliases: | |
| + - soil_taxonomic/FAO classification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Soil classification from the FAO World Reference Database for Soil | |
| + Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups | |
| + title: soil_taxonomic/FAO classification | |
| + examples: | |
| + - value: Luvisols | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001083 | |
| + multivalued: false | |
| + range: text value | |
| + fertilizer_regm: | |
| + name: fertilizer_regm | |
| + aliases: | |
| + - fertilizer regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: fertilizer name;fertilizer amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving the use of fertilizers; should | |
| + include the name of fertilizer, amount administered, treatment regimen including | |
| + how many times the treatment was repeated, how long each treatment lasted, and | |
| + the start and end time of the entire treatment; can include multiple fertilizer | |
| + regimens | |
| + title: fertilizer regimen | |
| + examples: | |
| + - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000556 | |
| + multivalued: false | |
| + range: quantity value | |
| + field: | |
| + name: field | |
| + aliases: | |
| + - field name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of the hydrocarbon field (e.g. Albacora) | |
| + title: field name | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000291 | |
| + multivalued: false | |
| + range: text value | |
| + filter_type: | |
| + name: filter_type | |
| + aliases: | |
| + - filter type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: A device which removes solid particulates or airborne molecular contaminants | |
| + title: filter type | |
| + examples: | |
| + - value: HEPA | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000765 | |
| + multivalued: false | |
| + range: text value | |
| + fire: | |
| + name: fire | |
| + aliases: | |
| + - history/fire | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: date | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Historical and/or physical evidence of fire | |
| + title: history/fire | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001086 | |
| + multivalued: false | |
| + range: timestamp value | |
| + fireplace_type: | |
| + name: fireplace_type | |
| + aliases: | |
| + - fireplace type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A firebox with chimney | |
| + title: fireplace type | |
| + examples: | |
| + - value: wood burning | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[gas burning|wood burning]' | |
| + slot_uri: MIXS:0000802 | |
| + multivalued: false | |
| + range: text value | |
| + flooding: | |
| + name: flooding | |
| + aliases: | |
| + - history/flooding | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: date | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Historical and/or physical evidence of flooding | |
| + title: history/flooding | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000319 | |
| + multivalued: false | |
| + range: timestamp value | |
| + floor_age: | |
| + name: floor_age | |
| + aliases: | |
| + - floor age | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: years, weeks, days | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The time period since installment of the carpet or flooring | |
| + title: floor age | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000164 | |
| + multivalued: false | |
| + range: quantity value | |
| + floor_area: | |
| + name: floor_area | |
| + aliases: | |
| + - floor area | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The area of the floor space within the room | |
| + title: floor area | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000165 | |
| + multivalued: false | |
| + range: quantity value | |
| + floor_cond: | |
| + name: floor_cond | |
| + aliases: | |
| + - floor condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The physical condition of the floor at the time of sampling; photos | |
| + or video preferred; use drawings to indicate location of damaged areas | |
| + title: floor condition | |
| + examples: | |
| + - value: new | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000803 | |
| + multivalued: false | |
| + range: text value | |
| + floor_count: | |
| + name: floor_count | |
| + aliases: | |
| + - floor count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of floors in the building, including basements and mechanical | |
| + penthouse | |
| + title: floor count | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000225 | |
| + multivalued: false | |
| + range: text value | |
| + floor_finish_mat: | |
| + name: floor_finish_mat | |
| + aliases: | |
| + - floor finish material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The floor covering type; the finished surface that is walked on | |
| + title: floor finish material | |
| + examples: | |
| + - value: carpet | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000804 | |
| + multivalued: false | |
| + range: text value | |
| + floor_struc: | |
| + name: floor_struc | |
| + aliases: | |
| + - floor structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Refers to the structural elements and subfloor upon which the finish | |
| + flooring is installed | |
| + title: floor structure | |
| + examples: | |
| + - value: concrete | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000806 | |
| + multivalued: false | |
| + range: text value | |
| + floor_thermal_mass: | |
| + name: floor_thermal_mass | |
| + aliases: | |
| + - floor thermal mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: joule per degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The ability of the floor to provide inertia against temperature fluctuations | |
| + title: floor thermal mass | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000166 | |
| + multivalued: false | |
| + range: quantity value | |
| + floor_water_mold: | |
| + name: floor_water_mold | |
| + aliases: | |
| + - floor signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew in a room | |
| + title: floor signs of water/mold | |
| + examples: | |
| + - value: ceiling discoloration | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000805 | |
| + multivalued: false | |
| + range: text value | |
| + fluor: | |
| + name: fluor | |
| + aliases: | |
| + - fluorescence | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram chlorophyll a per cubic meter, volts | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Raw or converted fluorescence of water | |
| + title: fluorescence | |
| + examples: | |
| + - value: 2.5 volts | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000704 | |
| + multivalued: false | |
| + range: quantity value | |
| + freq_clean: | |
| + name: freq_clean | |
| + aliases: | |
| + - frequency of cleaning | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration or {text} | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of times the sample location is cleaned. Frequency of | |
| + cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually. | |
| + title: frequency of cleaning | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000226 | |
| + multivalued: false | |
| + range: quantity value | |
| + freq_cook: | |
| + name: freq_cook | |
| + aliases: | |
| + - frequency of cooking | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of times a meal is cooked per week | |
| + title: frequency of cooking | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000227 | |
| + multivalued: false | |
| + range: quantity value | |
| + fungicide_regm: | |
| + name: fungicide_regm | |
| + aliases: | |
| + - fungicide regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: fungicide name;fungicide amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of fungicides; should include | |
| + the name of fungicide, amount administered, treatment regimen including how | |
| + many times the treatment was repeated, how long each treatment lasted, and the | |
| + start and end time of the entire treatment; can include multiple fungicide regimens | |
| + title: fungicide regimen | |
| + examples: | |
| + - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000557 | |
| + multivalued: false | |
| + range: quantity value | |
| + furniture: | |
| + name: furniture | |
| + aliases: | |
| + - furniture | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The types of furniture present in the sampled room | |
| + title: furniture | |
| + examples: | |
| + - value: chair | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000807 | |
| + multivalued: false | |
| + range: text value | |
| + gaseous_environment: | |
| + name: gaseous_environment | |
| + aliases: | |
| + - gaseous environment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gaseous compound name;gaseous compound amount;treatment interval and | |
| + duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Use of conditions with differing gaseous environments; should include | |
| + the name of gaseous compound, amount administered, treatment duration, interval | |
| + and total experimental duration; can include multiple gaseous environment regimens | |
| + title: gaseous environment | |
| + examples: | |
| + - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000558 | |
| + multivalued: false | |
| + range: quantity value | |
| + gaseous_substances: | |
| + name: gaseous_substances | |
| + aliases: | |
| + - gaseous substances | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gaseous substance name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Amount or concentration of substances such as hydrogen sulfide, carbon | |
| + dioxide, methane, etc.; can include multiple substances | |
| + title: gaseous substances | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000661 | |
| + multivalued: false | |
| + range: quantity value | |
| + gender_restroom: | |
| + name: gender_restroom | |
| + aliases: | |
| + - gender of restroom | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The gender type of the restroom | |
| + title: gender of restroom | |
| + examples: | |
| + - value: male | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000808 | |
| + multivalued: false | |
| + range: text value | |
| + genetic_mod: | |
| + name: genetic_mod | |
| + aliases: | |
| + - genetic modification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI,url or free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Genetic modifications of the genome of an organism, which may occur | |
| + naturally by spontaneous mutation, or be introduced by some experimental means, | |
| + e.g. specification of a transgene or the gene knocked-out or details of transient | |
| + transfection | |
| + title: genetic modification | |
| + examples: | |
| + - value: aox1A transgenic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}|{text}' | |
| + slot_uri: MIXS:0000859 | |
| + multivalued: false | |
| + range: text value | |
| + geo_loc_name: | |
| + name: geo_loc_name | |
| + aliases: | |
| + - geographic location (country and/or sea,region) | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location | |
| + name' | |
| + description: The geographical origin of the sample as defined by the country or | |
| + sea name followed by specific region name. Country or sea names should be chosen | |
| + from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology | |
| + (http://purl.bioontology.org/ontology/GAZ) | |
| + title: geographic location (country and/or sea,region) | |
| + examples: | |
| + - value: 'USA: Maryland, Bethesda' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{term}: {term}, {text}' | |
| + slot_uri: MIXS:0000010 | |
| + multivalued: false | |
| + range: text value | |
| + glucosidase_act: | |
| + name: glucosidase_act | |
| + aliases: | |
| + - glucosidase activity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mol per liter per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of glucosidase activity | |
| + title: glucosidase activity | |
| + examples: | |
| + - value: 5 mol per liter per hour | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000137 | |
| + multivalued: false | |
| + range: quantity value | |
| + gravidity: | |
| + name: gravidity | |
| + aliases: | |
| + - gravidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gravidity status;timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Whether or not subject is gravid, and if yes date due or date post-conception, | |
| + specifying which is used | |
| + title: gravidity | |
| + examples: | |
| + - value: yes;due date:2018-05-11 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{boolean};{timestamp}' | |
| + slot_uri: MIXS:0000875 | |
| + multivalued: false | |
| + range: text value | |
| + gravity: | |
| + name: gravity | |
| + aliases: | |
| + - gravity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gravity factor value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter per square second, g | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of gravity factor to study | |
| + various types of responses in presence, absence or modified levels of gravity; | |
| + treatment regimen including how many times the treatment was repeated, how long | |
| + each treatment lasted, and the start and end time of the entire treatment; can | |
| + include multiple treatments | |
| + title: gravity | |
| + examples: | |
| + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000559 | |
| + multivalued: false | |
| + range: quantity value | |
| + growth_facil: | |
| + name: growth_facil | |
| + aliases: | |
| + - growth facility | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text or CO | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Type of facility where the sampled plant was grown; controlled vocabulary: | |
| + growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively | |
| + use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' | |
| + title: growth facility | |
| + examples: | |
| + - value: Growth chamber [CO_715:0000189] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}|{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0001043 | |
| + multivalued: false | |
| + range: controlled term value | |
| + growth_habit: | |
| + name: growth_habit | |
| + aliases: | |
| + - growth habit | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Characteristic shape, appearance or growth form of a plant species | |
| + title: growth habit | |
| + examples: | |
| + - value: spreading | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001044 | |
| + multivalued: false | |
| + range: text value | |
| + growth_hormone_regm: | |
| + name: growth_hormone_regm | |
| + aliases: | |
| + - growth hormone regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: growth hormone name;growth hormone amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of growth hormones; should | |
| + include the name of growth hormone, amount administered, treatment regimen including | |
| + how many times the treatment was repeated, how long each treatment lasted, and | |
| + the start and end time of the entire treatment; can include multiple growth | |
| + hormone regimens | |
| + title: growth hormone regimen | |
| + examples: | |
| + - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000560 | |
| + multivalued: false | |
| + range: quantity value | |
| + hall_count: | |
| + name: hall_count | |
| + aliases: | |
| + - hallway/corridor count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The total count of hallways and cooridors in the built structure | |
| + title: hallway/corridor count | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000228 | |
| + multivalued: false | |
| + range: text value | |
| + handidness: | |
| + name: handidness | |
| + aliases: | |
| + - handidness | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The handidness of the individual sampled | |
| + title: handidness | |
| + examples: | |
| + - value: right handedness | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000809 | |
| + multivalued: false | |
| + range: text value | |
| + hc_produced: | |
| + name: hc_produced | |
| + aliases: | |
| + - hydrocarbon type produced | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, | |
| + etc). If "other" is specified, please propose entry in "additional info" field | |
| + title: hydrocarbon type produced | |
| + examples: | |
| + - value: Gas | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000989 | |
| + multivalued: false | |
| + range: text value | |
| + hcr: | |
| + name: hcr | |
| + aliases: | |
| + - hydrocarbon resource type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR | |
| + defined as a natural environmental feature containing large amounts of hydrocarbons | |
| + at high concentrations potentially suitable for commercial exploitation. This | |
| + term should not be confused with the Hydrocarbon Occurrence term which also | |
| + includes hydrocarbon-rich environments with currently limited commercial interest | |
| + such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose | |
| + entry in "additional info" field | |
| + title: hydrocarbon resource type | |
| + examples: | |
| + - value: Oil Sand | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000988 | |
| + multivalued: false | |
| + range: text value | |
| + hcr_fw_salinity: | |
| + name: hcr_fw_salinity | |
| + aliases: | |
| + - formation water salinity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original formation water salinity (prior to secondary recovery e.g. | |
| + Waterflooding) expressed as TDS | |
| + title: formation water salinity | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000406 | |
| + multivalued: false | |
| + range: quantity value | |
| + hcr_geol_age: | |
| + name: hcr_geol_age | |
| + aliases: | |
| + - hydrocarbon resource geological age | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). | |
| + If "other" is specified, please propose entry in "additional info" field' | |
| + title: hydrocarbon resource geological age | |
| + examples: | |
| + - value: Silurian | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000993 | |
| + multivalued: false | |
| + range: text value | |
| + hcr_pressure: | |
| + name: hcr_pressure | |
| + aliases: | |
| + - hydrocarbon resource original pressure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: atmosphere, kilopascal | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original pressure of the hydrocarbon resource | |
| + title: hydrocarbon resource original pressure | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} - {float} {unit}' | |
| + slot_uri: MIXS:0000395 | |
| + multivalued: false | |
| + range: quantity value | |
| + hcr_temp: | |
| + name: hcr_temp | |
| + aliases: | |
| + - hydrocarbon resource original temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original temperature of the hydrocarbon resource | |
| + title: hydrocarbon resource original temperature | |
| + examples: | |
| + - value: 150-295 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} - {float} {unit}' | |
| + slot_uri: MIXS:0000393 | |
| + multivalued: false | |
| + range: quantity value | |
| + heat_cool_type: | |
| + name: heat_cool_type | |
| + aliases: | |
| + - heating and cooling system type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Methods of conditioning or heating a room or building | |
| + title: heating and cooling system type | |
| + examples: | |
| + - value: heat pump | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000766 | |
| + multivalued: false | |
| + range: text value | |
| + heat_deliv_loc: | |
| + name: heat_deliv_loc | |
| + aliases: | |
| + - heating delivery locations | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The location of heat delivery within the room | |
| + title: heating delivery locations | |
| + examples: | |
| + - value: north | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000810 | |
| + multivalued: false | |
| + range: text value | |
| + heat_sys_deliv_meth: | |
| + name: heat_sys_deliv_meth | |
| + aliases: | |
| + - heating system delivery method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The method by which the heat is delivered through the system | |
| + title: heating system delivery method | |
| + examples: | |
| + - value: radiant | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '[conductive|radiant]' | |
| + slot_uri: MIXS:0000812 | |
| + multivalued: false | |
| + range: string | |
| + heat_system_id: | |
| + name: heat_system_id | |
| + aliases: | |
| + - heating system identifier | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: unique identifier | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The heating system identifier | |
| + title: heating system identifier | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000833 | |
| + multivalued: false | |
| + range: text value | |
| heavy_metals: | |
| - aliases: | |
| - - extreme_unusual_properties/heavy metals | |
| - description: >- | |
| - Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:heavy_metals | |
| - | |
| + name: heavy_metals | |
| + aliases: | |
| + - extreme_unusual_properties/heavy metals | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: heavy metal name;measurement value unit | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Heavy metals present in the sequenced sample and their concentrations. | |
| + For multiple heavy metals and concentrations, add multiple copies of this field. | |
| + title: extreme_unusual_properties/heavy metals | |
| + examples: | |
| + - value: mercury;0.09 micrograms per gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000652 | |
| + multivalued: false | |
| + range: quantity value | |
| heavy_metals_meth: | |
| - aliases: | |
| - - extreme_unusual_properties/heavy metals method | |
| - description: >- | |
| - Reference or method used in determining heavy metals | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:heavy_metals_meth | |
| - | |
| - al_sat: | |
| - aliases: | |
| - - extreme_unusual_properties/Al saturation | |
| - description: >- | |
| - Aluminum saturation (esp. For tropical soils) | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:al_sat | |
| - | |
| - al_sat_meth: | |
| - aliases: | |
| - - extreme_unusual_properties/Al saturation method | |
| - description: >- | |
| - Reference or method used in determining Al saturation | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {PMID}|{DOI}|{URL} | |
| - mappings: | |
| - - mixs:al_sat_meth | |
| - | |
| - biochem_oxygen_dem: | |
| - aliases: | |
| - - biochemical oxygen demand | |
| - description: >- | |
| - Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:biochem_oxygen_dem | |
| - | |
| - chem_oxygen_dem: | |
| - aliases: | |
| - - chemical oxygen demand | |
| - description: >- | |
| - A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:chem_oxygen_dem | |
| - | |
| - efficiency_percent: | |
| - aliases: | |
| - - efficiency percent | |
| - description: >- | |
| - Percentage of volatile solids removed from the anaerobic digestor | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:efficiency_percent | |
| - | |
| - emulsions: | |
| - aliases: | |
| - - emulsions | |
| - description: >- | |
| - Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:emulsions | |
| - | |
| - gaseous_substances: | |
| - aliases: | |
| - - gaseous substances | |
| - description: >- | |
| - Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:gaseous_substances | |
| - | |
| + name: heavy_metals_meth | |
| + aliases: | |
| + - extreme_unusual_properties/heavy metals method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining heavy metals | |
| + title: extreme_unusual_properties/heavy metals method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000343 | |
| + multivalued: false | |
| + range: text value | |
| + height_carper_fiber: | |
| + name: height_carper_fiber | |
| + aliases: | |
| + - height carpet fiber mat | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average carpet fiber height in the indoor environment | |
| + title: height carpet fiber mat | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000167 | |
| + multivalued: false | |
| + range: quantity value | |
| + herbicide_regm: | |
| + name: herbicide_regm | |
| + aliases: | |
| + - herbicide regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: herbicide name;herbicide amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of herbicides; information | |
| + about treatment involving use of growth hormones; should include the name of | |
| + herbicide, amount administered, treatment regimen including how many times the | |
| + treatment was repeated, how long each treatment lasted, and the start and end | |
| + time of the entire treatment; can include multiple regimens | |
| + title: herbicide regimen | |
| + examples: | |
| + - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000561 | |
| + multivalued: false | |
| + range: quantity value | |
| + horizon: | |
| + name: horizon | |
| + aliases: | |
| + - horizon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Specific layer in the land area which measures parallel to the soil | |
| + surface and possesses physical characteristics which differ from the layers | |
| + above and beneath | |
| + title: horizon | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001082 | |
| + multivalued: false | |
| + range: text value | |
| + horizon_meth: | |
| + name: horizon_meth | |
| + aliases: | |
| + - soil horizon method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining the horizon | |
| + title: soil horizon method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000321 | |
| + multivalued: false | |
| + range: text value | |
| + host_age: | |
| + name: host_age | |
| + aliases: | |
| + - host age | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: year, day, hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Age of host at the time of sampling; relevant scale depends on species | |
| + and study, e.g. Could be seconds for amoebae or centuries for trees | |
| + title: host age | |
| + examples: | |
| + - value: 10 days | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000255 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_body_habitat: | |
| + name: host_body_habitat | |
| + aliases: | |
| + - host body habitat | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original body habitat where the sample was obtained from | |
| + title: host body habitat | |
| + examples: | |
| + - value: nasopharynx | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000866 | |
| + multivalued: false | |
| + range: text value | |
| + host_body_product: | |
| + name: host_body_product | |
| + aliases: | |
| + - host body product | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: FMA or UBERON | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Substance produced by the body, e.g. Stool, mucus, where the sample | |
| + was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy | |
| + ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma | |
| + or https://www.ebi.ac.uk/ols/ontologies/uberon | |
| + title: host body product | |
| + examples: | |
| + - value: Portion of mucus [fma66938] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000888 | |
| + multivalued: false | |
| + range: controlled term value | |
| + host_body_site: | |
| + name: host_body_site | |
| + aliases: | |
| + - host body site | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: FMA or UBERON | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of body site where the sample was obtained from, such as a specific | |
| + organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology | |
| + (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, | |
| + please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON | |
| + title: host body site | |
| + examples: | |
| + - value: gill [UBERON:0002535] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000867 | |
| + multivalued: false | |
| + range: controlled term value | |
| + host_body_temp: | |
| + name: host_body_temp | |
| + aliases: | |
| + - host body temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Core body temperature of the host when sample was collected | |
| + title: host body temperature | |
| + examples: | |
| + - value: 15 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000274 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_color: | |
| + name: host_color | |
| + aliases: | |
| + - host color | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: color | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The color of host | |
| + title: host color | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000260 | |
| + multivalued: false | |
| + range: text value | |
| + host_common_name: | |
| + name: host_common_name | |
| + aliases: | |
| + - host common name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: common name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Common name of the host. | |
| + title: host common name | |
| + examples: | |
| + - value: human | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000248 | |
| + multivalued: false | |
| + range: text value | |
| + host_diet: | |
| + name: host_diet | |
| + aliases: | |
| + - host diet | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: diet type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Type of diet depending on the host, for animals omnivore, herbivore | |
| + etc., for humans high-fat, meditteranean etc.; can include multiple diet types | |
| + title: host diet | |
| + examples: | |
| + - value: herbivore | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000869 | |
| + multivalued: false | |
| + range: text value | |
| + host_dry_mass: | |
| + name: host_dry_mass | |
| + aliases: | |
| + - host dry mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: kilogram, gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of dry mass | |
| + title: host dry mass | |
| + examples: | |
| + - value: 500 gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000257 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_family_relation: | |
| + name: host_family_relation | |
| + aliases: | |
| + - host family relationship | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: relationship type;arbitrary identifier | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Familial relationships to other hosts in the same study; can include | |
| + multiple relationships | |
| + title: host family relationship | |
| + examples: | |
| + - value: offspring;Mussel25 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{text};{text}' | |
| + slot_uri: MIXS:0000872 | |
| + multivalued: true | |
| + range: string | |
| + host_genotype: | |
| + name: host_genotype | |
| + aliases: | |
| + - host genotype | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: genotype | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Observed genotype | |
| + title: host genotype | |
| + examples: | |
| + - value: C57BL/6 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000365 | |
| + multivalued: false | |
| + range: text value | |
| + host_growth_cond: | |
| + name: host_growth_cond | |
| + aliases: | |
| + - host growth conditions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI,url or free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Literature reference giving growth conditions of the host | |
| + title: host growth conditions | |
| + examples: | |
| + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}|{text}' | |
| + slot_uri: MIXS:0000871 | |
| + multivalued: false | |
| + range: text value | |
| + host_height: | |
| + name: host_height | |
| + aliases: | |
| + - host height | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: centimeter, millimeter, meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The height of subject | |
| + title: host height | |
| + examples: | |
| + - value: 0.1 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000264 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_last_meal: | |
| + name: host_last_meal | |
| + aliases: | |
| + - host last meal | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: content;duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Content of last meal and time since feeding; can include multiple | |
| + values | |
| + title: host last meal | |
| + examples: | |
| + - value: corn feed;P2H | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{duration}' | |
| + slot_uri: MIXS:0000870 | |
| + multivalued: false | |
| + range: text value | |
| + host_length: | |
| + name: host_length | |
| + aliases: | |
| + - host length | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: centimeter, millimeter, meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The length of subject | |
| + title: host length | |
| + examples: | |
| + - value: 1 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000256 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_life_stage: | |
| + name: host_life_stage | |
| + aliases: | |
| + - host life stage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: stage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Description of life stage of host | |
| + title: host life stage | |
| + examples: | |
| + - value: adult | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000251 | |
| + multivalued: false | |
| + range: text value | |
| + host_phenotype: | |
| + name: host_phenotype | |
| + aliases: | |
| + - host phenotype | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PATO or HP | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Phenotype of human or other host. For phenotypic quality ontology | |
| + (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. | |
| + For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP | |
| + title: host phenotype | |
| + examples: | |
| + - value: elongated [PATO:0001154] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000874 | |
| + multivalued: false | |
| + range: controlled term value | |
| + host_sex: | |
| + name: host_sex | |
| + aliases: | |
| + - host sex | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Gender or physical sex of the host. | |
| + title: host sex | |
| + examples: | |
| + - value: non-binary | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000811 | |
| + multivalued: false | |
| + range: text value | |
| + host_shape: | |
| + name: host_shape | |
| + aliases: | |
| + - host shape | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: shape | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Morphological shape of host | |
| + title: host shape | |
| + examples: | |
| + - value: round | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000261 | |
| + multivalued: false | |
| + range: text value | |
| + host_subject_id: | |
| + name: host_subject_id | |
| + aliases: | |
| + - host subject id | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: unique identifier | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A unique identifier by which each subject can be referred to, de-identified. | |
| + title: host subject id | |
| + examples: | |
| + - value: MPI123 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000861 | |
| + multivalued: false | |
| + range: text value | |
| + host_subspecf_genlin: | |
| + name: host_subspecf_genlin | |
| + aliases: | |
| + - host subspecific genetic lineage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, | |
| + e.g. serovar, biotype, ecotype, variety, cultivar. | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about the genetic distinctness of the host organism below | |
| + the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, | |
| + or any relevant genetic typing schemes like Group I plasmid. Subspecies should | |
| + not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage | |
| + name and the lineage rank separated by a colon, e.g., biovar:abc123. | |
| + title: host subspecific genetic lineage | |
| + examples: | |
| + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{rank name}:{text}' | |
| + slot_uri: MIXS:0001318 | |
| + multivalued: true | |
| + range: string | |
| + host_substrate: | |
| + name: host_substrate | |
| + aliases: | |
| + - host substrate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: substrate name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The growth substrate of the host. | |
| + title: host substrate | |
| + examples: | |
| + - value: rock | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000252 | |
| + multivalued: false | |
| + range: text value | |
| + host_symbiont: | |
| + name: host_symbiont | |
| + aliases: | |
| + - observed host symbionts | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: species name or common name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: The taxonomic name of the organism(s) found living in mutualistic, | |
| + commensalistic, or parasitic symbiosis with the specific host. | |
| + title: observed host symbionts | |
| + examples: | |
| + - value: flukeworms | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0001298 | |
| + multivalued: true | |
| + range: string | |
| + host_taxid: | |
| + name: host_taxid | |
| + aliases: | |
| + - host taxid | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: NCBI taxon identifier | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: NCBI taxon id of the host, e.g. 9606 | |
| + title: host taxid | |
| + examples: | |
| + - value: '7955' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{NCBI taxid}' | |
| + slot_uri: MIXS:0000250 | |
| + multivalued: false | |
| + range: text value | |
| + host_tot_mass: | |
| + name: host_tot_mass | |
| + aliases: | |
| + - host total mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: kilogram, gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total mass of the host at collection, the unit depends on host | |
| + title: host total mass | |
| + examples: | |
| + - value: 2500 gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000263 | |
| + multivalued: false | |
| + range: quantity value | |
| + host_wet_mass: | |
| + name: host_wet_mass | |
| + aliases: | |
| + - host wet mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: kilogram, gram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of wet mass | |
| + title: host wet mass | |
| + examples: | |
| + - value: 1500 gram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000567 | |
| + multivalued: false | |
| + range: quantity value | |
| + humidity: | |
| + name: humidity | |
| + aliases: | |
| + - humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per cubic meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Amount of water vapour in the air, at the time of sampling | |
| + title: humidity | |
| + examples: | |
| + - value: 25 gram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000100 | |
| + multivalued: false | |
| + range: quantity value | |
| + humidity_regm: | |
| + name: humidity_regm | |
| + aliases: | |
| + - humidity regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: humidity value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per cubic meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving an exposure to varying degree | |
| + of humidity; information about treatment involving use of growth hormones; should | |
| + include amount of humidity administered, treatment regimen including how many | |
| + times the treatment was repeated, how long each treatment lasted, and the start | |
| + and end time of the entire treatment; can include multiple regimens | |
| + title: humidity regimen | |
| + examples: | |
| + - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000568 | |
| + multivalued: false | |
| + range: quantity value | |
| + indoor_space: | |
| + name: indoor_space | |
| + aliases: | |
| + - indoor space | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A distinguishable space within a structure, the purpose for which | |
| + discrete areas of a building is used | |
| + title: indoor space | |
| + examples: | |
| + - value: foyer | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000763 | |
| + multivalued: false | |
| + range: text value | |
| + indoor_surf: | |
| + name: indoor_surf | |
| + aliases: | |
| + - indoor surface | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Type of indoor surface | |
| + title: indoor surface | |
| + examples: | |
| + - value: wall | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000764 | |
| + multivalued: false | |
| + range: text value | |
| indust_eff_percent: | |
| - aliases: | |
| - - industrial effluent percent | |
| - description: >- | |
| - Percentage of industrial effluents received by wastewater treatment plant | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:indust_eff_percent | |
| - | |
| + name: indust_eff_percent | |
| + aliases: | |
| + - industrial effluent percent | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Percentage of industrial effluents received by wastewater treatment | |
| + plant | |
| + title: industrial effluent percent | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000662 | |
| + multivalued: false | |
| + range: quantity value | |
| inorg_particles: | |
| - aliases: | |
| - - inorganic particles | |
| - description: >- | |
| - Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:inorg_particles | |
| - | |
| - org_particles: | |
| - aliases: | |
| - - organic particles | |
| - description: >- | |
| - Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:org_particles | |
| - | |
| - pre_treatment: | |
| - aliases: | |
| - - pre-treatment | |
| - description: >- | |
| - The process of pre-treatment removes materials that can be easily collected from the raw wastewater | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:pre_treatment | |
| - | |
| - primary_treatment: | |
| - aliases: | |
| - - primary treatment | |
| - description: >- | |
| - The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:primary_treatment | |
| - | |
| - reactor_type: | |
| - aliases: | |
| - - reactor type | |
| - description: >- | |
| - Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:reactor_type | |
| - | |
| - secondary_treatment: | |
| - aliases: | |
| - - secondary treatment | |
| - description: >- | |
| - The process for substantially degrading the biological content of the sewage | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:secondary_treatment | |
| - | |
| - sewage_type: | |
| - aliases: | |
| - - sewage type | |
| - description: >- | |
| - Type of wastewater treatment plant as municipial or industrial | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:sewage_type | |
| - | |
| - sludge_retent_time: | |
| - aliases: | |
| - - sludge retention time | |
| - description: >- | |
| - The time activated sludge remains in reactor | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:sludge_retent_time | |
| - | |
| - soluble_inorg_mat: | |
| - aliases: | |
| - - soluble inorganic material | |
| - description: >- | |
| - Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:soluble_inorg_mat | |
| - | |
| - soluble_org_mat: | |
| - aliases: | |
| - - soluble organic material | |
| - description: >- | |
| - Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:soluble_org_mat | |
| - | |
| - tertiary_treatment: | |
| - aliases: | |
| - - tertiary treatment | |
| - description: >- | |
| - The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:tertiary_treatment | |
| - | |
| - tot_phosphate: | |
| - aliases: | |
| - - total phosphate | |
| - description: >- | |
| - Total amount or concentration of phosphate | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_phosphate | |
| - | |
| - wastewater_type: | |
| - aliases: | |
| - - wastewater type | |
| - description: >- | |
| - The origin of wastewater such as human waste, rainfall, storm drains, etc. | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: text value ## syntax: {text} | |
| - mappings: | |
| - - mixs:wastewater_type | |
| - | |
| - atmospheric_data: | |
| - aliases: | |
| - - atmospheric data | |
| - description: >- | |
| - Measurement of atmospheric data; can include multiple data | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {text};{float} {unit} | |
| - string_serialization: "{text};{float} {unit}" | |
| - mappings: | |
| - - mixs:atmospheric_data | |
| - | |
| - bac_prod: | |
| - aliases: | |
| - - bacterial production | |
| - description: >- | |
| - Bacterial production in the water column measured by isotope uptake | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:bac_prod | |
| - | |
| - bac_resp: | |
| - aliases: | |
| - - bacterial respiration | |
| - description: >- | |
| - Measurement of bacterial respiration in the water column | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:bac_resp | |
| - | |
| - conduc: | |
| - aliases: | |
| - - conductivity | |
| - description: >- | |
| - Electrical conductivity of water | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:conduc | |
| - | |
| - diss_inorg_nitro: | |
| - aliases: | |
| - - dissolved inorganic nitrogen | |
| - description: >- | |
| - Concentration of dissolved inorganic nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:diss_inorg_nitro | |
| - | |
| - down_par: | |
| - aliases: | |
| - - downward PAR | |
| - description: >- | |
| - Visible waveband radiance and irradiance measurements in the water column | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:down_par | |
| - | |
| - fluor: | |
| - aliases: | |
| - - fluorescence | |
| - description: >- | |
| - Raw or converted fluorescence of water | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:fluor | |
| - | |
| + name: inorg_particles | |
| + aliases: | |
| + - inorganic particles | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: inorganic particle name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of particles such as sand, grit, metal particles, ceramics, | |
| + etc.; can include multiple particles | |
| + title: inorganic particles | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000664 | |
| + multivalued: false | |
| + range: quantity value | |
| + inside_lux: | |
| + name: inside_lux | |
| + aliases: | |
| + - inside lux light | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: kilowatt per square metre | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The recorded value at sampling time (power density) | |
| + title: inside lux light | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000168 | |
| + multivalued: false | |
| + range: quantity value | |
| + int_wall_cond: | |
| + name: int_wall_cond | |
| + aliases: | |
| + - interior wall condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The physical condition of the wall at the time of sampling; photos | |
| + or video preferred; use drawings to indicate location of damaged areas | |
| + title: interior wall condition | |
| + examples: | |
| + - value: damaged | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000813 | |
| + multivalued: false | |
| + range: text value | |
| + iw_bt_date_well: | |
| + name: iw_bt_date_well | |
| + aliases: | |
| + - injection water breakthrough date of specific well | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Injection water breakthrough date per well following a secondary | |
| + and/or tertiary recovery | |
| + title: injection water breakthrough date of specific well | |
| + examples: | |
| + - value: '2018-05-11' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001010 | |
| + multivalued: false | |
| + range: timestamp value | |
| + iwf: | |
| + name: iwf | |
| + aliases: | |
| + - injection water fraction | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Proportion of the produced fluids derived from injected water at | |
| + the time of sampling. (e.g. 87%) | |
| + title: injection water fraction | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000455 | |
| + multivalued: false | |
| + range: quantity value | |
| + last_clean: | |
| + name: last_clean | |
| + aliases: | |
| + - last time swept/mopped/vacuumed | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The last time the floor was cleaned (swept, mopped, vacuumed) | |
| + title: last time swept/mopped/vacuumed | |
| + examples: | |
| + - value: 2018-05-11:T14:30Z | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000814 | |
| + multivalued: false | |
| + range: timestamp value | |
| + lat_lon: | |
| + name: lat_lon | |
| + aliases: | |
| + - geographic location (latitude and longitude) | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: decimal degrees, limit to 8 decimal points | |
| + description: The geographical origin of the sample as defined by latitude and | |
| + longitude. The values should be reported in decimal degrees and in WGS84 system | |
| + title: geographic location (latitude and longitude) | |
| + examples: | |
| + - value: 50.586825 6.408977 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {float}' | |
| + slot_uri: MIXS:0000009 | |
| + multivalued: false | |
| + range: geolocation value | |
| light_intensity: | |
| - aliases: | |
| - - light intensity | |
| - description: >- | |
| - Measurement of light intensity | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:light_intensity | |
| - | |
| + name: light_intensity | |
| + aliases: | |
| + - light intensity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: lux | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of light intensity | |
| + title: light intensity | |
| + examples: | |
| + - value: 0.3 lux | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000706 | |
| + multivalued: false | |
| + range: quantity value | |
| + light_regm: | |
| + name: light_regm | |
| + aliases: | |
| + - light regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: exposure type;light intensity;light quality | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: lux; micrometer, nanometer, angstrom | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Information about treatment(s) involving exposure to light, including | |
| + both light intensity and quality. | |
| + title: light regimen | |
| + examples: | |
| + - value: incandescant light;10 lux;450 nanometer | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{float} {unit}' | |
| + slot_uri: MIXS:0000569 | |
| + multivalued: false | |
| + range: quantity value | |
| + light_type: | |
| + name: light_type | |
| + aliases: | |
| + - light type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Application of light to achieve some practical or aesthetic effect. | |
| + Lighting includes the use of both artificial light sources such as lamps and | |
| + light fixtures, as well as natural illumination by capturing daylight. Can also | |
| + include absence of light | |
| + title: light type | |
| + examples: | |
| + - value: desk lamp | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000769 | |
| + multivalued: false | |
| + range: text value | |
| + link_addit_analys: | |
| + name: link_addit_analys | |
| + aliases: | |
| + - links to additional analysis | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Link to additional analysis results performed on the sample | |
| + title: links to additional analysis | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000340 | |
| + multivalued: false | |
| + range: text value | |
| + link_class_info: | |
| + name: link_class_info | |
| + aliases: | |
| + - link to classification information | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Link to digitized soil maps or other soil classification information | |
| + title: link to classification information | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000329 | |
| + multivalued: false | |
| + range: text value | |
| + link_climate_info: | |
| + name: link_climate_info | |
| + aliases: | |
| + - link to climate information | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Link to climate resource | |
| + title: link to climate information | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000328 | |
| + multivalued: false | |
| + range: text value | |
| + lithology: | |
| + name: lithology | |
| + aliases: | |
| + - lithology | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). | |
| + If "other" is specified, please propose entry in "additional info" field' | |
| + title: lithology | |
| + examples: | |
| + - value: Volcanic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000990 | |
| + multivalued: false | |
| + range: text value | |
| + local_class: | |
| + name: local_class | |
| + aliases: | |
| + - soil_taxonomic/local classification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: local classification name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Soil classification based on local soil classification system | |
| + title: soil_taxonomic/local classification | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000330 | |
| + multivalued: false | |
| + range: text value | |
| + local_class_meth: | |
| + name: local_class_meth | |
| + aliases: | |
| + - soil_taxonomic/local classification method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining the local soil classification | |
| + title: soil_taxonomic/local classification method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000331 | |
| + multivalued: false | |
| + range: text value | |
| + magnesium: | |
| + name: magnesium | |
| + aliases: | |
| + - magnesium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mole per liter, milligram per liter, parts per million, micromole per | |
| + kilogram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of magnesium in the sample | |
| + title: magnesium | |
| + examples: | |
| + - value: 52.8 micromole per kilogram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000431 | |
| + multivalued: false | |
| + range: quantity value | |
| + max_occup: | |
| + name: max_occup | |
| + aliases: | |
| + - maximum occupancy | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The maximum amount of people allowed in the indoor environment | |
| + title: maximum occupancy | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000229 | |
| + multivalued: false | |
| + range: quantity value | |
| + mean_frict_vel: | |
| + name: mean_frict_vel | |
| + aliases: | |
| + - mean friction velocity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter per second | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of mean friction velocity | |
| + title: mean friction velocity | |
| + examples: | |
| + - value: 0.5 meter per second | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000498 | |
| + multivalued: false | |
| + range: quantity value | |
| + mean_peak_frict_vel: | |
| + name: mean_peak_frict_vel | |
| + aliases: | |
| + - mean peak friction velocity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter per second | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of mean peak friction velocity | |
| + title: mean peak friction velocity | |
| + examples: | |
| + - value: 1 meter per second | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000502 | |
| + multivalued: false | |
| + range: quantity value | |
| + mech_struc: | |
| + name: mech_struc | |
| + aliases: | |
| + - mechanical structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'mechanical structure: a moving structure' | |
| + title: mechanical structure | |
| + examples: | |
| + - value: elevator | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000815 | |
| + multivalued: false | |
| + range: text value | |
| + mechanical_damage: | |
| + name: mechanical_damage | |
| + aliases: | |
| + - mechanical damage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: damage type;body site | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about any mechanical damage exerted on the plant; can | |
| + include multiple damages and sites | |
| + title: mechanical damage | |
| + examples: | |
| + - value: pruning;bark | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{text}' | |
| + slot_uri: MIXS:0001052 | |
| + multivalued: false | |
| + range: text value | |
| + methane: | |
| + name: methane | |
| + aliases: | |
| + - methane | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, parts per billion, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Methane (gas) amount or concentration at the time of sampling | |
| + title: methane | |
| + examples: | |
| + - value: 1800 parts per billion | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000101 | |
| + multivalued: false | |
| + range: quantity value | |
| + micro_biomass_meth: | |
| + name: micro_biomass_meth | |
| + aliases: | |
| + - microbial biomass method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining microbial biomass | |
| + title: microbial biomass method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000339 | |
| + multivalued: false | |
| + range: string | |
| + microbial_biomass: | |
| + name: microbial_biomass | |
| + aliases: | |
| + - microbial biomass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: ton, kilogram, gram per kilogram soil | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The part of the organic matter in the soil that constitutes living | |
| + microorganisms smaller than 5-10 micrometer. If you keep this, you would need | |
| + to have correction factors used for conversion to the final units | |
| + title: microbial biomass | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000650 | |
| + multivalued: false | |
| + range: quantity value | |
| + microbial_biomass_meth: | |
| + name: microbial_biomass_meth | |
| + aliases: | |
| + - microbial biomass method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining microbial biomass | |
| + title: microbial biomass method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID|DOI|URL}' | |
| + slot_uri: MIXS:0000339 | |
| + multivalued: false | |
| + range: text value | |
| + mineral_nutr_regm: | |
| + name: mineral_nutr_regm | |
| + aliases: | |
| + - mineral nutrient regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: mineral nutrient name;mineral nutrient amount;treatment interval and | |
| + duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving the use of mineral supplements; | |
| + should include the name of mineral nutrient, amount administered, treatment | |
| + regimen including how many times the treatment was repeated, how long each treatment | |
| + lasted, and the start and end time of the entire treatment; can include multiple | |
| + mineral nutrient regimens | |
| + title: mineral nutrient regimen | |
| + examples: | |
| + - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000570 | |
| + multivalued: false | |
| + range: quantity value | |
| + misc_param: | |
| + name: misc_param | |
| + aliases: | |
| + - miscellaneous parameter | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: parameter name;measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Any other measurement performed or parameter collected, that is not | |
| + listed here | |
| + title: miscellaneous parameter | |
| + examples: | |
| + - value: Bicarbonate ion concentration;2075 micromole per kilogram | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000752 | |
| + multivalued: false | |
| + range: quantity value | |
| + n_alkanes: | |
| + name: n_alkanes | |
| + aliases: | |
| + - n-alkanes | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: n-alkane name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of n-alkanes; can include multiple n-alkanes | |
| + title: n-alkanes | |
| + examples: | |
| + - value: n-hexadecane;100 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000503 | |
| + multivalued: false | |
| + range: quantity value | |
| + nitrate: | |
| + name: nitrate | |
| + aliases: | |
| + - nitrate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of nitrate in the sample | |
| + title: nitrate | |
| + examples: | |
| + - value: 65 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000425 | |
| + multivalued: false | |
| + range: quantity value | |
| + nitrite: | |
| + name: nitrite | |
| + aliases: | |
| + - nitrite | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of nitrite in the sample | |
| + title: nitrite | |
| + examples: | |
| + - value: 0.5 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000426 | |
| + multivalued: false | |
| + range: quantity value | |
| + nitro: | |
| + name: nitro | |
| + aliases: | |
| + - nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of nitrogen (total) | |
| + title: nitrogen | |
| + examples: | |
| + - value: 4.2 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000504 | |
| + multivalued: false | |
| + range: quantity value | |
| + non_min_nutr_regm: | |
| + name: non_min_nutr_regm | |
| + aliases: | |
| + - non-mineral nutrient regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval | |
| + and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving the exposure of plant to non-mineral | |
| + nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral | |
| + nutrient, amount administered, treatment regimen including how many times the | |
| + treatment was repeated, how long each treatment lasted, and the start and end | |
| + time of the entire treatment; can include multiple non-mineral nutrient regimens | |
| + title: non-mineral nutrient regimen | |
| + examples: | |
| + - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000571 | |
| + multivalued: true | |
| + range: string | |
| + nucl_acid_amp: | |
| + name: nucl_acid_amp | |
| + aliases: | |
| + - nucleic acid amplification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID, DOI or URL | |
| + description: A link to a literature reference, electronic resource or a standard | |
| + operating procedure (SOP), that describes the enzymatic amplification (PCR, | |
| + TMA, NASBA) of specific nucleic acids | |
| + title: nucleic acid amplification | |
| + examples: | |
| + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000038 | |
| + multivalued: false | |
| + range: text value | |
| + nucl_acid_ext: | |
| + name: nucl_acid_ext | |
| + aliases: | |
| + - nucleic acid extraction | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID, DOI or URL | |
| + description: A link to a literature reference, electronic resource or a standard | |
| + operating procedure (SOP), that describes the material separation to recover | |
| + the nucleic acid fraction from a sample | |
| + title: nucleic acid extraction | |
| + examples: | |
| + - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000037 | |
| + multivalued: false | |
| + range: text value | |
| + number_pets: | |
| + name: number_pets | |
| + aliases: | |
| + - number of pets | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of pets residing in the sampled space | |
| + title: number of pets | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000231 | |
| + multivalued: false | |
| + range: quantity value | |
| + number_plants: | |
| + name: number_plants | |
| + aliases: | |
| + - number of houseplants | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of plant(s) in the sampling space | |
| + title: number of houseplants | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000230 | |
| + multivalued: false | |
| + range: quantity value | |
| + number_resident: | |
| + name: number_resident | |
| + aliases: | |
| + - number of residents | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of individuals currently occupying in the sampling location | |
| + title: number of residents | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000232 | |
| + multivalued: false | |
| + range: quantity value | |
| + occup_density_samp: | |
| + name: occup_density_samp | |
| + aliases: | |
| + - occupant density at sampling | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Average number of occupants at time of sampling per square footage | |
| + title: occupant density at sampling | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000217 | |
| + multivalued: false | |
| + range: quantity value | |
| + occup_document: | |
| + name: occup_document | |
| + aliases: | |
| + - occupancy documentation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of documentation of occupancy | |
| + title: occupancy documentation | |
| + examples: | |
| + - value: estimate | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000816 | |
| + multivalued: false | |
| + range: text value | |
| + occup_samp: | |
| + name: occup_samp | |
| + aliases: | |
| + - occupancy at sampling | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Number of occupants present at time of sample within the given space | |
| + title: occupancy at sampling | |
| + examples: | |
| + - value: '10' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000772 | |
| + multivalued: false | |
| + range: quantity value | |
| + org_carb: | |
| + name: org_carb | |
| + aliases: | |
| + - organic carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of organic carbon | |
| + title: organic carbon | |
| + examples: | |
| + - value: 1.5 microgram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000508 | |
| + multivalued: false | |
| + range: quantity value | |
| + org_count_qpcr_info: | |
| + name: org_count_qpcr_info | |
| + aliases: | |
| + - organism count qPCR information | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial | |
| + denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final | |
| + elongation:degrees_minutes; total cycles | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: number of cells per gram (or ml or cm^2) | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'If qpcr was used for the cell count, the target gene name, the primer | |
| + sequence and the cycling conditions should also be provided. (Example: 16S rrna; | |
| + FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; | |
| + annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; | |
| + 30 cycles)' | |
| + title: organism count qPCR information | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final | |
| + elongation:degrees_minutes; total cycles' | |
| + slot_uri: MIXS:0000099 | |
| + multivalued: false | |
| + range: string | |
| + org_matter: | |
| + name: org_matter | |
| + aliases: | |
| + - organic matter | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of organic matter | |
| + title: organic matter | |
| + examples: | |
| + - value: 1.75 milligram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000204 | |
| + multivalued: false | |
| + range: quantity value | |
| + org_nitro: | |
| + name: org_nitro | |
| + aliases: | |
| + - organic nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of organic nitrogen | |
| + title: organic nitrogen | |
| + examples: | |
| + - value: 4 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000205 | |
| + multivalued: false | |
| + range: quantity value | |
| + org_particles: | |
| + name: org_particles | |
| + aliases: | |
| + - organic particles | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: particle name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of particles such as faeces, hairs, food, vomit, paper | |
| + fibers, plant material, humus, etc. | |
| + title: organic particles | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000665 | |
| + multivalued: false | |
| + range: quantity value | |
| + organism_count: | |
| + name: organism_count | |
| + aliases: | |
| + - organism count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: organism name;measurement value;enumeration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: number of cells per cubic meter, number of cells per milliliter, number | |
| + of cells per cubic centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: 'Total cell count of any organism (or group of organisms) per gram, | |
| + volume or area of sample, should include name of organism followed by count. | |
| + The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should | |
| + also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' | |
| + title: organism count | |
| + examples: | |
| + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000103 | |
| + multivalued: false | |
| + range: quantity value | |
| + owc_tvdss: | |
| + name: owc_tvdss | |
| + aliases: | |
| + - oil water contact depth | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) | |
| + title: oil water contact depth | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000405 | |
| + multivalued: false | |
| + range: quantity value | |
| + oxy_stat_samp: | |
| + name: oxy_stat_samp | |
| + aliases: | |
| + - oxygenation status of sample | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Oxygenation status of sample | |
| + title: oxygenation status of sample | |
| + examples: | |
| + - value: aerobic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000753 | |
| + multivalued: false | |
| + range: text value | |
| + oxygen: | |
| + name: oxygen | |
| + aliases: | |
| + - oxygen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Oxygen (gas) amount or concentration at the time of sampling | |
| + title: oxygen | |
| + examples: | |
| + - value: 600 parts per million | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000104 | |
| + multivalued: false | |
| + range: quantity value | |
| + part_org_carb: | |
| + name: part_org_carb | |
| + aliases: | |
| + - particulate organic carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of particulate organic carbon | |
| + title: particulate organic carbon | |
| + examples: | |
| + - value: 1.92 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000515 | |
| + multivalued: false | |
| + range: quantity value | |
| part_org_nitro: | |
| - aliases: | |
| - - particulate organic nitrogen | |
| - description: >- | |
| - Concentration of particulate organic nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:part_org_nitro | |
| - | |
| + name: part_org_nitro | |
| + aliases: | |
| + - particulate organic nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of particulate organic nitrogen | |
| + title: particulate organic nitrogen | |
| + examples: | |
| + - value: 0.3 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000719 | |
| + multivalued: false | |
| + range: quantity value | |
| + particle_class: | |
| + name: particle_class | |
| + aliases: | |
| + - particle classification | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: particle name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micrometer | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Particles are classified, based on their size, into six general categories:clay, | |
| + silt, sand, gravel, cobbles, and boulders; should include amount of particle | |
| + preceded by the name of the particle type; can include multiple values | |
| + title: particle classification | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000206 | |
| + multivalued: false | |
| + range: quantity value | |
| + pcr_cond: | |
| + name: pcr_cond | |
| + aliases: | |
| + - pcr conditions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final | |
| + elongation:degrees_minutes;total cycles | |
| + description: Description of reaction conditions and components of PCR in the form | |
| + of 'initial denaturation:94degC_1.5min; annealing=...' | |
| + title: pcr conditions | |
| + examples: | |
| + - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final | |
| + elongation:degrees_minutes;total cycles | |
| + slot_uri: MIXS:0000049 | |
| + multivalued: false | |
| + range: text value | |
| + pcr_primers: | |
| + name: pcr_primers | |
| + aliases: | |
| + - pcr primers | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: 'FWD: forward primer sequence;REV:reverse primer sequence' | |
| + description: PCR primers that were used to amplify the sequence of the targeted | |
| + gene, locus or subfragment. This field should contain all the primers used for | |
| + a single PCR reaction if multiple forward or reverse primers are present in | |
| + a single PCR reaction. The primer sequence should be reported in uppercase letters | |
| + title: pcr primers | |
| + examples: | |
| + - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: FWD:{dna};REV:{dna} | |
| + slot_uri: MIXS:0000046 | |
| + multivalued: false | |
| + range: text value | |
| + permeability: | |
| + name: permeability | |
| + aliases: | |
| + - permeability | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mD | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Measure of the ability of a hydrocarbon resource to allow fluids | |
| + to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' | |
| + title: permeability | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer} - {integer} {unit}' | |
| + slot_uri: MIXS:0000404 | |
| + multivalued: false | |
| + range: quantity value | |
| + perturbation: | |
| + name: perturbation | |
| + aliases: | |
| + - perturbation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: perturbation type name;perturbation interval and duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Type of perturbation, e.g. chemical administration, physical disturbance, | |
| + etc., coupled with perturbation regimen including how many times the perturbation | |
| + was repeated, how long each perturbation lasted, and the start and end time | |
| + of the entire perturbation period; can include multiple perturbation types | |
| + title: perturbation | |
| + examples: | |
| + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000754 | |
| + multivalued: false | |
| + range: text value | |
| + pesticide_regm: | |
| + name: pesticide_regm | |
| + aliases: | |
| + - pesticide regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: pesticide name;pesticide amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of insecticides; should | |
| + include the name of pesticide, amount administered, treatment regimen including | |
| + how many times the treatment was repeated, how long each treatment lasted, and | |
| + the start and end time of the entire treatment; can include multiple pesticide | |
| + regimens | |
| + title: pesticide regimen | |
| + examples: | |
| + - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000573 | |
| + multivalued: false | |
| + range: quantity value | |
| + petroleum_hydrocarb: | |
| + name: petroleum_hydrocarb | |
| + aliases: | |
| + - petroleum hydrocarbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of petroleum hydrocarbon | |
| + title: petroleum hydrocarbon | |
| + examples: | |
| + - value: 0.05 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000516 | |
| + multivalued: false | |
| + range: quantity value | |
| + ph: | |
| + name: ph | |
| + aliases: | |
| + - pH | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Ph measurement of the sample, or liquid portion of sample, or aqueous | |
| + phase of the fluid | |
| + title: pH | |
| + examples: | |
| + - value: '7.2' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001001 | |
| + multivalued: false | |
| + range: quantity value | |
| + ph_meth: | |
| + name: ph_meth | |
| + aliases: | |
| + - pH method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining ph | |
| + title: pH method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0001106 | |
| + multivalued: false | |
| + range: text value | |
| + ph_regm: | |
| + name: ph_regm | |
| + aliases: | |
| + - pH regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;treatment interval and duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving exposure of plants to varying | |
| + levels of ph of the growth media, treatment regimen including how many times | |
| + the treatment was repeated, how long each treatment lasted, and the start and | |
| + end time of the entire treatment; can include multiple regimen | |
| + title: pH regimen | |
| + examples: | |
| + - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0001056 | |
| + multivalued: false | |
| + range: text value | |
| + phaeopigments: | |
| + name: phaeopigments | |
| + aliases: | |
| + - phaeopigments | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: phaeopigment name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per cubic meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of phaeopigments; can include multiple phaeopigments | |
| + title: phaeopigments | |
| + examples: | |
| + - value: 2.5 milligram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000180 | |
| + multivalued: false | |
| + range: quantity value | |
| + phosphate: | |
| + name: phosphate | |
| + aliases: | |
| + - phosphate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of phosphate | |
| + title: phosphate | |
| + examples: | |
| + - value: 0.7 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000505 | |
| + multivalued: false | |
| + range: quantity value | |
| + phosplipid_fatt_acid: | |
| + name: phosplipid_fatt_acid | |
| + aliases: | |
| + - phospholipid fatty acid | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: phospholipid fatty acid name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: mole per gram, mole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of phospholipid fatty acids; can include multiple values | |
| + title: phospholipid fatty acid | |
| + examples: | |
| + - value: 2.98 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000181 | |
| + multivalued: false | |
| + range: quantity value | |
| photon_flux: | |
| - aliases: | |
| - - photon flux | |
| - description: >- | |
| - Measurement of photon flux | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:photon_flux | |
| - | |
| + name: photon_flux | |
| + aliases: | |
| + - photon flux | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: number of photons per second per unit area | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of photon flux | |
| + title: photon flux | |
| + examples: | |
| + - value: 3.926 micromole photons per second per square meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000725 | |
| + multivalued: false | |
| + range: quantity value | |
| + plant_growth_med: | |
| + name: plant_growth_med | |
| + aliases: | |
| + - plant growth medium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: EO or enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Specification of the media for growing the plants or tissue cultured | |
| + samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in | |
| + vitro liquid culture medium. Recommended value is a specific value from EO:plant | |
| + growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) | |
| + or other controlled vocabulary | |
| + title: plant growth medium | |
| + examples: | |
| + - value: hydroponic plant culture media [EO:0007067] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001057 | |
| + multivalued: false | |
| + range: controlled term value | |
| + plant_product: | |
| + name: plant_product | |
| + aliases: | |
| + - plant product | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: product name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Substance produced by the plant, where the sample was obtained from | |
| + title: plant product | |
| + examples: | |
| + - value: xylem sap [PO:0025539] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0001058 | |
| + multivalued: false | |
| + range: text value | |
| + plant_sex: | |
| + name: plant_sex | |
| + aliases: | |
| + - plant sex | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, | |
| + staminate, monoecieous, hermaphrodite. | |
| + title: plant sex | |
| + examples: | |
| + - value: Hermaphroditic | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001059 | |
| + multivalued: false | |
| + range: text value | |
| + plant_struc: | |
| + name: plant_struc | |
| + aliases: | |
| + - plant structure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PO | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of plant structure the sample was obtained from; for Plant Ontology | |
| + (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, | |
| + e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the | |
| + sex of it can be recorded here. | |
| + title: plant structure | |
| + examples: | |
| + - value: epidermis [PO:0005679] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0001060 | |
| + multivalued: false | |
| + range: controlled term value | |
| + pollutants: | |
| + name: pollutants | |
| + aliases: | |
| + - pollutants | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: pollutant name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, mole per liter, milligram per liter, microgram per cubic meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Pollutant types and, amount or concentrations measured at the time | |
| + of sampling; can report multiple pollutants by entering numeric values preceded | |
| + by name of pollutant | |
| + title: pollutants | |
| + examples: | |
| + - value: lead;0.15 microgram per cubic meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000107 | |
| + multivalued: false | |
| + range: quantity value | |
| + pool_dna_extracts: | |
| + name: pool_dna_extracts | |
| + aliases: | |
| + - pooling of DNA extracts (if done) | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: pooling status;number of pooled extracts | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Indicate whether multiple DNA extractions were mixed. If the answer | |
| + yes, the number of extracts that were pooled should be given | |
| + title: pooling of DNA extracts (if done) | |
| + examples: | |
| + - value: yes;5 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{boolean};{integer}' | |
| + slot_uri: MIXS:0000325 | |
| + multivalued: false | |
| + range: text value | |
| + porosity: | |
| + name: porosity | |
| + aliases: | |
| + - porosity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value or range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Porosity of deposited sediment is volume of voids divided by the | |
| + total volume of sample | |
| + title: porosity | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} - {float} {unit}' | |
| + slot_uri: MIXS:0000211 | |
| + multivalued: false | |
| + range: quantity value | |
| + potassium: | |
| + name: potassium | |
| + aliases: | |
| + - potassium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of potassium in the sample | |
| + title: potassium | |
| + examples: | |
| + - value: 463 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000430 | |
| + multivalued: false | |
| + range: quantity value | |
| + pour_point: | |
| + name: pour_point | |
| + aliases: | |
| + - pour point | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Temperature at which a liquid becomes semi solid and loses its flow | |
| + characteristics. In crude oil a high pour point is generally associated with | |
| + a high paraffin content, typically found in crude deriving from a larger proportion | |
| + of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' | |
| + title: pour point | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000127 | |
| + multivalued: false | |
| + range: quantity value | |
| + pre_treatment: | |
| + name: pre_treatment | |
| + aliases: | |
| + - pre-treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: pre-treatment type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The process of pre-treatment removes materials that can be easily | |
| + collected from the raw wastewater | |
| + title: pre-treatment | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000348 | |
| + multivalued: false | |
| + range: text value | |
| + pres_animal_insect: | |
| + name: pres_animal_insect | |
| + aliases: | |
| + - presence of pets, animals, or insects | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration;count | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type and number of animals or insects present in the sampling | |
| + space. | |
| + title: presence of pets, animals, or insects | |
| + examples: | |
| + - value: cat;5 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000819 | |
| + multivalued: false | |
| + range: string | |
| + pattern: ^(cat|dog|rodent|snake|other);\d+$ | |
| + pressure: | |
| + name: pressure | |
| + aliases: | |
| + - pressure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: atmosphere | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Pressure to which the sample is subject to, in atmospheres | |
| + title: pressure | |
| + examples: | |
| + - value: 50 atmosphere | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000412 | |
| + multivalued: false | |
| + range: quantity value | |
| + prev_land_use_meth: | |
| + name: prev_land_use_meth | |
| + aliases: | |
| + - history/previous land use method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining previous land use and dates | |
| + title: history/previous land use method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000316 | |
| + multivalued: false | |
| + range: string | |
| + previous_land_use: | |
| + name: previous_land_use | |
| + aliases: | |
| + - history/previous land use | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: land use name;date | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Previous land use and dates | |
| + title: history/previous land use | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{timestamp}' | |
| + slot_uri: MIXS:0000315 | |
| + multivalued: false | |
| + range: text value | |
| + previous_land_use_meth: | |
| + name: previous_land_use_meth | |
| + aliases: | |
| + - history/previous land use method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining previous land use and dates | |
| + title: history/previous land use method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID|DOI|URL}' | |
| + slot_uri: MIXS:0000316 | |
| + multivalued: false | |
| + range: text value | |
| primary_prod: | |
| - aliases: | |
| - - primary production | |
| - description: >- | |
| - Measurement of primary production, generally measured as isotope uptake | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:primary_prod | |
| - | |
| + name: primary_prod | |
| + aliases: | |
| + - primary production | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per cubic meter per day, gram per square meter per day | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of primary production, generally measured as isotope | |
| + uptake | |
| + title: primary production | |
| + examples: | |
| + - value: 100 milligram per cubic meter per day | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000728 | |
| + multivalued: false | |
| + range: quantity value | |
| + primary_treatment: | |
| + name: primary_treatment | |
| + aliases: | |
| + - primary treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: primary treatment type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The process to produce both a generally homogeneous liquid capable | |
| + of being treated biologically and a sludge that can be separately treated or | |
| + processed | |
| + title: primary treatment | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000349 | |
| + multivalued: false | |
| + range: text value | |
| + prod_rate: | |
| + name: prod_rate | |
| + aliases: | |
| + - production rate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cubic meter per day | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Oil and/or gas production rates per well (e.g. 524 m3 / day) | |
| + title: production rate | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000452 | |
| + multivalued: false | |
| + range: quantity value | |
| + prod_start_date: | |
| + name: prod_start_date | |
| + aliases: | |
| + - production start date | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: timestamp | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Date of field's first production | |
| + title: production start date | |
| + examples: | |
| + - value: '2018-05-11' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001008 | |
| + multivalued: false | |
| + range: timestamp value | |
| + profile_position: | |
| + name: profile_position | |
| + aliases: | |
| + - profile position | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Cross-sectional position in the hillslope where sample was collected.sample | |
| + area position in relation to surrounding areas | |
| + title: profile position | |
| + examples: | |
| + - value: summit | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001084 | |
| + multivalued: false | |
| + range: text value | |
| + quad_pos: | |
| + name: quad_pos | |
| + aliases: | |
| + - quadrant position | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The quadrant position of the sampling room within the building | |
| + title: quadrant position | |
| + examples: | |
| + - value: West side | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000820 | |
| + multivalued: false | |
| + range: text value | |
| + radiation_regm: | |
| + name: radiation_regm | |
| + aliases: | |
| + - radiation regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: radiation type name;radiation amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: rad, gray | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving exposure of plant or a plant | |
| + part to a particular radiation regimen; should include the radiation type, amount | |
| + or intensity administered, treatment regimen including how many times the treatment | |
| + was repeated, how long each treatment lasted, and the start and end time of | |
| + the entire treatment; can include multiple radiation regimens | |
| + title: radiation regimen | |
| + examples: | |
| + - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000575 | |
| + multivalued: false | |
| + range: quantity value | |
| + rainfall_regm: | |
| + name: rainfall_regm | |
| + aliases: | |
| + - rainfall regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving an exposure to a given amount | |
| + of rainfall, treatment regimen including how many times the treatment was repeated, | |
| + how long each treatment lasted, and the start and end time of the entire treatment; | |
| + can include multiple regimens | |
| + title: rainfall regimen | |
| + examples: | |
| + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000576 | |
| + multivalued: false | |
| + range: quantity value | |
| + reactor_type: | |
| + name: reactor_type | |
| + aliases: | |
| + - reactor type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: reactor type name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Anaerobic digesters can be designed and engineered to operate using | |
| + a number of different process configurations, as batch or continuous, mesophilic, | |
| + high solid or low solid, and single stage or multistage | |
| + title: reactor type | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000350 | |
| + multivalued: false | |
| + range: text value | |
| + redox_potential: | |
| + name: redox_potential | |
| + aliases: | |
| + - redox potential | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millivolt | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Redox potential, measured relative to a hydrogen cell, indicating | |
| + oxidation or reduction potential | |
| + title: redox potential | |
| + examples: | |
| + - value: 300 millivolt | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000182 | |
| + multivalued: false | |
| + range: quantity value | |
| + rel_air_humidity: | |
| + name: rel_air_humidity | |
| + aliases: | |
| + - relative air humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Partial vapor and air pressure, density of the vapor and air, or | |
| + by the actual mass of the vapor and air | |
| + title: relative air humidity | |
| + examples: | |
| + - value: 80% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000121 | |
| + multivalued: false | |
| + range: quantity value | |
| + rel_humidity_out: | |
| + name: rel_humidity_out | |
| + aliases: | |
| + - outside relative humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram of air, kilogram of air | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The recorded outside relative humidity value at the time of sampling | |
| + title: outside relative humidity | |
| + examples: | |
| + - value: 12 per kilogram of air | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000188 | |
| + multivalued: false | |
| + range: quantity value | |
| + rel_samp_loc: | |
| + name: rel_samp_loc | |
| + aliases: | |
| + - relative sampling location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The sampling location within the train car | |
| + title: relative sampling location | |
| + examples: | |
| + - value: center of car | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000821 | |
| + multivalued: false | |
| + range: text value | |
| + rel_to_oxygen: | |
| + name: rel_to_oxygen | |
| + aliases: | |
| + - relationship to oxygen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + description: Is this organism an aerobe, anaerobe? Please note that aerobic and | |
| + anaerobic are valid descriptors for microbial environments | |
| + title: relationship to oxygen | |
| + examples: | |
| + - value: aerobe | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000015 | |
| + multivalued: false | |
| + range: text value | |
| + reservoir: | |
| + name: reservoir | |
| + aliases: | |
| + - reservoir name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of the reservoir (e.g. Carapebus) | |
| + title: reservoir name | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000303 | |
| + multivalued: false | |
| + range: text value | |
| + resins_pc: | |
| + name: resins_pc | |
| + aliases: | |
| + - resins wt% | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis | |
| + method that divides crude oil components according to their polarizability | |
| + and polarity. There are three main methods to obtain SARA results. The most | |
| + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: | |
| + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' | |
| + title: resins wt% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000134 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_air_exch_rate: | |
| + name: room_air_exch_rate | |
| + aliases: | |
| + - room air exchange rate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: liter per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The rate at which outside air replaces indoor air in a given space | |
| + title: room air exchange rate | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000169 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_architec_elem: | |
| + name: room_architec_elem | |
| + aliases: | |
| + - room architectural elements | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The unique details and component parts that, together, form the architecture | |
| + of a distinguisahable space within a built structure | |
| + title: room architectural elements | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000233 | |
| + multivalued: false | |
| + range: string | |
| + room_condt: | |
| + name: room_condt | |
| + aliases: | |
| + - room condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The condition of the room at the time of sampling | |
| + title: room condition | |
| + examples: | |
| + - value: new | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000822 | |
| + multivalued: false | |
| + range: text value | |
| + room_connected: | |
| + name: room_connected | |
| + aliases: | |
| + - rooms connected by a doorway | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of rooms connected to the sampling room by a doorway | |
| + title: rooms connected by a doorway | |
| + examples: | |
| + - value: office | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000826 | |
| + multivalued: false | |
| + range: text value | |
| + room_count: | |
| + name: room_count | |
| + aliases: | |
| + - room count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The total count of rooms in the built structure including all room | |
| + types | |
| + title: room count | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000234 | |
| + multivalued: false | |
| + range: text value | |
| + room_dim: | |
| + name: room_dim | |
| + aliases: | |
| + - room dimensions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The length, width and height of sampling room | |
| + title: room dimensions | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' | |
| + slot_uri: MIXS:0000192 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_door_dist: | |
| + name: room_door_dist | |
| + aliases: | |
| + - room door distance | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Distance between doors (meters) in the hallway between the sampling | |
| + room and adjacent rooms | |
| + title: room door distance | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer} {unit}' | |
| + slot_uri: MIXS:0000193 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_door_share: | |
| + name: room_door_share | |
| + aliases: | |
| + - rooms that share a door with sampling room | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: room name;room number | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of room(s) (room number, room name) sharing a door with the | |
| + sampling room | |
| + title: rooms that share a door with sampling room | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{integer}' | |
| + slot_uri: MIXS:0000242 | |
| + multivalued: false | |
| + range: text value | |
| + room_hallway: | |
| + name: room_hallway | |
| + aliases: | |
| + - rooms that are on the same hallway | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: room name;room number | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of room(s) (room number, room name) located in the same hallway | |
| + as sampling room | |
| + title: rooms that are on the same hallway | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{integer}' | |
| + slot_uri: MIXS:0000238 | |
| + multivalued: false | |
| + range: text value | |
| + room_loc: | |
| + name: room_loc | |
| + aliases: | |
| + - room location in building | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The position of the room within the building | |
| + title: room location in building | |
| + examples: | |
| + - value: interior room | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000823 | |
| + multivalued: false | |
| + range: text value | |
| + room_moist_dam_hist: | |
| + name: room_moist_dam_hist | |
| + aliases: | |
| + - room moisture damage or mold history | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The history of moisture damage or mold in the past 12 months. Number | |
| + of events of moisture damage or mold observed | |
| + title: room moisture damage or mold history | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000235 | |
| + multivalued: false | |
| + range: integer | |
| + room_net_area: | |
| + name: room_net_area | |
| + aliases: | |
| + - room net area | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square feet, square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The net floor area of sampling room. Net area excludes wall thicknesses | |
| + title: room net area | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer} {unit}' | |
| + slot_uri: MIXS:0000194 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_occup: | |
| + name: room_occup | |
| + aliases: | |
| + - room occupancy | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Count of room occupancy at time of sampling | |
| + title: room occupancy | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000236 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_samp_pos: | |
| + name: room_samp_pos | |
| + aliases: | |
| + - room sampling position | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The horizontal sampling position in the room relative to architectural | |
| + elements | |
| + title: room sampling position | |
| + examples: | |
| + - value: south corner | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000824 | |
| + multivalued: false | |
| + range: text value | |
| + room_type: | |
| + name: room_type | |
| + aliases: | |
| + - room type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The main purpose or activity of the sampling room. A room is any | |
| + distinguishable space within a structure | |
| + title: room type | |
| + examples: | |
| + - value: bathroom | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000825 | |
| + multivalued: false | |
| + range: text value | |
| + room_vol: | |
| + name: room_vol | |
| + aliases: | |
| + - room volume | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cubic feet, cubic meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Volume of sampling room | |
| + title: room volume | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{integer} {unit}' | |
| + slot_uri: MIXS:0000195 | |
| + multivalued: false | |
| + range: quantity value | |
| + room_wall_share: | |
| + name: room_wall_share | |
| + aliases: | |
| + - rooms that share a wall with sampling room | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: room name;room number | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: List of room(s) (room number, room name) sharing a wall with the | |
| + sampling room | |
| + title: rooms that share a wall with sampling room | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{integer}' | |
| + slot_uri: MIXS:0000243 | |
| + multivalued: false | |
| + range: text value | |
| + room_window_count: | |
| + name: room_window_count | |
| + aliases: | |
| + - room window count | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Number of windows in the room | |
| + title: room window count | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000237 | |
| + multivalued: false | |
| + range: text value | |
| + root_cond: | |
| + name: root_cond | |
| + aliases: | |
| + - rooting conditions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI,url or free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Relevant rooting conditions such as field plot size, sowing density, | |
| + container dimensions, number of plants per container. | |
| + title: rooting conditions | |
| + examples: | |
| + - value: http://himedialabs.com/TD/PT158.pdf | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}|{text}' | |
| + slot_uri: MIXS:0001061 | |
| + multivalued: false | |
| + range: text value | |
| + root_med_carbon: | |
| + name: root_med_carbon | |
| + aliases: | |
| + - rooting medium carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: carbon source name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Source of organic carbon in the culture rooting medium; e.g. sucrose. | |
| + title: rooting medium carbon | |
| + examples: | |
| + - value: sucrose | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000577 | |
| + multivalued: false | |
| + range: quantity value | |
| + root_med_macronutr: | |
| + name: root_med_macronutr | |
| + aliases: | |
| + - rooting medium macronutrients | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: macronutrient name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of the culture rooting medium macronutrients (N,P, K, | |
| + Ca, Mg, S); e.g. KH2PO4 (170 mg/L). | |
| + title: rooting medium macronutrients | |
| + examples: | |
| + - value: KH2PO4;170 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000578 | |
| + multivalued: false | |
| + range: quantity value | |
| + root_med_micronutr: | |
| + name: root_med_micronutr | |
| + aliases: | |
| + - rooting medium micronutrients | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: micronutrient name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of the culture rooting medium micronutrients (Fe, Mn, | |
| + Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). | |
| + title: rooting medium micronutrients | |
| + examples: | |
| + - value: H3BO3;6.2 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000579 | |
| + multivalued: false | |
| + range: quantity value | |
| + root_med_ph: | |
| + name: root_med_ph | |
| + aliases: | |
| + - rooting medium pH | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: pH measurement of the culture rooting medium; e.g. 5.5. | |
| + title: rooting medium pH | |
| + examples: | |
| + - value: '7.5' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001062 | |
| + multivalued: false | |
| + range: quantity value | |
| + root_med_regl: | |
| + name: root_med_regl | |
| + aliases: | |
| + - rooting medium regulators | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: regulator name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Growth regulators in the culture rooting medium such as cytokinins, | |
| + auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. | |
| + title: rooting medium regulators | |
| + examples: | |
| + - value: abscisic acid;0.75 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000581 | |
| + multivalued: false | |
| + range: quantity value | |
| + root_med_solid: | |
| + name: root_med_solid | |
| + aliases: | |
| + - rooting medium solidifier | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Specification of the solidifying agent in the culture rooting medium; | |
| + e.g. agar. | |
| + title: rooting medium solidifier | |
| + examples: | |
| + - value: agar | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0001063 | |
| + multivalued: false | |
| + range: text value | |
| + root_med_suppl: | |
| + name: root_med_suppl | |
| + aliases: | |
| + - rooting medium organic supplements | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: supplement name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Organic supplements of the culture rooting medium, such as vitamins, | |
| + amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid | |
| + (0.5 mg/L). | |
| + title: rooting medium organic supplements | |
| + examples: | |
| + - value: nicotinic acid;0.5 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000580 | |
| + multivalued: false | |
| + range: quantity value | |
| + salinity: | |
| + name: salinity | |
| + aliases: | |
| + - salinity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: practical salinity unit, percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The total concentration of all dissolved salts in a liquid or solid | |
| + sample. While salinity can be measured by a complete chemical analysis, this | |
| + method is difficult and time consuming. More often, it is instead derived from | |
| + the conductivity measurement. This is known as practical salinity. These derivations | |
| + compare the specific conductance of the sample to a salinity standard such as | |
| + seawater. | |
| + title: salinity | |
| + examples: | |
| + - value: 25 practical salinity unit | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000183 | |
| + multivalued: false | |
| + range: quantity value | |
| + salinity_meth: | |
| + name: salinity_meth | |
| + aliases: | |
| + - salinity method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining salinity | |
| + title: salinity method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000341 | |
| + multivalued: false | |
| + range: text value | |
| + salt_regm: | |
| + name: salt_regm | |
| + aliases: | |
| + - salt regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: salt name;salt amount;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, microgram, mole per liter, gram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving use of salts as supplement | |
| + to liquid and soil growth media; should include the name of salt, amount administered, | |
| + treatment regimen including how many times the treatment was repeated, how long | |
| + each treatment lasted, and the start and end time of the entire treatment; can | |
| + include multiple salt regimens | |
| + title: salt regimen | |
| + examples: | |
| + - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000582 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_capt_status: | |
| + name: samp_capt_status | |
| + aliases: | |
| + - sample capture status | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reason for the sample | |
| + title: sample capture status | |
| + examples: | |
| + - value: farm sample | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000860 | |
| + multivalued: false | |
| + range: text value | |
| + samp_collec_device: | |
| + name: samp_collec_device | |
| + aliases: | |
| + - sample collection device | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: device name | |
| + description: The device used to collect an environmental sample. This field accepts | |
| + terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). | |
| + This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). | |
| + title: sample collection device | |
| + examples: | |
| + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: nucleic acid sequence source field | |
| + string_serialization: '{termLabel} {[termID]}|{text}' | |
| + slot_uri: MIXS:0000002 | |
| + multivalued: false | |
| + range: string | |
| + samp_collec_method: | |
| + name: samp_collec_method | |
| + aliases: | |
| + - sample collection method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI,url , or text | |
| + description: The method employed for collecting the sample. | |
| + title: sample collection method | |
| + examples: | |
| + - value: swabbing | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: nucleic acid sequence source field | |
| + string_serialization: '{PMID}|{DOI}|{URL}|{text}' | |
| + slot_uri: MIXS:0001225 | |
| + multivalued: false | |
| + range: string | |
| + samp_collect_device: | |
| + name: samp_collect_device | |
| + aliases: | |
| + - sample collection device | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: device name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The device used to collect an environmental sample. This field accepts | |
| + terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). | |
| + This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). | |
| + title: sample collection device | |
| + examples: | |
| + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}|{text}' | |
| + slot_uri: MIXS:0000002 | |
| + multivalued: false | |
| + range: text value | |
| + samp_collect_point: | |
| + name: samp_collect_point | |
| + aliases: | |
| + - sample collection point | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Sampling point on the asset were sample was collected (e.g. Wellhead, | |
| + storage tank, separator, etc). If "other" is specified, please propose entry | |
| + in "additional info" field | |
| + title: sample collection point | |
| + examples: | |
| + - value: well | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0001015 | |
| + multivalued: false | |
| + range: samp_collect_point_enum | |
| + samp_dis_stage: | |
| + name: samp_dis_stage | |
| + aliases: | |
| + - sample disease stage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Stage of the disease at the time of sample collection, e.g. inoculation, | |
| + penetration, infection, growth and reproduction, dissemination of pathogen. | |
| + title: sample disease stage | |
| + examples: | |
| + - value: infection | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000249 | |
| + multivalued: false | |
| + range: text value | |
| + samp_floor: | |
| + name: samp_floor | |
| + aliases: | |
| + - sampling floor | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The floor of the building, where the sampling room is located | |
| + title: sampling floor | |
| + examples: | |
| + - value: 4th floor | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000828 | |
| + multivalued: false | |
| + range: text value | |
| + samp_loc_corr_rate: | |
| + name: samp_loc_corr_rate | |
| + aliases: | |
| + - corrosion rate at sample location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter per year | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Metal corrosion rate is the speed of metal deterioration due to environmental | |
| + conditions. As environmental conditions change corrosion rates change accordingly. | |
| + Therefore, long term corrosion rates are generally more informative than short | |
| + term rates and for that reason they are preferred during reporting. In the case | |
| + of suspected MIC, corrosion rate measurements at the time of sampling might | |
| + provide insights into the involvement of certain microbial community members | |
| + in MIC as well as potential microbial interplays | |
| + title: corrosion rate at sample location | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} - {float} {unit}' | |
| + slot_uri: MIXS:0000136 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_mat_process: | |
| + name: samp_mat_process | |
| + aliases: | |
| + - sample material processing | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: text | |
| + description: A brief description of any processing applied to the sample during | |
| + or after retrieving the sample from environment, or a link to the relevant protocol(s) | |
| + performed. | |
| + title: sample material processing | |
| + examples: | |
| + - value: filtering of seawater, storing samples in ethanol | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000016 | |
| + multivalued: false | |
| + range: controlled term value | |
| + samp_md: | |
| + name: samp_md | |
| + aliases: | |
| + - sample measured depth | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;enumeration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: In non deviated well, measured depth is equal to the true vertical | |
| + depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated | |
| + wells, the MD is the length of trajectory of the borehole measured from the | |
| + same reference or datum. Common datums used are ground level (GL), drilling | |
| + rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). | |
| + If "other" is specified, please propose entry in "additional info" field | |
| + title: sample measured depth | |
| + examples: | |
| + - value: 1534 meter;MSL | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000413 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_name: | |
| + name: samp_name | |
| + aliases: | |
| + - sample name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: text | |
| + description: A local identifier or name that for the material sample used for | |
| + extracting nucleic acids, and subsequent sequencing. It can refer either to | |
| + the original material collected or to any derived sub-samples. It can have any | |
| + format, but we suggest that you make it concise, unique and consistent within | |
| + your lab, and as informative as possible. INSDC requires every sample name from | |
| + a single Submitter to be unique. Use of a globally unique identifier for the | |
| + field source_mat_id is recommended in addition to sample_name. | |
| + title: sample name | |
| + examples: | |
| + - value: ISDsoil1 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: investigation field | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0001107 | |
| + multivalued: false | |
| + range: string | |
| + samp_preserv: | |
| + name: samp_preserv | |
| + aliases: | |
| + - preservative added to sample | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milliliter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, | |
| + etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) | |
| + title: preservative added to sample | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000463 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_room_id: | |
| + name: samp_room_id | |
| + aliases: | |
| + - sampling room ID or name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Sampling room number. This ID should be consistent with the designations | |
| + on the building floor plans | |
| + title: sampling room ID or name | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000244 | |
| + multivalued: false | |
| + range: text value | |
| + samp_size: | |
| + name: samp_size | |
| + aliases: | |
| + - amount or size of sample collected | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millliter, gram, milligram, liter | |
| + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of | |
| + sample collected. | |
| + title: amount or size of sample collected | |
| + examples: | |
| + - value: 5 liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000001 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_sort_meth: | |
| + name: samp_sort_meth | |
| + aliases: | |
| + - sample size sorting method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: description of method | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Method by which samples are sorted; open face filter collecting total | |
| + suspended particles, prefilter to remove particles larger than X micrometers | |
| + in diameter, where common values of X would be 10 and 2.5 full size sorting | |
| + in a cascade impactor. | |
| + title: sample size sorting method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000216 | |
| + multivalued: false | |
| + range: text value | |
| + samp_store_dur: | |
| + name: samp_store_dur | |
| + aliases: | |
| + - sample storage duration | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Duration for which the sample was stored | |
| + title: sample storage duration | |
| + examples: | |
| + - value: P1Y6M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{duration}' | |
| + slot_uri: MIXS:0000116 | |
| + multivalued: false | |
| + range: text value | |
| + samp_store_loc: | |
| + name: samp_store_loc | |
| + aliases: | |
| + - sample storage location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: location name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Location at which sample was stored, usually name of a specific freezer/room | |
| + title: sample storage location | |
| + examples: | |
| + - value: Freezer no:5 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000755 | |
| + multivalued: false | |
| + range: text value | |
| + samp_store_temp: | |
| + name: samp_store_temp | |
| + aliases: | |
| + - sample storage temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Temperature at which sample was stored, e.g. -80 degree Celsius | |
| + title: sample storage temperature | |
| + examples: | |
| + - value: -80 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000110 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_subtype: | |
| + name: samp_subtype | |
| + aliases: | |
| + - sample subtype | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of sample sub-type. For example if "sample type" is "Produced | |
| + Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, | |
| + please propose entry in "additional info" field | |
| + title: sample subtype | |
| + examples: | |
| + - value: biofilm | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000999 | |
| + multivalued: false | |
| + range: text value | |
| + samp_time_out: | |
| + name: samp_time_out | |
| + aliases: | |
| + - sampling time outside | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: time | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The recent and long term history of outside sampling | |
| + title: sampling time outside | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000196 | |
| + multivalued: false | |
| + range: text value | |
| + samp_transport_cond: | |
| + name: samp_transport_cond | |
| + aliases: | |
| + - sample transport conditions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: days;degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Sample transport duration (in days or hrs) and temperature the sample | |
| + was exposed to (e.g. 5.5 days; 20 °C) | |
| + title: sample transport conditions | |
| + examples: | |
| + - value: 5 days;-20 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{float} {unit}' | |
| + slot_uri: MIXS:0000410 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_tvdss: | |
| + name: samp_tvdss | |
| + aliases: | |
| + - sample true vertical depth subsea | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value or measurement value range | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Depth of the sample i.e. The vertical distance between the sea level | |
| + and the sampled position in the subsurface. Depth can be reported as an interval | |
| + for subsurface samples e.g. 1325.75-1362.25 m | |
| + title: sample true vertical depth subsea | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float}-{float} {unit}' | |
| + slot_uri: MIXS:0000409 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_type: | |
| + name: samp_type | |
| + aliases: | |
| + - sample type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: GENEPIO:0001246 | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of material from which the sample was obtained. For the | |
| + Hydrocarbon package, samples include types like core, rock trimmings, drill | |
| + cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, | |
| + produced water, injected water, swabs, etc. For the Food Package, samples are | |
| + usually categorized as food, body products or tissues, or environmental material. | |
| + This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246). | |
| + title: sample type | |
| + examples: | |
| + - value: built environment sample [GENEPIO:0001248] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000998 | |
| + multivalued: false | |
| + range: text value | |
| + samp_vol_we_dna_ext: | |
| + name: samp_vol_we_dna_ext | |
| + aliases: | |
| + - sample volume or weight for DNA extraction | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millliter, gram, milligram, square centimeter | |
| + description: 'Volume (ml) or mass (g) of total collected sample processed for | |
| + DNA extraction. Note: total sample collected should be entered under the term | |
| + Sample Size (MIXS:0000001).' | |
| + title: sample volume or weight for DNA extraction | |
| + examples: | |
| + - value: 1500 milliliter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000111 | |
| + multivalued: false | |
| + range: quantity value | |
| + samp_weather: | |
| + name: samp_weather | |
| + aliases: | |
| + - sampling day weather | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The weather on the sampling day | |
| + title: sampling day weather | |
| + examples: | |
| + - value: foggy | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000827 | |
| + multivalued: false | |
| + range: text value | |
| + samp_well_name: | |
| + name: samp_well_name | |
| + aliases: | |
| + - sample well name | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Name of the well (e.g. BXA1123) where sample was taken | |
| + title: sample well name | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000296 | |
| + multivalued: false | |
| + range: text value | |
| + saturates_pc: | |
| + name: saturates_pc | |
| + aliases: | |
| + - saturates wt% | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis | |
| + method that divides crude oil components according to their polarizability | |
| + and polarity. There are three main methods to obtain SARA results. The most | |
| + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: | |
| + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' | |
| + title: saturates wt% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000131 | |
| + multivalued: false | |
| + range: quantity value | |
| + season: | |
| + name: season | |
| + aliases: | |
| + - season | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: NCIT:C94729 | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The season when sampling occurred. Any of the four periods into which | |
| + the year is divided by the equinoxes and solstices. This field accepts terms | |
| + listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). | |
| + title: season | |
| + examples: | |
| + - value: autumn [NCIT:C94733] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000829 | |
| + multivalued: false | |
| + range: text value | |
| + season_environment: | |
| + name: season_environment | |
| + aliases: | |
| + - seasonal environment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: seasonal environment name;treatment interval and duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Treatment involving an exposure to a particular season (e.g. Winter, | |
| + summer, rabi, rainy etc.), treatment regimen including how many times the treatment | |
| + was repeated, how long each treatment lasted, and the start and end time of | |
| + the entire treatment | |
| + title: seasonal environment | |
| + examples: | |
| + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0001068 | |
| + multivalued: false | |
| + range: text value | |
| + season_precpt: | |
| + name: season_precpt | |
| + aliases: | |
| + - mean seasonal precipitation | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: millimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average of all seasonal precipitation values known, or an estimated | |
| + equivalent value derived by such methods as regional indexes or Isohyetal maps. | |
| + title: mean seasonal precipitation | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000645 | |
| + multivalued: false | |
| + range: quantity value | |
| + season_temp: | |
| + name: season_temp | |
| + aliases: | |
| + - mean seasonal temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Mean seasonal temperature | |
| + title: mean seasonal temperature | |
| + examples: | |
| + - value: 18 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000643 | |
| + multivalued: false | |
| + range: quantity value | |
| + season_use: | |
| + name: season_use | |
| + aliases: | |
| + - seasonal use | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The seasons the space is occupied | |
| + title: seasonal use | |
| + examples: | |
| + - value: Winter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000830 | |
| + multivalued: false | |
| + range: text value | |
| + secondary_treatment: | |
| + name: secondary_treatment | |
| + aliases: | |
| + - secondary treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: secondary treatment type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The process for substantially degrading the biological content of | |
| + the sewage | |
| + title: secondary treatment | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000351 | |
| + multivalued: false | |
| + range: text value | |
| + sediment_type: | |
| + name: sediment_type | |
| + aliases: | |
| + - sediment type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Information about the sediment type based on major constituents | |
| + title: sediment type | |
| + examples: | |
| + - value: biogenous | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001078 | |
| + multivalued: false | |
| + range: text value | |
| + seq_meth: | |
| + name: seq_meth | |
| + aliases: | |
| + - sequencing method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: Text or OBI | |
| + description: Sequencing machine used. Where possible the term should be taken | |
| + from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103). | |
| + title: sequencing method | |
| + examples: | |
| + - value: 454 Genome Sequencer FLX [OBI:0000702] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}|{text}' | |
| + slot_uri: MIXS:0000050 | |
| + multivalued: false | |
| + range: text value | |
| + seq_quality_check: | |
| + name: seq_quality_check | |
| + aliases: | |
| + - sequence quality check | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: none or manually edited | |
| + description: Indicate if the sequence has been called by automatic systems (none) | |
| + or undergone a manual editing procedure (e.g. by inspecting the raw data or | |
| + chromatograms). Applied only for sequences that are not submitted to SRA,ENA | |
| + or DRA | |
| + title: sequence quality check | |
| + examples: | |
| + - value: none | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[none|manually edited]' | |
| + slot_uri: MIXS:0000051 | |
| + multivalued: false | |
| + range: text value | |
| + sewage_type: | |
| + name: sewage_type | |
| + aliases: | |
| + - sewage type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: sewage type name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Type of wastewater treatment plant as municipial or industrial | |
| + title: sewage type | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000215 | |
| + multivalued: false | |
| + range: text value | |
| + shad_dev_water_mold: | |
| + name: shad_dev_water_mold | |
| + aliases: | |
| + - shading device signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew on the shading device | |
| + title: shading device signs of water/mold | |
| + examples: | |
| + - value: no presence of mold visible | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '[presence of mold visible|no presence of mold visible]' | |
| + slot_uri: MIXS:0000834 | |
| + multivalued: false | |
| + range: string | |
| + shading_device_cond: | |
| + name: shading_device_cond | |
| + aliases: | |
| + - shading device condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The physical condition of the shading device at the time of sampling | |
| + title: shading device condition | |
| + examples: | |
| + - value: new | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000831 | |
| + multivalued: false | |
| + range: text value | |
| + shading_device_loc: | |
| + name: shading_device_loc | |
| + aliases: | |
| + - shading device location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The location of the shading device in relation to the built structure | |
| + title: shading device location | |
| + examples: | |
| + - value: exterior | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[exterior|interior]' | |
| + slot_uri: MIXS:0000832 | |
| + multivalued: false | |
| + range: text value | |
| + shading_device_mat: | |
| + name: shading_device_mat | |
| + aliases: | |
| + - shading device material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: material name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The material the shading device is composed of | |
| + title: shading device material | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000245 | |
| + multivalued: false | |
| + range: text value | |
| + shading_device_type: | |
| + name: shading_device_type | |
| + aliases: | |
| + - shading device type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of shading device | |
| + title: shading device type | |
| + examples: | |
| + - value: slatted aluminum awning | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000835 | |
| + multivalued: false | |
| + range: text value | |
| + sieving: | |
| + name: sieving | |
| + aliases: | |
| + - composite design/sieving | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: design name and/or size;amount | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Collection design of pooled samples and/or sieve size and amount | |
| + of sample sieved | |
| + title: composite design/sieving | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{{text}|{float} {unit}};{float} {unit}' | |
| + slot_uri: MIXS:0000322 | |
| + multivalued: false | |
| + range: quantity value | |
| + silicate: | |
| + name: silicate | |
| + aliases: | |
| + - silicate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of silicate | |
| + title: silicate | |
| + examples: | |
| + - value: 0.05 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000184 | |
| + multivalued: false | |
| + range: quantity value | |
| + size_frac: | |
| + name: size_frac | |
| + aliases: | |
| + - size fraction selected | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: filter size value range | |
| + description: Filtering pore size used in sample preparation | |
| + title: size fraction selected | |
| + examples: | |
| + - value: 0-0.22 micrometer | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float}-{float} {unit}' | |
| + slot_uri: MIXS:0000017 | |
| + multivalued: false | |
| + range: quantity value | |
| size_frac_low: | |
| - aliases: | |
| - - size-fraction lower threshold | |
| - description: >- | |
| - Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:size_frac_low | |
| - | |
| + name: size_frac_low | |
| + aliases: | |
| + - size-fraction lower threshold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micrometer | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. | |
| + Materials larger than the size threshold are excluded from the sample | |
| + title: size-fraction lower threshold | |
| + examples: | |
| + - value: 0.2 micrometer | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000735 | |
| + multivalued: false | |
| + range: quantity value | |
| size_frac_up: | |
| - aliases: | |
| - - size-fraction upper threshold | |
| - description: >- | |
| - Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:size_frac_up | |
| - | |
| + name: size_frac_up | |
| + aliases: | |
| + - size-fraction upper threshold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micrometer | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Refers to the mesh/pore size used to retain the sample. Materials | |
| + smaller than the size threshold are excluded from the sample | |
| + title: size-fraction upper threshold | |
| + examples: | |
| + - value: 20 micrometer | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000736 | |
| + multivalued: false | |
| + range: quantity value | |
| + slope_aspect: | |
| + name: slope_aspect | |
| + aliases: | |
| + - slope aspect | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The direction a slope faces. While looking down a slope use a compass | |
| + to record the direction you are facing (direction or degrees); e.g., nw or 315 | |
| + degrees. This measure provides an indication of sun and wind exposure that will | |
| + influence soil temperature and evapotranspiration. | |
| + title: slope aspect | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000647 | |
| + multivalued: false | |
| + range: quantity value | |
| + slope_gradient: | |
| + name: slope_gradient | |
| + aliases: | |
| + - slope gradient | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Commonly called 'slope'. The angle between ground surface and a horizontal | |
| + line (in percent). This is the direction that overland water would flow. This | |
| + measure is usually taken with a hand level meter or clinometer | |
| + title: slope gradient | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000646 | |
| + multivalued: false | |
| + range: quantity value | |
| + sludge_retent_time: | |
| + name: sludge_retent_time | |
| + aliases: | |
| + - sludge retention time | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: hours | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The time activated sludge remains in reactor | |
| + title: sludge retention time | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000669 | |
| + multivalued: false | |
| + range: quantity value | |
| + sodium: | |
| + name: sodium | |
| + aliases: | |
| + - sodium | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Sodium concentration in the sample | |
| + title: sodium | |
| + examples: | |
| + - value: 10.5 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000428 | |
| + multivalued: false | |
| + range: quantity value | |
| + soil_horizon: | |
| + name: soil_horizon | |
| + aliases: | |
| + - soil horizon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Specific layer in the land area which measures parallel to the soil | |
| + surface and possesses physical characteristics which differ from the layers | |
| + above and beneath | |
| + title: soil horizon | |
| + examples: | |
| + - value: A horizon | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0001082 | |
| + multivalued: false | |
| + range: soil_horizon_enum | |
| + soil_text_measure: | |
| + name: soil_text_measure | |
| + aliases: | |
| + - soil texture measurement | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The relative proportion of different grain sizes of mineral particles | |
| + in a soil, as described using a standard system; express as % sand (50 um to | |
| + 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty | |
| + clay loam) optional. | |
| + title: soil texture measurement | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000335 | |
| + multivalued: false | |
| + range: quantity value | |
| + soil_texture_meth: | |
| + name: soil_texture_meth | |
| + aliases: | |
| + - soil texture method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining soil texture | |
| + title: soil texture method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000336 | |
| + multivalued: false | |
| + range: string | |
| + soil_type: | |
| + name: soil_type | |
| + aliases: | |
| + - soil type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: ENVO_00001998 | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Description of the soil type or classification. This field accepts | |
| + terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms | |
| + can be separated by pipes. | |
| + title: soil type | |
| + examples: | |
| + - value: plinthosol [ENVO:00002250] | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{termLabel} {[termID]}' | |
| + slot_uri: MIXS:0000332 | |
| + multivalued: false | |
| + range: text value | |
| + soil_type_meth: | |
| + name: soil_type_meth | |
| + aliases: | |
| + - soil type method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining soil series name or other | |
| + lower-level classification | |
| + title: soil type method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000334 | |
| + multivalued: false | |
| + range: text value | |
| + solar_irradiance: | |
| + name: solar_irradiance | |
| + aliases: | |
| + - solar irradiance | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: kilowatts per square meter per day, ergs per square centimeter per | |
| + second | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The amount of solar energy that arrives at a specific area of a surface | |
| + during a specific time interval | |
| + title: solar irradiance | |
| + examples: | |
| + - value: 1.36 kilowatts per square meter per day | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000112 | |
| + multivalued: false | |
| + range: quantity value | |
| + soluble_inorg_mat: | |
| + name: soluble_inorg_mat | |
| + aliases: | |
| + - soluble inorganic material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: soluble inorganic material name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, microgram, mole per liter, gram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of substances such as ammonia, road-salt, sea-salt, | |
| + cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. | |
| + title: soluble inorganic material | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000672 | |
| + multivalued: false | |
| + range: quantity value | |
| + soluble_org_mat: | |
| + name: soluble_org_mat | |
| + aliases: | |
| + - soluble organic material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: soluble organic material name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, microgram, mole per liter, gram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of substances such as urea, fruit sugars, soluble proteins, | |
| + drugs, pharmaceuticals, etc. | |
| + title: soluble organic material | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000673 | |
| + multivalued: false | |
| + range: quantity value | |
| soluble_react_phosp: | |
| - aliases: | |
| - - soluble reactive phosphorus | |
| - description: >- | |
| - Concentration of soluble reactive phosphorus | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:soluble_react_phosp | |
| - | |
| + name: soluble_react_phosp | |
| + aliases: | |
| + - soluble reactive phosphorus | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of soluble reactive phosphorus | |
| + title: soluble reactive phosphorus | |
| + examples: | |
| + - value: 0.1 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000738 | |
| + multivalued: false | |
| + range: quantity value | |
| + source_mat_id: | |
| + name: source_mat_id | |
| + aliases: | |
| + - source material identifiers | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: 'for cultures of microorganisms: identifiers for two culture collections; | |
| + for other material a unique arbitrary identifer' | |
| + description: A unique identifier assigned to a material sample (as defined by | |
| + http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular | |
| + digital record of a material sample) used for extracting nucleic acids, and | |
| + subsequent sequencing. The identifier can refer either to the original material | |
| + collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, | |
| + /bio_material, or /culture_collection may or may not share the same value as | |
| + the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id | |
| + may both contain 'UAM:Herps:14' , referring to both the specimen voucher and | |
| + sampled tissue with the same identifier. However, the /culture_collection qualifier | |
| + may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id | |
| + would refer to an identifier from some derived culture from which the nucleic | |
| + acids were extracted (e.g. xatc123 or ark:/2154/R2). | |
| + title: source material identifiers | |
| + examples: | |
| + - value: MPI012345 | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000026 | |
| + multivalued: false | |
| + range: text value | |
| + space_typ_state: | |
| + name: space_typ_state | |
| + aliases: | |
| + - space typical state | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Customary or normal state of the space | |
| + title: space typical state | |
| + examples: | |
| + - value: typically occupied | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[typically occupied|typically unoccupied]' | |
| + slot_uri: MIXS:0000770 | |
| + multivalued: false | |
| + range: text value | |
| + specific: | |
| + name: specific | |
| + aliases: | |
| + - specifications | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'The building specifications. If design is chosen, indicate phase: | |
| + conceptual, schematic, design development, construction documents' | |
| + title: specifications | |
| + examples: | |
| + - value: construction | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000836 | |
| + multivalued: false | |
| + range: text value | |
| + specific_humidity: | |
| + name: specific_humidity | |
| + aliases: | |
| + - specific humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram of air, kilogram of air | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The mass of water vapour in a unit mass of moist air, usually expressed | |
| + as grams of vapour per kilogram of air, or, in air conditioning, as grains per | |
| + pound. | |
| + title: specific humidity | |
| + examples: | |
| + - value: 15 per kilogram of air | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000214 | |
| + multivalued: false | |
| + range: quantity value | |
| + sr_dep_env: | |
| + name: sr_dep_env | |
| + aliases: | |
| + - source rock depositional environment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). | |
| + If "other" is specified, please propose entry in "additional info" field | |
| + title: source rock depositional environment | |
| + examples: | |
| + - value: Marine | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000996 | |
| + multivalued: false | |
| + range: text value | |
| + sr_geol_age: | |
| + name: sr_geol_age | |
| + aliases: | |
| + - source rock geological age | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). | |
| + If "other" is specified, please propose entry in "additional info" field' | |
| + title: source rock geological age | |
| + examples: | |
| + - value: Silurian | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000997 | |
| + multivalued: false | |
| + range: text value | |
| + sr_kerog_type: | |
| + name: sr_kerog_type | |
| + aliases: | |
| + - source rock kerogen type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic | |
| + and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ | |
| + fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris | |
| + (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). | |
| + If "other" is specified, please propose entry in "additional info" field' | |
| + title: source rock kerogen type | |
| + examples: | |
| + - value: Type IV | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000994 | |
| + multivalued: false | |
| + range: text value | |
| + sr_lithology: | |
| + name: sr_lithology | |
| + aliases: | |
| + - source rock lithology | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). | |
| + If "other" is specified, please propose entry in "additional info" field | |
| + title: source rock lithology | |
| + examples: | |
| + - value: Coal | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000995 | |
| + multivalued: false | |
| + range: text value | |
| + standing_water_regm: | |
| + name: standing_water_regm | |
| + aliases: | |
| + - standing water regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: standing water type;treatment interval and duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Treatment involving an exposure to standing water during a plant's | |
| + life span, types can be flood water or standing water, treatment regimen including | |
| + how many times the treatment was repeated, how long each treatment lasted, and | |
| + the start and end time of the entire treatment; can include multiple regimens | |
| + title: standing water regimen | |
| + examples: | |
| + - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0001069 | |
| + multivalued: false | |
| + range: text value | |
| + store_cond: | |
| + name: store_cond | |
| + aliases: | |
| + - storage conditions | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: storage condition type;duration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Explain how and for how long the soil sample was stored before DNA | |
| + extraction (fresh/frozen/other). | |
| + title: storage conditions | |
| + examples: | |
| + - value: -20 degree Celsius freezer;P2Y10D | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{duration}' | |
| + slot_uri: MIXS:0000327 | |
| + multivalued: false | |
| + range: text value | |
| + substructure_type: | |
| + name: substructure_type | |
| + aliases: | |
| + - substructure type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: The substructure or under building is that largely hidden section | |
| + of the building which is built off the foundations to the ground floor level | |
| + title: substructure type | |
| + examples: | |
| + - value: basement | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000767 | |
| + multivalued: false | |
| + range: text value | |
| + sulfate: | |
| + name: sulfate | |
| + aliases: | |
| + - sulfate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of sulfate in the sample | |
| + title: sulfate | |
| + examples: | |
| + - value: 5 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000423 | |
| + multivalued: false | |
| + range: quantity value | |
| + sulfate_fw: | |
| + name: sulfate_fw | |
| + aliases: | |
| + - sulfate in formation water | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original sulfate concentration in the hydrocarbon resource | |
| + title: sulfate in formation water | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000407 | |
| + multivalued: false | |
| + range: quantity value | |
| + sulfide: | |
| + name: sulfide | |
| + aliases: | |
| + - sulfide | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of sulfide in the sample | |
| + title: sulfide | |
| + examples: | |
| + - value: 2 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000424 | |
| + multivalued: false | |
| + range: quantity value | |
| + surf_air_cont: | |
| + name: surf_air_cont | |
| + aliases: | |
| + - surface-air contaminant | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Contaminant identified on surface | |
| + title: surface-air contaminant | |
| + examples: | |
| + - value: radon | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000759 | |
| + multivalued: false | |
| + range: text value | |
| + surf_humidity: | |
| + name: surf_humidity | |
| + aliases: | |
| + - surface humidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percentage | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Surfaces: water activity as a function of air and material moisture' | |
| + title: surface humidity | |
| + examples: | |
| + - value: 10% | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000123 | |
| + multivalued: false | |
| + range: quantity value | |
| + surf_material: | |
| + name: surf_material | |
| + aliases: | |
| + - surface material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Surface materials at the point of sampling | |
| + title: surface material | |
| + examples: | |
| + - value: wood | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000758 | |
| + multivalued: false | |
| + range: text value | |
| + surf_moisture: | |
| + name: surf_moisture | |
| + aliases: | |
| + - surface moisture | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: parts per million, gram per cubic meter, gram per square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Water held on a surface | |
| + title: surface moisture | |
| + examples: | |
| + - value: 0.01 gram per square meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000128 | |
| + multivalued: false | |
| + range: quantity value | |
| + surf_moisture_ph: | |
| + name: surf_moisture_ph | |
| + aliases: | |
| + - surface moisture pH | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: ph measurement of surface | |
| + title: surface moisture pH | |
| + examples: | |
| + - value: '7' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000760 | |
| + multivalued: false | |
| + range: quantity value | |
| + surf_temp: | |
| + name: surf_temp | |
| + aliases: | |
| + - surface temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Temperature of the surface at the time of sampling | |
| + title: surface temperature | |
| + examples: | |
| + - value: 15 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000125 | |
| + multivalued: false | |
| + range: quantity value | |
| suspend_part_matter: | |
| - aliases: | |
| - - suspended particulate matter | |
| - description: >- | |
| - Concentration of suspended particulate matter | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:suspend_part_matter | |
| - | |
| + name: suspend_part_matter | |
| + aliases: | |
| + - suspended particulate matter | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of suspended particulate matter | |
| + title: suspended particulate matter | |
| + examples: | |
| + - value: 0.5 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000741 | |
| + multivalued: false | |
| + range: quantity value | |
| + suspend_solids: | |
| + name: suspend_solids | |
| + aliases: | |
| + - suspended solids | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: suspended solid name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram, microgram, milligram per liter, mole per liter, gram per liter, | |
| + part per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of substances including a wide variety of material, | |
| + such as silt, decaying plant and animal matter; can include multiple substances | |
| + title: suspended solids | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000150 | |
| + multivalued: false | |
| + range: quantity value | |
| + tan: | |
| + name: tan | |
| + aliases: | |
| + - total acid number | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Total Acid Number (TAN) is a measurement of acidity that is determined | |
| + by the amount of potassium hydroxide in milligrams that is needed to neutralize | |
| + the acids in one gram of oil. It is an important quality measurement of crude | |
| + oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' | |
| + title: total acid number | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000120 | |
| + multivalued: false | |
| + range: quantity value | |
| + target_gene: | |
| + name: target_gene | |
| + aliases: | |
| + - target gene | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gene name | |
| + description: Targeted gene or locus name for marker gene studies | |
| + title: target gene | |
| + examples: | |
| + - value: 16S rRNA, 18S rRNA, nif, amoA, rpo | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000044 | |
| + multivalued: false | |
| + range: text value | |
| + target_subfragment: | |
| + name: target_subfragment | |
| + aliases: | |
| + - target subfragment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: gene fragment name | |
| + description: Name of subfragment of a gene or locus. Important to e.g. identify | |
| + special regions on marker genes like V6 on 16S rRNA | |
| + title: target subfragment | |
| + examples: | |
| + - value: V6, V9, ITS | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000045 | |
| + multivalued: false | |
| + range: text value | |
| + temp: | |
| + name: temp | |
| + aliases: | |
| + - temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + description: Temperature of the sample at the time of sampling. | |
| + title: temperature | |
| + examples: | |
| + - value: 25 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000113 | |
| + multivalued: false | |
| + range: quantity value | |
| + temp_out: | |
| + name: temp_out | |
| + aliases: | |
| + - temperature outside house | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The recorded temperature value at sampling time outside | |
| + title: temperature outside house | |
| + examples: | |
| + - value: 5 degree Celsius | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000197 | |
| + multivalued: false | |
| + range: quantity value | |
| + tertiary_treatment: | |
| + name: tertiary_treatment | |
| + aliases: | |
| + - tertiary treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: tertiary treatment type | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The process providing a final treatment stage to raise the effluent | |
| + quality before it is discharged to the receiving environment | |
| + title: tertiary treatment | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000352 | |
| + multivalued: false | |
| + range: text value | |
| + texture: | |
| + name: texture | |
| + aliases: | |
| + - texture | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The relative proportion of different grain sizes of mineral particles | |
| + in a soil, as described using a standard system; express as % sand (50 um to | |
| + 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty | |
| + clay loam) optional. | |
| + title: texture | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000335 | |
| + multivalued: false | |
| + range: quantity value | |
| + texture_meth: | |
| + name: texture_meth | |
| + aliases: | |
| + - texture method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining soil texture. | |
| + title: texture method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000336 | |
| + multivalued: false | |
| + range: text value | |
| + tidal_stage: | |
| + name: tidal_stage | |
| + aliases: | |
| + - tidal stage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Stage of tide | |
| + title: tidal stage | |
| + examples: | |
| + - value: high tide | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000750 | |
| + multivalued: false | |
| + range: text value | |
| + tillage: | |
| + name: tillage | |
| + aliases: | |
| + - history/tillage | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Note method(s) used for tilling | |
| + title: history/tillage | |
| + examples: | |
| + - value: chisel | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0001081 | |
| + multivalued: false | |
| + range: text value | |
| + tiss_cult_growth_med: | |
| + name: tiss_cult_growth_med | |
| + aliases: | |
| + - tissue culture growth media | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI,url or free text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Description of plant tissue culture growth media used | |
| + title: tissue culture growth media | |
| + examples: | |
| + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}|{text}' | |
| + slot_uri: MIXS:0001070 | |
| + multivalued: false | |
| + range: text value | |
| + toluene: | |
| + name: toluene | |
| + aliases: | |
| + - toluene | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of toluene in the sample | |
| + title: toluene | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000154 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_carb: | |
| + name: tot_carb | |
| + aliases: | |
| + - total carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total carbon content | |
| + title: total carbon | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000525 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_depth_water_col: | |
| + name: tot_depth_water_col | |
| + aliases: | |
| + - total depth of water column | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of total depth of water column | |
| + title: total depth of water column | |
| + examples: | |
| + - value: 500 meter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000634 | |
| + multivalued: false | |
| + range: quantity value | |
| tot_diss_nitro: | |
| - aliases: | |
| - - total dissolved nitrogen | |
| - description: >- | |
| - Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_diss_nitro | |
| - | |
| + name: tot_diss_nitro | |
| + aliases: | |
| + - total dissolved nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured | |
| + by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' | |
| + title: total dissolved nitrogen | |
| + examples: | |
| + - value: 40 microgram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000744 | |
| + multivalued: false | |
| + range: quantity value | |
| tot_inorg_nitro: | |
| - aliases: | |
| - - total inorganic nitrogen | |
| - description: >- | |
| - Total inorganic nitrogen content | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| - mappings: | |
| - - mixs:tot_inorg_nitro | |
| - | |
| + name: tot_inorg_nitro | |
| + aliases: | |
| + - total inorganic nitrogen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total inorganic nitrogen content | |
| + title: total inorganic nitrogen | |
| + examples: | |
| + - value: 40 microgram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000745 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_iron: | |
| + name: tot_iron | |
| + aliases: | |
| + - total iron | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, milligram per kilogram | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of total iron in the sample | |
| + title: total iron | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000105 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_nitro: | |
| + name: tot_nitro | |
| + aliases: | |
| + - total nitrogen concentration | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Total nitrogen concentration of water samples, calculated by: total | |
| + nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured | |
| + without filtering, reported as nitrogen' | |
| + title: total nitrogen concentration | |
| + examples: | |
| + - value: 50 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000102 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_nitro_cont_meth: | |
| + name: tot_nitro_cont_meth | |
| + aliases: | |
| + - total nitrogen content method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + mixs_5_name: | |
| + tag: mixs_5_name | |
| + value: tot_nitro_content_meth | |
| + description: Reference or method used in determining the total nitrogen | |
| + title: total nitrogen content method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000338 | |
| + multivalued: false | |
| + range: string | |
| + tot_nitro_content: | |
| + name: tot_nitro_content | |
| + aliases: | |
| + - total nitrogen content | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter, milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total nitrogen content of the sample | |
| + title: total nitrogen content | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000530 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_org_c_meth: | |
| + name: tot_org_c_meth | |
| + aliases: | |
| + - total organic carbon method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Reference or method used in determining total organic carbon | |
| + title: total organic carbon method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000337 | |
| + multivalued: false | |
| + range: text value | |
| + tot_org_carb: | |
| + name: tot_org_carb | |
| + aliases: | |
| + - total organic carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram Carbon per kilogram sample material | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Definition for soil: total organic carbon content of the soil, definition | |
| + otherwise: total organic carbon content' | |
| + title: total organic carbon | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000533 | |
| + multivalued: false | |
| + range: quantity value | |
| tot_part_carb: | |
| + name: tot_part_carb | |
| + aliases: | |
| + - total particulate carbon | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total particulate carbon content | |
| + title: total particulate carbon | |
| + examples: | |
| + - value: 35 micromole per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000747 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_phosp: | |
| + name: tot_phosp | |
| + aliases: | |
| + - total phosphorus | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: micromole per liter, milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'Total phosphorus concentration in the sample, calculated by: total | |
| + phosphorus = total dissolved phosphorus + particulate phosphorus' | |
| + title: total phosphorus | |
| + examples: | |
| + - value: 0.03 milligram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000117 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_phosphate: | |
| + name: tot_phosphate | |
| + aliases: | |
| + - total phosphate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per liter, micromole per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Total amount or concentration of phosphate | |
| + title: total phosphate | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000689 | |
| + multivalued: false | |
| + range: quantity value | |
| + tot_sulfur: | |
| + name: tot_sulfur | |
| + aliases: | |
| + - total sulfur | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of total sulfur in the sample | |
| + title: total sulfur | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000419 | |
| + multivalued: false | |
| + range: quantity value | |
| + train_line: | |
| + name: train_line | |
| + aliases: | |
| + - train line | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The subway line name | |
| + title: train line | |
| + examples: | |
| + - value: red | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000837 | |
| + multivalued: false | |
| + range: text value | |
| + train_stat_loc: | |
| + name: train_stat_loc | |
| + aliases: | |
| + - train station collection location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The train station collection location | |
| + title: train station collection location | |
| + examples: | |
| + - value: forest hills | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000838 | |
| + multivalued: false | |
| + range: text value | |
| + train_stop_loc: | |
| + name: train_stop_loc | |
| + aliases: | |
| + - train stop collection location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The train stop collection location | |
| + title: train stop collection location | |
| + examples: | |
| + - value: end | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000839 | |
| + multivalued: false | |
| + range: text value | |
| + turbidity: | |
| + name: turbidity | |
| + aliases: | |
| + - turbidity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: formazin turbidity unit, formazin nephelometric units | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measure of the amount of cloudiness or haziness in water caused by | |
| + individual particles | |
| + title: turbidity | |
| + examples: | |
| + - value: 0.3 nephelometric turbidity units | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000191 | |
| + multivalued: false | |
| + range: quantity value | |
| + tvdss_of_hcr_press: | |
| + name: tvdss_of_hcr_press | |
| + aliases: | |
| + - depth (TVDSS) of hydrocarbon resource pressure | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where | |
| + the original pressure was measured (e.g. 1578 m). | |
| + title: depth (TVDSS) of hydrocarbon resource pressure | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000397 | |
| + multivalued: false | |
| + range: quantity value | |
| + tvdss_of_hcr_temp: | |
| + name: tvdss_of_hcr_temp | |
| + aliases: | |
| + - depth (TVDSS) of hydrocarbon resource temperature | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where | |
| + the original temperature was measured (e.g. 1345 m). | |
| + title: depth (TVDSS) of hydrocarbon resource temperature | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000394 | |
| + multivalued: false | |
| + range: quantity value | |
| + typ_occup_density: | |
| + name: typ_occup_density | |
| + aliases: | |
| + - typical occupant density | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Customary or normal density of occupants | |
| + title: typical occupant density | |
| + examples: | |
| + - value: '25' | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000771 | |
| + multivalued: false | |
| + range: quantity value | |
| + ventilation_rate: | |
| + name: ventilation_rate | |
| + aliases: | |
| + - ventilation rate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cubic meter per minute, liters per second | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Ventilation rate of the system in the sampled premises | |
| + title: ventilation rate | |
| + examples: | |
| + - value: 750 cubic meter per minute | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000114 | |
| + multivalued: false | |
| + range: quantity value | |
| + ventilation_type: | |
| + name: ventilation_type | |
| + aliases: | |
| + - ventilation type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: ventilation type name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Ventilation system used in the sampled premises | |
| + title: ventilation type | |
| + examples: | |
| + - value: Operable windows | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000756 | |
| + multivalued: false | |
| + range: text value | |
| + vfa: | |
| + name: vfa | |
| + aliases: | |
| + - volatile fatty acids | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of Volatile Fatty Acids in the sample | |
| + title: volatile fatty acids | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000152 | |
| + multivalued: false | |
| + range: quantity value | |
| + vfa_fw: | |
| + name: vfa_fw | |
| + aliases: | |
| + - vfa in formation water | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Original volatile fatty acid concentration in the hydrocarbon resource | |
| + title: vfa in formation water | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000408 | |
| + multivalued: false | |
| + range: quantity value | |
| + vis_media: | |
| + name: vis_media | |
| + aliases: | |
| + - visual media | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The building visual media | |
| + title: visual media | |
| + examples: | |
| + - value: 3D scans | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000840 | |
| + multivalued: false | |
| + range: text value | |
| + viscosity: | |
| + name: viscosity | |
| + aliases: | |
| + - viscosity | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cP at degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: A measure of oil's resistance to gradual deformation by shear stress or tensile | |
| + stress (e.g. 3.5 cp; 100 °C) | |
| + title: viscosity | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{float} {unit}' | |
| + slot_uri: MIXS:0000126 | |
| + multivalued: false | |
| + range: quantity value | |
| + volatile_org_comp: | |
| + name: volatile_org_comp | |
| + aliases: | |
| + - volatile organic compounds | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: volatile organic compound name;measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: microgram per cubic meter, parts per million, nanogram per liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Concentration of carbon-based chemicals that easily evaporate at | |
| + room temperature; can report multiple volatile organic compounds by entering | |
| + numeric values preceded by name of compound | |
| + title: volatile organic compounds | |
| + examples: | |
| + - value: formaldehyde;500 nanogram per liter | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_uri: MIXS:0000115 | |
| + multivalued: false | |
| + range: quantity value | |
| + wall_area: | |
| + name: wall_area | |
| + aliases: | |
| + - wall area | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The total area of the sampled room's walls | |
| + title: wall area | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000198 | |
| + multivalued: false | |
| + range: quantity value | |
| + wall_const_type: | |
| + name: wall_const_type | |
| + aliases: | |
| + - wall construction type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The building class of the wall defined by the composition of the | |
| + building elements and fire-resistance rating. | |
| + title: wall construction type | |
| + examples: | |
| + - value: fire resistive | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000841 | |
| + multivalued: false | |
| + range: text value | |
| + wall_finish_mat: | |
| + name: wall_finish_mat | |
| + aliases: | |
| + - wall finish material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The material utilized to finish the outer most layer of the wall | |
| + title: wall finish material | |
| + examples: | |
| + - value: wood | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000842 | |
| + multivalued: false | |
| + range: text value | |
| + wall_height: | |
| + name: wall_height | |
| + aliases: | |
| + - wall height | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The average height of the walls in the sampled room | |
| + title: wall height | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000221 | |
| + multivalued: false | |
| + range: quantity value | |
| + wall_loc: | |
| + name: wall_loc | |
| + aliases: | |
| + - wall location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The relative location of the wall within the room | |
| + title: wall location | |
| + examples: | |
| + - value: north | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000843 | |
| + multivalued: false | |
| + range: text value | |
| + wall_surf_treatment: | |
| + name: wall_surf_treatment | |
| + aliases: | |
| + - wall surface treatment | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The surface treatment of interior wall | |
| + title: wall surface treatment | |
| + examples: | |
| + - value: paneling | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000845 | |
| + multivalued: false | |
| + range: text value | |
| + wall_texture: | |
| + name: wall_texture | |
| + aliases: | |
| + - wall texture | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The feel, appearance, or consistency of a wall surface | |
| + title: wall texture | |
| + examples: | |
| + - value: popcorn | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000846 | |
| + multivalued: false | |
| + range: text value | |
| + wall_thermal_mass: | |
| + name: wall_thermal_mass | |
| + aliases: | |
| + - wall thermal mass | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: joule per degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The ability of the wall to provide inertia against temperature fluctuations. | |
| + Generally this means concrete or concrete block that is either exposed or covered | |
| + only with paint | |
| + title: wall thermal mass | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000222 | |
| + multivalued: false | |
| + range: quantity value | |
| + wall_water_mold: | |
| + name: wall_water_mold | |
| + aliases: | |
| + - wall signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew on a wall | |
| + title: wall signs of water/mold | |
| + examples: | |
| + - value: no presence of mold visible | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[presence of mold visible|no presence of mold visible]' | |
| + slot_uri: MIXS:0000844 | |
| + multivalued: false | |
| + range: text value | |
| + wastewater_type: | |
| + name: wastewater_type | |
| + aliases: | |
| + - wastewater type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: wastewater type name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The origin of wastewater such as human waste, rainfall, storm drains, | |
| + etc. | |
| + title: wastewater type | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000353 | |
| + multivalued: false | |
| + range: text value | |
| + water_cont_soil_meth: | |
| + name: water_cont_soil_meth | |
| + aliases: | |
| + - water content method | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: PMID,DOI or url | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + mixs_5_name: | |
| + tag: mixs_5_name | |
| + value: water_content_soil_meth | |
| + description: Reference or method used in determining the water content of soil | |
| + title: water content method | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_uri: MIXS:0000323 | |
| + multivalued: false | |
| + range: string | |
| + water_content: | |
| + name: water_content | |
| + aliases: | |
| + - water content | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: gram per gram or cubic centimeter per cubic centimeter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Water content measurement | |
| + title: water content | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000185 | |
| + multivalued: false | |
| + range: quantity value | |
| + water_current: | |
| + name: water_current | |
| + aliases: | |
| + - water current | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cubic meter per second, knots | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Measurement of magnitude and direction of flow within a fluid | |
| + title: water current | |
| + examples: | |
| + - value: 10 cubic meter per second | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000203 | |
| + multivalued: false | |
| + range: quantity value | |
| + water_cut: | |
| + name: water_cut | |
| + aliases: | |
| + - water cut | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: percent | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Current amount of water (%) in a produced fluid stream; or the average | |
| + of the combined streams | |
| + title: water cut | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000454 | |
| + multivalued: false | |
| + range: quantity value | |
| + water_feat_size: | |
| + name: water_feat_size | |
| + aliases: | |
| + - water feature size | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: square meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The size of the water feature | |
| + title: water feature size | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000223 | |
| + multivalued: false | |
| + range: quantity value | |
| + water_feat_type: | |
| + name: water_feat_type | |
| + aliases: | |
| + - water feature type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of water feature present within the building being sampled | |
| + title: water feature type | |
| + examples: | |
| + - value: stream | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000847 | |
| + multivalued: false | |
| + range: text value | |
| + water_prod_rate: | |
| + name: water_prod_rate | |
| + aliases: | |
| + - water production rate | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: cubic meter per day | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Water production rates per well (e.g. 987 m3 / day) | |
| + title: water production rate | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: core field | |
| + slot_uri: MIXS:0000453 | |
| + multivalued: false | |
| + range: quantity value | |
| + water_temp_regm: | |
| + name: water_temp_regm | |
| + aliases: | |
| + - water temperature regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: degree Celsius | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving an exposure to water with varying | |
| + degree of temperature, treatment regimen including how many times the treatment | |
| + was repeated, how long each treatment lasted, and the start and end time of | |
| + the entire treatment; can include multiple regimens | |
| + title: water temperature regimen | |
| + examples: | |
| + - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000590 | |
| + multivalued: false | |
| + range: quantity value | |
| + watering_regm: | |
| + name: watering_regm | |
| + aliases: | |
| + - watering regimen | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value;treatment interval and duration | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milliliter, liter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: m | |
| + description: Information about treatment involving an exposure to watering frequencies, | |
| + treatment regimen including how many times the treatment was repeated, how long | |
| + each treatment lasted, and the start and end time of the entire treatment; can | |
| + include multiple regimens | |
| + title: watering regimen | |
| + examples: | |
| + - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' | |
| + slot_uri: MIXS:0000591 | |
| + multivalued: false | |
| + range: quantity value | |
| + weekday: | |
| + name: weekday | |
| + aliases: | |
| + - weekday | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The day of the week when sampling occurred | |
| + title: weekday | |
| + examples: | |
| + - value: Sunday | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000848 | |
| + multivalued: false | |
| + range: text value | |
| + win: | |
| + name: win | |
| + aliases: | |
| + - well identification number | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: text | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: 'A unique identifier of a well or wellbore. This is part of the Global | |
| + Framework for Well Identification initiative which is compiled by the Professional | |
| + Petroleum Data Management Association (PPDM) in an effort to improve well identification | |
| + systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' | |
| + title: well identification number | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000297 | |
| + multivalued: false | |
| + range: text value | |
| + wind_direction: | |
| + name: wind_direction | |
| + aliases: | |
| + - wind direction | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: wind direction name | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Wind direction is the direction from which a wind originates | |
| + title: wind direction | |
| + examples: | |
| + - value: Northwest | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{text}' | |
| + slot_uri: MIXS:0000757 | |
| + multivalued: false | |
| + range: text value | |
| + wind_speed: | |
| + name: wind_speed | |
| + aliases: | |
| + - wind speed | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: meter per second, kilometer per hour | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Speed of wind measured at the time of sampling | |
| + title: wind speed | |
| + examples: | |
| + - value: 21 kilometer per hour | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000118 | |
| + multivalued: false | |
| + range: quantity value | |
| + window_cond: | |
| + name: window_cond | |
| + aliases: | |
| + - window condition | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The physical condition of the window at the time of sampling | |
| + title: window condition | |
| + examples: | |
| + - value: rupture | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000849 | |
| + multivalued: false | |
| + range: text value | |
| + window_cover: | |
| + name: window_cover | |
| + aliases: | |
| + - window covering | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of window covering | |
| + title: window covering | |
| + examples: | |
| + - value: curtains | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000850 | |
| + multivalued: false | |
| + range: text value | |
| + window_horiz_pos: | |
| + name: window_horiz_pos | |
| + aliases: | |
| + - window horizontal position | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The horizontal position of the window on the wall | |
| + title: window horizontal position | |
| + examples: | |
| + - value: middle | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000851 | |
| + multivalued: false | |
| + range: text value | |
| + window_loc: | |
| + name: window_loc | |
| + aliases: | |
| + - window location | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The relative location of the window within the room | |
| + title: window location | |
| + examples: | |
| + - value: west | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000852 | |
| + multivalued: false | |
| + range: text value | |
| + window_mat: | |
| + name: window_mat | |
| + aliases: | |
| + - window material | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of material used to finish a window | |
| + title: window material | |
| + examples: | |
| + - value: wood | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000853 | |
| + multivalued: false | |
| + range: text value | |
| + window_open_freq: | |
| + name: window_open_freq | |
| + aliases: | |
| + - window open frequency | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: value | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The number of times windows are opened per week | |
| + title: window open frequency | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000246 | |
| + multivalued: false | |
| + range: text value | |
| + window_size: | |
| + name: window_size | |
| + aliases: | |
| + - window area/size | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: inch, meter | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The window's length and width | |
| + title: window area/size | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '{float} {unit} x {float} {unit}' | |
| + slot_uri: MIXS:0000224 | |
| + multivalued: false | |
| + range: quantity value | |
| + window_status: | |
| + name: window_status | |
| + aliases: | |
| + - window status | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Defines whether the windows were open or closed during environmental | |
| + testing | |
| + title: window status | |
| + examples: | |
| + - value: open | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[closed|open]' | |
| + slot_uri: MIXS:0000855 | |
| + multivalued: false | |
| + range: text value | |
| + window_type: | |
| + name: window_type | |
| + aliases: | |
| + - window type | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The type of windows | |
| + title: window type | |
| + examples: | |
| + - value: fixed window | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000856 | |
| + multivalued: false | |
| + range: text value | |
| + window_vert_pos: | |
| + name: window_vert_pos | |
| + aliases: | |
| + - window vertical position | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: The vertical position of the window on the wall | |
| + title: window vertical position | |
| + examples: | |
| + - value: middle | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000857 | |
| + multivalued: false | |
| + range: text value | |
| + window_water_mold: | |
| + name: window_water_mold | |
| + aliases: | |
| + - window signs of water/mold | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: enumeration | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Signs of the presence of mold or mildew on the window. | |
| + title: window signs of water/mold | |
| + examples: | |
| + - value: no presence of mold visible | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + string_serialization: '[presence of mold visible|no presence of mold visible]' | |
| + slot_uri: MIXS:0000854 | |
| + multivalued: false | |
| + range: text value | |
| + xylene: | |
| + name: xylene | |
| + aliases: | |
| + - xylene | |
| + annotations: | |
| + expected_value: | |
| + tag: expected_value | |
| + value: measurement value | |
| + preferred_unit: | |
| + tag: preferred_unit | |
| + value: milligram per liter, parts per million | |
| + occurrence: | |
| + tag: occurrence | |
| + value: '1' | |
| + description: Concentration of xylene in the sample | |
| + title: xylene | |
| + from_schema: http://w3id.org/mixs/terms | |
| + source: http://w3id.org/mixs/terms | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + slot_uri: MIXS:0000156 | |
| + multivalued: false | |
| + range: quantity value | |
| + env_package: | |
| + name: env_package | |
| aliases: | |
| - - total particulate carbon | |
| - description: >- | |
| - Total particulate carbon content | |
| - multivalued: false | |
| - is_a: attribute | |
| - range: quantity value ## syntax: {float} {unit} | |
| - pattern: "\\d+[.\\d+] \\S+" | |
| - string_serialization: "{float} {unit}" | |
| + - environmental package | |
| mappings: | |
| - - mixs:tot_part_carb | |
| - | |
| + - mixs:env_package | |
| + description: MIxS extension for reporting of measurements and observations obtained | |
| + from one or more of the environments where the sample was obtained. All environmental | |
| + packages listed here are further defined in separate subtables. By giving the | |
| + name of the environmental package, a selection of fields can be made from the | |
| + subtables and can be reported | |
| + in_subset: | |
| + - mixs extension | |
| + from_schema: https://microbiomedata/schema/mixs | |
| + source: https://microbiomedata/schema/mixs | |
| + see_also: | |
| + - https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py | |
| + is_a: attribute | |
| + multivalued: false | |
| + range: text value | |
| + pattern: '[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon | |
| + resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc | |
| + environment|plant\-associated|sediment|soil|wastewater\/sludge|water]' | |
| diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml | |
| index 36dc324..b766d06 100644 | |
| --- a/src/schema/nmdc.yaml | |
| +++ b/src/schema/nmdc.yaml | |
| @@ -4,17 +4,16 @@ title: NMDC Schema | |
| description: >- | |
| Schema for National Microbiome Data Collaborative (NMDC). | |
| - | |
| + | |
| This schema is organized into distinct modules: | |
| - | |
| + | |
| * a set of core types for representing data values | |
| * the mixs schema (auto-translated from mixs excel) | |
| * annotation schema | |
| * the NMDC schema itself | |
| - | |
| -license: https://creativecommons.org/publicdomain/zero/1.0/ | |
| -version: 2.1.0 | |
| +license: https://creativecommons.org/publicdomain/zero/1.0/ | |
| +version: 4.0.0 | |
| prefixes: | |
| nmdc: https://microbiomedata/meta/ | |
| GOLD: https://identifiers.org/gold/ | |
| @@ -28,52 +27,48 @@ prefixes: | |
| NCIT: http://purl.obolibrary.org/obo/NCIT_ | |
| igsn: https://app.geosamples.org/sample/igsn/ | |
| img.taxon: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid= | |
| - | |
| default_prefix: nmdc | |
| default_range: string | |
| - | |
| default_curi_maps: | |
| - obo_context | |
| - idot_context | |
| - | |
| emit_prefixes: | |
| - rdf | |
| - rdfs | |
| - xsd | |
| - skos | |
| - | |
| -# This file organizes the main NMDC schema. | |
| -# It brings in the mixs schema plus a schemaa | |
| -# of core types | |
| imports: | |
| + - annotation | |
| + - bioscales | |
| + - core | |
| + - external_identifiers | |
| - linkml:types | |
| - mixs | |
| - - core | |
| + - portal/emsl | |
| + - portal/jgi_metagenomics | |
| + - portal/jgi_metatranscriptomics | |
| + - portal/mixs_inspired | |
| + - portal/sample_id | |
| - prov | |
| - workflow_execution_activity | |
| - - annotation | |
| - - external_identifiers | |
| subsets: | |
| sample subset: | |
| - description: >- | |
| - Subset consisting of entities linked to the processing of samples. | |
| - Currently, this subset consists of study, omics process, and biosample. | |
| - | |
| + description: Subset consisting of entities linked to the processing of samples. Currently, | |
| + this subset consists of study, omics process, and biosample. | |
| data object subset: | |
| - description: >- | |
| - Subset consisting of the data objects that either inputs or outputs of processes or workflows. | |
| + description: Subset consisting of the data objects that either inputs or outputs | |
| + of processes or workflows. | |
| classes: | |
| - | |
| database: | |
| - tree_root: true ## this forms the root of the json object tree | |
| + tree_root: true | |
| aliases: | |
| - - "NMDC metadata object" | |
| - description: >- | |
| - An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed databse | |
| - top level holder class. When translated to JSON-Schema this is the 'root' object. | |
| - It should contain pointers to other objects of interest | |
| + - NMDC metadata object | |
| + description: An abstract holder for any set of metadata and data. It does not | |
| + need to correspond to an actual managed databse top level holder class. When | |
| + translated to JSON-Schema this is the 'root' object. It should contain pointers | |
| + to other objects of interest | |
| slots: | |
| - biosample set | |
| - study set | |
| @@ -93,22 +88,17 @@ classes: | |
| - genome feature set | |
| slot_usage: | |
| nmdc schema version: | |
| - description: >- | |
| - TODO | |
| + description: TODO | |
| date created: | |
| - description: >- | |
| - TODO | |
| + description: TODO | |
| etl software version: | |
| - description: >- | |
| - TODO | |
| - | |
| + description: TODO | |
| data object: | |
| is_a: named thing | |
| in_subset: | |
| - data object subset | |
| - description: >- | |
| - An object that primarily consists of symbols that represent information. | |
| - Files, records, and omics data are examples of data objects. | |
| + description: 'An object that primarily consists of symbols that represent information. Files, | |
| + records, and omics data are examples of data objects. ' | |
| slots: | |
| - file size bytes | |
| - md5 checksum | |
| @@ -116,7 +106,7 @@ classes: | |
| - compression type | |
| - was generated by | |
| - url | |
| - - type # custom slot that specifies object type | |
| + - type | |
| slot_usage: | |
| name: | |
| required: true | |
| @@ -127,20 +117,26 @@ classes: | |
| biosample: | |
| is_a: named thing | |
| - in_subset: | |
| + in_subset: | |
| - sample subset | |
| - aliases: ['sample', 'material sample', 'specimen', 'biospecimen'] | |
| + aliases: | |
| + - sample | |
| + - material sample | |
| + - specimen | |
| + - biospecimen | |
| description: >- | |
| A material sample. It may be environmental (encompassing many organisms) or isolate or tissue. | |
| An environmental sample containing genetic material from multiple individuals is commonly referred to as a biosample. | |
| alt_descriptions: | |
| - embl.ena: >- | |
| - A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon. | |
| + embl.ena: A sample contains information about the sequenced source material. | |
| + Samples are associated with checklists, which define the fields used to annotate | |
| + the samples. Samples are always associated with a taxon. | |
| slots: | |
| - type # custom slot that specifies object type | |
| - alternative identifiers | |
| - part of | |
| - | |
| + - canary | |
| + | |
| # MIXS slots | |
| - agrochem_addition | |
| - alkalinity | |
| @@ -151,7 +147,7 @@ classes: | |
| - al_sat_meth | |
| - aminopept_act | |
| - ammonium | |
| - - annual_precpt | |
| + - annual_precpt | |
| - annual_temp | |
| - bacteria_carb_prod | |
| - bishomohopanol | |
| @@ -175,25 +171,25 @@ classes: | |
| - diss_org_carb | |
| - diss_org_nitro | |
| - diss_oxygen | |
| - - drainage_class | |
| + - drainage_class | |
| - elev | |
| - env_package | |
| - env_broad_scale | |
| - env_local_scale | |
| - env_medium | |
| - - extreme_event | |
| - - fao_class | |
| + - extreme_event | |
| + - fao_class | |
| - fire | |
| - - flooding | |
| + - flooding | |
| - geo_loc_name | |
| - glucosidase_act | |
| - heavy_metals | |
| - heavy_metals_meth | |
| - horizon | |
| - - horizon_meth | |
| + - horizon_meth | |
| - lat_lon | |
| - - link_addit_analys | |
| - - link_class_info | |
| + - link_addit_analys | |
| + - link_class_info | |
| - link_climate_info | |
| - local_class | |
| - local_class_meth | |
| @@ -201,7 +197,7 @@ classes: | |
| - mean_frict_vel | |
| - mean_peak_frict_vel | |
| - microbial_biomass | |
| - - microbial_biomass_meth | |
| + - microbial_biomass_meth | |
| - misc_param | |
| - n_alkanes | |
| - nitrate | |
| @@ -230,10 +226,10 @@ classes: | |
| - samp_mat_process | |
| - samp_store_dur | |
| - samp_store_loc | |
| - - samp_store_temp | |
| + - samp_store_temp | |
| - samp_vol_we_dna_ext | |
| - season_temp | |
| - - season_precpt | |
| + - season_precpt | |
| - sieving | |
| - size_frac_low | |
| - size_frac_up | |
| @@ -245,9 +241,9 @@ classes: | |
| - store_cond | |
| - sulfate | |
| - sulfide | |
| - - temp | |
| + - temp | |
| - texture | |
| - - texture_meth | |
| + - texture_meth | |
| - tillage | |
| - tidal_stage | |
| - tot_carb | |
| @@ -256,11 +252,11 @@ classes: | |
| - tot_org_carb | |
| - tot_org_c_meth | |
| - tot_nitro_content | |
| - - tot_nitro_content_meth | |
| + - tot_nitro_cont_meth # MAM 2022-05-06 | |
| - tot_phosp | |
| - water_content | |
| - - water_content_soil_meth | |
| - | |
| + - water_cont_soil_meth # MAM 2022-05-06 | |
| + | |
| # GOLD path fields | |
| - ecosystem | |
| - ecosystem_category | |
| @@ -285,39 +281,148 @@ classes: | |
| - subsurface_depth | |
| - subsurface_depth2 | |
| - # external IDs | |
| + # external IDs | |
| - GOLD sample identifiers | |
| - INSDC biosample identifiers | |
| - INSDC secondary sample identifiers | |
| + | |
| + | |
| + # MIxS terms initially used in | |
| + # sample metadata submission portal (aka DataHarmonizer) | |
| + - air_temp_regm | |
| + - biotic_regm | |
| + - biotic_relationship | |
| + - climate_environment | |
| + - experimental_factor | |
| + - gaseous_environment | |
| + - growth_facil | |
| + - humidity_regm | |
| + - light_regm | |
| + - micro_biomass_meth | |
| + - phosphate | |
| + - rel_to_oxygen | |
| + - samp_collec_method | |
| + - samp_size | |
| + - soil_text_measure | |
| + - soil_texture_meth | |
| + - source_mat_id | |
| + - watering_regm | |
| + | |
| + # sample metadata submission portal (aka DataHarmonizer) terms (EMSL, JGI, etc.) | |
| + - dna_absorb1 | |
| + - dna_absorb2 | |
| + - dna_collect_site | |
| + - dna_concentration | |
| + - dna_cont_type | |
| + - dna_cont_well | |
| + - dna_container_ID | |
| + - dna_dnase | |
| + - dna_isolate_meth | |
| + - dna_organisms | |
| + - dna_project_contact | |
| + - dna_samp_ID | |
| + - dna_sample_format | |
| + - dna_sample_name | |
| + - dna_seq_project | |
| + - dna_seq_project_PI | |
| + - dna_seq_project_name | |
| + - dna_volume | |
| + - proposal_dna | |
| + - dnase_rna | |
| + - proposal_rna | |
| + - rna_absorb1 | |
| + - rna_absorb2 | |
| + - rna_collect_site | |
| + - rna_concentration | |
| + - rna_cont_type | |
| + - rna_cont_well | |
| + - rna_container_ID | |
| + - rna_isolate_meth | |
| + - rna_organisms | |
| + - rna_project_contact | |
| + - rna_samp_ID | |
| + - rna_sample_format | |
| + - rna_sample_name | |
| + - rna_seq_project | |
| + - rna_seq_project_PI | |
| + - rna_seq_project_name | |
| + - rna_volume | |
| + - collection_date_inc | |
| + - collection_time | |
| + - collection_time_inc | |
| + - experimental_factor_other | |
| + - filter_method | |
| + - isotope_exposure | |
| + - micro_biomass_C_meth | |
| + - micro_biomass_N_meth | |
| + - microbial_biomass_C | |
| + - microbial_biomass_N | |
| + - non_microb_biomass | |
| + - non_microb_biomass_method | |
| + - org_nitro_method | |
| + - other_treatment | |
| + - start_date_inc | |
| + - start_time_inc | |
| + - EMSL_store_temp | |
| + - project_ID | |
| + - replicate_number | |
| + - sample_shipped | |
| + - sample_type | |
| + - technical_reps | |
| + - analysis_type | |
| + - sample_link | |
| + # bioscales | |
| + # tot_phosp, tot_carb, tot_nitro_content, pH already associated with biosamples | |
| + - zinc | |
| + - manganese | |
| + - ammonium nitrogen | |
| + - nitrate nitrogen | |
| + - nitrite nitrogen | |
| + - lbc_thirty | |
| + - lbceq | |
| + | |
| slot_usage: | |
| lat_lon: | |
| required: false | |
| - description: >- | |
| - This is currently a required field but it's not clear if this should be required for human hosts | |
| + description: This is currently a required field but it's not clear if this | |
| + should be required for human hosts | |
| env_broad_scale: | |
| required: true | |
| env_local_scale: | |
| required: true | |
| env_medium: | |
| required: true | |
| - part of: | |
| + sample_link: | |
| required: true | |
| + # canary: | |
| + # required: true | |
| + # part of: | |
| + # required: false | |
| + | |
| id_prefixes: | |
| - GOLD | |
| exact_mappings: | |
| - OBI:0000747 | |
| - NCIT:C43412 | |
| + | |
| study: | |
| is_a: named thing | |
| - in_subset: | |
| + in_subset: | |
| - sample subset | |
| - aliases: ['proposal', 'research proposal', 'research study', 'investigation', 'project', 'umbrella project'] | |
| + aliases: | |
| + - proposal | |
| + - research proposal | |
| + - research study | |
| + - investigation | |
| + - project | |
| + - umbrella project | |
| description: >- | |
| - A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects. | |
| + A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects. | |
| alt_descriptions: | |
| - embl.ena: >- | |
| - A study (project) groups together data submitted to the archive and controls its release date. A study accession is typically used when citing data submitted to ENA | |
| + embl.ena: A study (project) groups together data submitted to the archive and | |
| + controls its release date. A study accession is typically used when citing | |
| + data submitted to ENA | |
| slots: | |
| - ecosystem | |
| - ecosystem_category | |
| @@ -335,11 +440,9 @@ classes: | |
| - websites | |
| - publications | |
| - ess dive datasets | |
| - - type # custom slot that specifies object type | |
| + - type | |
| - relevant protocols | |
| - funding sources | |
| - | |
| - # external IDs | |
| - INSDC bioproject identifiers | |
| - INSDC SRA ENA study identifiers | |
| - GOLD study identifiers | |
| @@ -350,52 +453,101 @@ classes: | |
| doi: | |
| description: >- | |
| The dataset citation for this study | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + DOI associated with the data in this study. This is required when data is already generated. | |
| + name: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: Provide a name for the study your samples will belong with. | |
| + | |
| + websites: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Link to the Principal Investigator's research lab webpage | |
| + or the study webpage associated with this collection of samples. | |
| + Multiple links can be provided. | |
| + description: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Provide a brief description of your study. | |
| + notes: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Add any additional notes or comments about this study. | |
| + alternative names: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Project, study, or sample set names the are also associated with this submission | |
| + or other names / identifiers for this study. | |
| + GOLD sample identifiers: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Provide the GOLD study IDs associated with samples for this study. | |
| + INSDC bioproject identifiers: | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Provide the NCBI BioProject Accession Number associated with the listed NCBI BioProject Title. | |
| exact_mappings: | |
| - - SIO:001066 ## study | |
| - - NCIT:C63536 ## study | |
| - - OBI:0000066 ## investigation | |
| + - SIO:001066 | |
| + - NCIT:C63536 | |
| + - OBI:0000066 | |
| - ISA:Study | |
| close_mappings: | |
| - - NCIT:C41198 ## investigation | |
| + - NCIT:C41198 | |
| - ISA:Investigation | |
| broad_mappings: | |
| - prov:Activity | |
| todos: | |
| - - determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor | |
| + - determine how to get data values for submitted_to_insdc, investigation_type, | |
| + experimental_factor | |
| - project_name is redundant with name, so excluding it | |
| id_prefixes: | |
| - GOLD ## https://identifiers.org/gold:Gs0110115 | |
| - insdc.srs ## https://www.ebi.ac.uk/ena/browser/view/PRJEB45055? | |
| - mgnify ## https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757 | |
| - | |
| biosample processing: | |
| aliases: | |
| - material processing | |
| is_a: named thing | |
| - description: >- | |
| - A process that takes one or more biosamples as inputs and generates one or as outputs. | |
| - Examples of outputs include samples cultivated from another sample or data objects created by instruments runs. | |
| + description: A process that takes one or more biosamples as inputs and generates | |
| + one or as outputs. Examples of outputs include samples cultivated from another | |
| + sample or data objects created by instruments runs. | |
| slots: | |
| - has input | |
| slot_usage: | |
| has input: | |
| range: biosample | |
| broad_mappings: | |
| - - OBI:0000094 ## material processing: https://github.com/microbiomedata/nmdc-metadata/issues/171 | |
| - | |
| + - OBI:0000094 | |
| omics processing: | |
| aliases: | |
| - omics assay | |
| - sequencing project | |
| - experiment | |
| is_a: biosample processing | |
| - in_subset: | |
| + in_subset: | |
| - sample subset | |
| description: >- | |
| The methods and processes used to generate omics data from a biosample or organism. | |
| alt_descriptions: | |
| - embl.ena: >- | |
| - An experiment contains information about a sequencing experiment including library and instrument details. | |
| + embl.ena: An experiment contains information about a sequencing experiment including | |
| + library and instrument details. | |
| comments: | |
| - The IDs for objects coming from GOLD will have prefixes gold:GpNNNN | |
| slots: | |
| @@ -409,13 +561,9 @@ classes: | |
| - part of | |
| - principal investigator | |
| - processing_institution | |
| - - type # custom slot that specifies object type | |
| - | |
| - # external IDs | |
| + - type | |
| - GOLD sequencing project identifiers | |
| - INSDC experiment identifiers | |
| - | |
| - # amplicon slots | |
| - samp_vol_we_dna_ext | |
| - nucl_acid_ext | |
| - nucl_acid_amp | |
| @@ -430,21 +578,23 @@ classes: | |
| has input: | |
| required: true | |
| broad_mappings: | |
| - - OBI:0000070 ## assay: https://github.com/microbiomedata/nmdc-metadata/issues/171 | |
| + - OBI:0000070 | |
| - ISA:Assay | |
| - | |
| credit association: | |
| - aliases: ['study role', 'credit table', 'associated researchers'] | |
| + aliases: | |
| + - study role | |
| + - credit table | |
| + - associated researchers | |
| description: >- | |
| This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value | |
| - Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0 | |
| + Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0 | |
| slots: | |
| - applies to person | |
| - applied role | |
| - applied roles | |
| - type | |
| class_uri: prov:Association | |
| - | |
| + | |
| enums: | |
| file type enum: | |
| permissible_values: | |
| @@ -510,31 +660,30 @@ enums: | |
| description: Reads QC summary statistics | |
| TIGRFam Annotation GFF: | |
| description: GFF3 format file with TIGRfam | |
| - annotations: | |
| - file_name_pattern: "[GOLD-AP]_tigrfam.gff" | |
| + annotations: | |
| + file_name_pattern: '[GOLD-AP]_tigrfam.gff' | |
| Clusters of Orthologous Groups (COG) Annotation GFF: | |
| description: GFF3 format file with COGs | |
| annotations: | |
| - file_name_pattern: "[GOLD-AP]_cog.gff" | |
| + file_name_pattern: '[GOLD-AP]_cog.gff' | |
| CATH FunFams (Functional Families) Annotation GFF: | |
| description: GFF3 format file with CATH FunFams | |
| annotations: | |
| - file_name_pattern: "[GOLD-AP]_cath_funfam.gff" | |
| + file_name_pattern: '[GOLD-AP]_cath_funfam.gff' | |
| SUPERFam Annotation GFF: | |
| description: GFF3 format file with SUPERFam | |
| annotations: | |
| - file_name_pattern: "[GOLD-AP]_supfam.gff" | |
| + file_name_pattern: '[GOLD-AP]_supfam.gff' | |
| SMART Annotation GFF: | |
| description: GFF3 format file with SMART | |
| annotations: | |
| - file_name_pattern: "[GOLD-AP]_smart.gff" | |
| + file_name_pattern: '[GOLD-AP]_smart.gff' | |
| Pfam Annotation GFF: | |
| description: GFF3 format file with Pfam | |
| annotations: | |
| - file_name_pattern: "[GOLD-AP]_pfam.gff" | |
| + file_name_pattern: '[GOLD-AP]_pfam.gff' | |
| Direct Infusion FT ICR-MS Raw Data: | |
| description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spectrometry raw data acquired in broadband full scan mode | |
| - | |
| credit enum: | |
| permissible_values: | |
| Conceptualization: | |
| @@ -562,188 +711,192 @@ enums: | |
| Visualization: | |
| description: Visualization | |
| Writing original draft: | |
| - description: Writing – original draft | |
| + description: "Writing \u2013 original draft" | |
| Writing review and editing: | |
| - description: Writing – review & editing | |
| + description: "Writing \u2013 review & editing" | |
| Principal Investigator: | |
| description: principal investigator role | |
| meaning: OBI:0000103 | |
| comments: | |
| - credit enums come from https://casrai.org/credit/ | |
| - | |
| -slots: | |
| + processing_institution_enum: | |
| + name: processing_institution_enum | |
| + comments: | |
| + - This will become the range of processing_institution.omics processing | |
| + - use ROR meanings like https://ror.org/0168r3w48 for UCSD | |
| + from_schema: NMDC_enums_roundtrip | |
| + permissible_values: | |
| + UCSD: | |
| + text: UCSD | |
| + title: University of California, San Diego | |
| + meaning: https://ror.org/0168r3w48 | |
| + JGI: | |
| + text: JGI | |
| + title: Joint Genome Institute | |
| + meaning: https://ror.org/04xm1d337 | |
| + EMSL: | |
| + text: EMSL | |
| + title: Environmental Molecular Sciences Laboratory | |
| + meaning: https://ror.org/04rc0xn13 | |
| + comments: | |
| + - replaces Environmental Molecular Science Laboratory | |
| + - replaces Environmental Molecular Sciences Lab | |
| +slots: | |
| + canary: | |
| ess dive datasets: | |
| multivalued: true | |
| - description: >- | |
| - List of ESS-DIVE dataset DOIs | |
| - | |
| + description: List of ESS-DIVE dataset DOIs | |
| has credit associations: | |
| domain: study | |
| range: credit association | |
| multivalued: true | |
| - inlined: true | |
| - description: >- | |
| - This slot links a study to a credit association. | |
| - The credit association will be linked to a person value and to a CRediT Contributor Roles term. | |
| - Overall semantics: person should get credit X for their participation in the study | |
| + # was just "inlined: true" | |
| + inlined_as_list: true | |
| + description: 'This slot links a study to a credit association. The credit association | |
| + will be linked to a person value and to a CRediT Contributor Roles term. Overall | |
| + semantics: person should get credit X for their participation in the study' | |
| slot_uri: prov:qualifiedAssociation | |
| - | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: Other researchers associated with this study. | |
| study image: | |
| domain: study | |
| range: image value | |
| multivalued: true | |
| inlined: true | |
| - description: >- | |
| - Links a study to one or more images. | |
| - | |
| + description: Links a study to one or more images. | |
| relevant protocols: | |
| multivalued: true | |
| - range: string | |
| - | |
| + range: string | |
| funding sources: | |
| multivalued: true | |
| - range: string | |
| - | |
| + range: string | |
| applied role: | |
| domain: credit association | |
| range: credit enum | |
| slot_uri: prov:hadRole | |
| - deprecated: A credit association may have multiple roles. So, use the applied roles slot. | |
| + deprecated: A credit association may have multiple roles. So, use the applied | |
| + roles slot. | |
| multivalued: false | |
| required: false | |
| - | |
| applied roles: | |
| domain: credit association | |
| range: credit enum | |
| multivalued: true | |
| required: true | |
| - | |
| + annotations: | |
| + display_hint: | |
| + tag: display_hint | |
| + value: >- | |
| + Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/ | |
| applies to person: | |
| domain: credit association | |
| range: person value | |
| - todos: >- | |
| - prov:agent takes an Agent object. Is a person value an Agent? Also try to relate to principal investigator slot? | |
| - could include OBI:0000103 principal investigator role... do we need to define the OBI prefix? | |
| + todos: prov:agent takes an Agent object. Is a person value an Agent? Also try | |
| + to relate to principal investigator slot? could include OBI:0000103 principal | |
| + investigator role... do we need to define the OBI prefix? | |
| multivalued: false | |
| required: true | |
| slot_uri: prov:agent | |
| - | |
| - | |
| object set: | |
| mixin: true | |
| domain: database | |
| multivalued: true | |
| inlined_as_list: true | |
| - description: | |
| - Applies to a property that links a database object to a set of objects. | |
| - This is necessary in a json document to provide context for a list, and | |
| - to allow for a single json object that combines multiple object types | |
| - | |
| + description: Applies to a property that links a database object to a set of objects. | |
| + This is necessary in a json document to provide context for a list, and to allow | |
| + for a single json object that combines multiple object types | |
| biosample set: | |
| mixins: object set | |
| domain: database | |
| range: biosample | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of samples within it. | |
| - | |
| + description: This property links a database object to the set of samples within | |
| + it. | |
| study set: | |
| mixins: object set | |
| domain: database | |
| range: study | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of studies within it. | |
| - | |
| + description: This property links a database object to the set of studies within | |
| + it. | |
| data object set: | |
| mixins: object set | |
| domain: database | |
| range: data object | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of data objects within it. | |
| - | |
| + description: This property links a database object to the set of data objects | |
| + within it. | |
| genome feature set: | |
| mixins: object set | |
| domain: database | |
| range: genome feature | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of all features | |
| - | |
| + description: This property links a database object to the set of all features | |
| functional annotation set: | |
| mixins: object set | |
| domain: database | |
| range: functional annotation | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of all functional annotations | |
| - | |
| + description: This property links a database object to the set of all functional | |
| + annotations | |
| activity set: | |
| mixins: object set | |
| domain: database | |
| range: workflow execution activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of workflow activities. | |
| - | |
| + description: This property links a database object to the set of workflow activities. | |
| mags activity set: | |
| mixins: object set | |
| domain: database | |
| range: MAGs analysis activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of MAGs analysis activities. | |
| - | |
| + description: This property links a database object to the set of MAGs analysis | |
| + activities. | |
| metabolomics analysis activity set: | |
| mixins: object set | |
| domain: database | |
| range: metabolomics analysis activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of metabolomics analysis activities. | |
| - | |
| + description: This property links a database object to the set of metabolomics | |
| + analysis activities. | |
| metaproteomics analysis activity set: | |
| mixins: object set | |
| domain: database | |
| range: metaproteomics analysis activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of metaproteomics analysis activities. | |
| - | |
| + description: This property links a database object to the set of metaproteomics | |
| + analysis activities. | |
| metagenome annotation activity set: | |
| mixins: object set | |
| domain: database | |
| range: metagenome annotation activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of metagenome annotation activities. | |
| - | |
| + description: This property links a database object to the set of metagenome annotation | |
| + activities. | |
| metagenome assembly set: | |
| mixins: object set | |
| domain: database | |
| range: metagenome assembly | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of metagenome assembly activities. | |
| - | |
| + description: This property links a database object to the set of metagenome assembly | |
| + activities. | |
| metatranscriptome activity set: | |
| mixins: object set | |
| domain: database | |
| range: metatranscriptome activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of metatranscriptome analysis activities. | |
| - | |
| + description: This property links a database object to the set of metatranscriptome | |
| + analysis activities. | |
| read QC analysis activity set: | |
| mixins: object set | |
| domain: database | |
| range: read QC analysis activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of read QC analysis activities. | |
| - | |
| + description: This property links a database object to the set of read QC analysis | |
| + activities. | |
| read based analysis activity set: | |
| mixins: object set | |
| domain: database | |
| @@ -751,202 +904,173 @@ slots: | |
| multivalued: true | |
| description: >- | |
| This property links a database object to the set of read based analysis activities. | |
| - | |
| nom analysis activity set: | |
| mixins: object set | |
| domain: database | |
| range: nom analysis activity | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of natural organic matter (NOM) analysis activities. | |
| - | |
| + description: This property links a database object to the set of natural organic | |
| + matter (NOM) analysis activities. | |
| omics processing set: | |
| mixins: object set | |
| domain: database | |
| range: omics processing | |
| multivalued: true | |
| - description: >- | |
| - This property links a database object to the set of omics processings within it. | |
| - | |
| + description: This property links a database object to the set of omics processings | |
| + within it. | |
| omics type: | |
| - range: controlled term value | |
| - description: >- | |
| - The type of omics data | |
| + range: controlled term value | |
| + description: The type of omics data | |
| examples: | |
| - value: metatranscriptome | |
| - value: metagenome | |
| - | |
| data object type: | |
| range: file type enum | |
| - description: >- | |
| - The type of file represented by the data object. | |
| + description: The type of file represented by the data object. | |
| examples: | |
| - value: FT ICR-MS Analysis Results | |
| - value: GC-MS Metabolomics Results | |
| - | |
| compression type: | |
| range: string | |
| - description: >- | |
| - If provided, specifies the compression type | |
| + description: If provided, specifies the compression type | |
| examples: | |
| - value: gzip | |
| todos: | |
| - consider enum | |
| - | |
| instrument_name: | |
| description: >- | |
| The name of the instrument that was used for processing the sample. | |
| - | |
| ## GOLD PATHS | |
| gold_path_field: | |
| is_a: attribute | |
| range: string | |
| abstract: true | |
| description: >- | |
| - This is a grouping for any of the gold path fields | |
| - | |
| + This is a grouping for any of the gold path fields | |
| ecosystem: | |
| is_a: gold_path_field | |
| - description: >- | |
| - An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path. | |
| - comments: The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. | |
| + description: An ecosystem is a combination of a physical environment (abiotic | |
| + factors) and all the organisms (biotic factors) that interact with this environment. | |
| + Ecosystem is in position 1/5 in a GOLD path. | |
| + comments: The abiotic factors play a profound role on the type and composition | |
| + of organisms in a given environment. The GOLD Ecosystem at the top of the five-level | |
| + classification system is aimed at capturing the broader environment from which | |
| + an organism or environmental sample is collected. The three broad groups under | |
| + Ecosystem are Environmental, Host-associated, and Engineered. They represent | |
| + samples collected from a natural environment or from another organism or from | |
| + engineered environments like bioreactors respectively. | |
| see_also: https://gold.jgi.doe.gov/help | |
| - | |
| ecosystem_category: | |
| is_a: gold_path_field | |
| - description: >- | |
| - Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path. | |
| - comments: The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. | |
| + description: Ecosystem categories represent divisions within the ecosystem based | |
| + on specific characteristics of the environment from where an organism or sample | |
| + is isolated. Ecosystem category is in position 2/5 in a GOLD path. | |
| + comments: The Environmental ecosystem (for example) is divided into Air, Aquatic | |
| + and Terrestrial. Ecosystem categories for Host-associated samples can be individual | |
| + hosts or phyla and for engineered samples it may be manipulated environments | |
| + like bioreactors, solid waste etc. | |
| see_also: https://gold.jgi.doe.gov/help | |
| - | |
| ecosystem_type: | |
| is_a: gold_path_field | |
| - description: >- | |
| - Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path. | |
| - comments: The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. | |
| + description: Ecosystem types represent things having common characteristics within | |
| + the Ecosystem Category. These common characteristics based grouping is still | |
| + broad but specific to the characteristics of a given environment. Ecosystem | |
| + type is in position 3/5 in a GOLD path. | |
| + comments: The Aquatic ecosystem category (for example) may have ecosystem types | |
| + like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air | |
| + or Outdoor air as different Ecosystem Types. In the case of Host-associated | |
| + samples, ecosystem type can represent Respiratory system, Digestive system, | |
| + Roots etc. | |
| see_also: https://gold.jgi.doe.gov/help | |
| - | |
| ecosystem_subtype: | |
| is_a: gold_path_field | |
| - description: >- | |
| - Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. | |
| - comments: Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. | |
| + description: Ecosystem subtypes represent further subdivision of Ecosystem types | |
| + into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD | |
| + path. | |
| + comments: Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further | |
| + divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone | |
| + etc. in the Ecosystem subtype category. | |
| see_also: https://gold.jgi.doe.gov/help | |
| - | |
| specific_ecosystem: | |
| is_a: gold_path_field | |
| - description: >- | |
| - Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path. | |
| - comments: Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. | |
| + description: Specific ecosystems represent specific features of the environment | |
| + like aphotic zone in an ocean or gastric mucosa within a host digestive system. | |
| + Specific ecosystem is in position 5/5 in a GOLD path. | |
| + comments: Specific ecosystems help to define samples based on very specific characteristics | |
| + of an environment under the five-level classification system. | |
| see_also: https://gold.jgi.doe.gov/help | |
| - | |
| - ## GOLD DATABASE SPECFIC FIELDS | |
| principal investigator: | |
| aliases: | |
| - PI | |
| is_a: attribute | |
| range: person value | |
| - description: >- | |
| - Principal Investigator who led the study and/or generated the dataset. | |
| - | |
| + description: Principal Investigator who led the study and/or generated the dataset. | |
| doi: | |
| is_a: attribute | |
| range: attribute value | |
| - | |
| add_date: | |
| range: string | |
| - description: >- | |
| - The date on which the information was added to the database. | |
| - | |
| + description: The date on which the information was added to the database. | |
| mod_date: | |
| range: string | |
| - description: >- | |
| - The last date on which the database information was modified. | |
| - | |
| + description: The last date on which the database information was modified. | |
| ecosystem_path_id: | |
| range: string | |
| - description: >- | |
| - A unique id representing the GOLD classifers associated with a sample. | |
| - | |
| + description: A unique id representing the GOLD classifers associated with a sample. | |
| habitat: | |
| range: string | |
| - | |
| location: | |
| range: string | |
| - | |
| community: | |
| range: string | |
| - | |
| ncbi_taxonomy_name: | |
| range: string | |
| - | |
| ncbi_project_name: | |
| range: string | |
| - | |
| sample_collection_site: | |
| range: string | |
| - | |
| identifier: | |
| range: string | |
| - | |
| sample_collection_year: | |
| range: integer | |
| - | |
| sample_collection_month: | |
| range: integer | |
| - | |
| sample_collection_day: | |
| range: integer | |
| - | |
| sample_collection_hour: | |
| range: integer | |
| - | |
| sample_collection_minute: | |
| range: integer | |
| - | |
| salinity_category: | |
| - description: >- | |
| - Categorcial description of the sample's salinity. | |
| - Examples: halophile, halotolerant, hypersaline, huryhaline | |
| + description: 'Categorcial description of the sample''s salinity. Examples: halophile, | |
| + halotolerant, hypersaline, huryhaline' | |
| range: string | |
| see_also: | |
| - https://github.com/microbiomedata/nmdc-metadata/pull/297 | |
| - | |
| soluble_iron_micromol: | |
| range: string | |
| - | |
| host_name: | |
| range: string | |
| - | |
| depth2: | |
| range: quantity value | |
| - | |
| subsurface_depth: | |
| range: quantity value | |
| - | |
| subsurface_depth2: | |
| range: quantity value | |
| - | |
| proport_woa_temperature: | |
| range: string | |
| - | |
| + | |
| biogas_temperature: | |
| range: string | |
| - | |
| soil_annual_season_temp: | |
| range: string | |
| - | |
| + | |
| biogas_retention_time: | |
| range: string | |
| - | |
| processing_institution: | |
| - range: string | |
| - description: >- | |
| - The organization that processed the sample. | |
| - | |
| + range: processing_institution_enum | |
| + description: The organization that processed the sample. | |
| omics_type: | |
| range: string | |
| - | |
| completion_date: | |
| range: string | |
| - | |
| diff --git a/src/schema/portal/README.md b/src/schema/portal/README.md | |
| new file mode 100644 | |
| index 0000000..23c93c4 | |
| --- /dev/null | |
| +++ b/src/schema/portal/README.md | |
| @@ -0,0 +1 @@ | |
| +don't delete this directory | |
| diff --git a/src/schema/portal/emsl.yaml b/src/schema/portal/emsl.yaml | |
| new file mode 100644 | |
| index 0000000..68fe9f1 | |
| --- /dev/null | |
| +++ b/src/schema/portal/emsl.yaml | |
| @@ -0,0 +1,96 @@ | |
| +name: emsl | |
| +description: This file defines terms that appear in the 'EMSL' section of the NMDC | |
| + sample metadata submission portal, which is implemented with DataHarmonizer as of | |
| + Spring 2022 | |
| +title: 'NMDC Schema supplement for Submission Portal: EMSL' | |
| +id: https://microbiomedata/schema/emsl | |
| +imports: | |
| +- linkml:types | |
| +license: 'license: https://creativecommons.org/publicdomain/zero/1.0/' | |
| +prefixes: | |
| +- prefix_prefix: linkml | |
| + prefix_reference: https://w3id.org/linkml/ | |
| +- prefix_prefix: nmdc | |
| + prefix_reference: https://microbiomedata/meta/ | |
| +default_prefix: nmdc | |
| +default_range: string | |
| +enums: | |
| + sample_type_enum: | |
| + name: sample_type_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + soil: | |
| + text: soil | |
| + water_extract_soil: | |
| + text: water_extract_soil | |
| +slots: | |
| + EMSL_store_temp: | |
| + name: EMSL_store_temp | |
| + description: Temperature at which the sample sent to EMSL should be stored | |
| + title: EMSL sample storage temperature, deg. C | |
| + comments: | |
| + - Enter a temperature in celsius. Numeric portion only. | |
| + examples: | |
| + - value: '-80' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 4 | |
| + string_serialization: '{float}' | |
| + slot_group: EMSL | |
| + required: false | |
| + recommended: true | |
| + project_ID: | |
| + name: project_ID | |
| + description: Proposal IDs or names associated with dataset | |
| + title: project ID | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 1 | |
| + string_serialization: '{text}' | |
| + slot_group: EMSL | |
| + required: false | |
| + recommended: true | |
| + replicate_number: | |
| + name: replicate_number | |
| + description: If sending biological replicates, indicate the rep number here. | |
| + title: replicate number | |
| + comments: | |
| + - This will guide staff in ensuring your samples are block & randomized correctly | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 6 | |
| + string_serialization: '{integer}' | |
| + slot_group: EMSL | |
| + recommended: true | |
| + sample_shipped: | |
| + name: sample_shipped | |
| + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of | |
| + sample sent to EMSL | |
| + title: sample shipped amount | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 3 | |
| + string_serialization: '{float} {unit}' | |
| + slot_group: EMSL | |
| + required: false | |
| + recommended: true | |
| + sample_type: | |
| + name: sample_type | |
| + description: Type of sample being submitted | |
| + title: sample type | |
| + comments: | |
| + - This can vary from 'environmental package' if the sample is an extraction. | |
| + examples: | |
| + - value: water extracted soil | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 2 | |
| + slot_group: EMSL | |
| + range: sample_type_enum | |
| + required: false | |
| + recommended: true | |
| + technical_reps: | |
| + name: technical_reps | |
| + description: If sending multiple technical replicates of the same sample, indicate | |
| + how many replicates are being sent | |
| + title: number technical replicate | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 5 | |
| + string_serialization: '{integer}' | |
| + slot_group: EMSL | |
| + recommended: true | |
| diff --git a/src/schema/portal/jgi_metagenomics.yaml b/src/schema/portal/jgi_metagenomics.yaml | |
| new file mode 100644 | |
| index 0000000..ddbc2e7 | |
| --- /dev/null | |
| +++ b/src/schema/portal/jgi_metagenomics.yaml | |
| @@ -0,0 +1,320 @@ | |
| +name: jgi_metagenomics | |
| +description: This file defines terms that appear in the 'JGI-Metagenomics' section | |
| + of the NMDC sample metadata submission portal, which is implemented with DataHarmonizer | |
| + as of Spring 2022 | |
| +title: 'NMDC Schema supplement for Submission Portal: JGI-Metagenomics' | |
| +id: https://microbiomedata/schema/jgi_metagenomics | |
| +imports: | |
| +- linkml:types | |
| +license: 'license: https://creativecommons.org/publicdomain/zero/1.0/' | |
| +prefixes: | |
| +- prefix_prefix: linkml | |
| + prefix_reference: https://w3id.org/linkml/ | |
| +- prefix_prefix: nmdc | |
| + prefix_reference: https://microbiomedata/meta/ | |
| +default_prefix: nmdc | |
| +default_range: string | |
| +enums: | |
| + dna_cont_type_enum: | |
| + name: dna_cont_type_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + plate: | |
| + text: plate | |
| + tube: | |
| + text: tube | |
| + dna_dnase_enum: | |
| + name: dna_dnase_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + 'no': | |
| + text: 'no' | |
| + 'yes': | |
| + text: 'yes' | |
| + dna_sample_format_enum: | |
| + name: dna_sample_format_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + 10 mM Tris-HCl: | |
| + text: 10 mM Tris-HCl | |
| + DNAStable: | |
| + text: DNAStable | |
| + Ethanol: | |
| + text: Ethanol | |
| + Low EDTA TE: | |
| + text: Low EDTA TE | |
| + MDA reaction buffer: | |
| + text: MDA reaction buffer | |
| + PBS: | |
| + text: PBS | |
| + Pellet: | |
| + text: Pellet | |
| + RNAStable: | |
| + text: RNAStable | |
| + TE: | |
| + text: TE | |
| + Water: | |
| + text: Water | |
| +slots: | |
| + dna_absorb1: | |
| + name: dna_absorb1 | |
| + description: 260/280 measurement of DNA sample purity | |
| + title: DNA absorbance 260/280 | |
| + comments: | |
| + - Recommended value is between 1 and 3. | |
| + examples: | |
| + - value: '2.02' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 7 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metagenomics | |
| + recommended: true | |
| + dna_absorb2: | |
| + name: dna_absorb2 | |
| + description: 260/230 measurement of DNA sample purity | |
| + title: DNA absorbance 260/230 | |
| + comments: | |
| + - Recommended value is between 1 and 3. | |
| + examples: | |
| + - value: '2.02' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 8 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metagenomics | |
| + recommended: true | |
| + dna_collect_site: | |
| + name: dna_collect_site | |
| + description: Provide information on the site your DNA sample was collected from | |
| + title: DNA collection site | |
| + examples: | |
| + - value: untreated pond water | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 15 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_concentration: | |
| + name: dna_concentration | |
| + title: DNA concentration in ng/ul | |
| + comments: | |
| + - Units must be in ng/uL. Enter the numerical part only. Must be calculated using | |
| + a fluorometric method. Acceptable values are 0-2000. | |
| + examples: | |
| + - value: '100' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 5 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + minimum_value: 0 | |
| + maximum_value: 2000 | |
| + dna_cont_type: | |
| + name: dna_cont_type | |
| + description: Tube or plate (96-well) | |
| + title: DNA container type | |
| + examples: | |
| + - value: plate | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 10 | |
| + slot_group: JGI-Metagenomics | |
| + range: dna_cont_type_enum | |
| + required: false | |
| + recommended: true | |
| + dna_cont_well: | |
| + name: dna_cont_well | |
| + title: DNA well number | |
| + comments: | |
| + - Required when 'plate' is selected for container type. Corner wells must be blank. | |
| + For partial plates, fill by columns. Leave blank if the sample will be shipped | |
| + in a tube. | |
| + examples: | |
| + - value: B2 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 11 | |
| + string_serialization: '{96 well plate pos}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_container_ID: | |
| + name: dna_container_ID | |
| + title: DNA container label | |
| + comments: | |
| + - Must be unique across all tubes and plates, and <20 characters. All samples | |
| + in a plate should have the same plate label. | |
| + examples: | |
| + - value: Pond_MT_041618 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 9 | |
| + string_serialization: '{text < 20 characters}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_dnase: | |
| + name: dna_dnase | |
| + title: DNase treatment DNA | |
| + comments: | |
| + - Note DNAse treatment is required for all RNA samples. | |
| + examples: | |
| + - value: 'no' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 13 | |
| + slot_group: JGI-Metagenomics | |
| + range: dna_dnase_enum | |
| + required: false | |
| + recommended: true | |
| + dna_isolate_meth: | |
| + name: dna_isolate_meth | |
| + description: Describe the method/protocol/kit used to extract DNA/RNA. | |
| + title: DNA isolation method | |
| + examples: | |
| + - value: phenol/chloroform extraction | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 16 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_organisms: | |
| + name: dna_organisms | |
| + description: List any organisms known or suspected to grow in co-culture, as well | |
| + as estimated % of the organism in that culture. | |
| + title: DNA expected organisms | |
| + examples: | |
| + - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles | |
| + (1%) | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 14 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + recommended: true | |
| + dna_project_contact: | |
| + name: dna_project_contact | |
| + title: DNA seq project contact | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: John Jones | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 18 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_samp_ID: | |
| + name: dna_samp_ID | |
| + title: DNA sample ID | |
| + todos: | |
| + - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't | |
| + have two identifiers. How to force uniqueness? Moot because that column will | |
| + be prefilled? | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '187654' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 3 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_sample_format: | |
| + name: dna_sample_format | |
| + description: Solution in which the DNA sample has been suspended | |
| + title: DNA sample format | |
| + examples: | |
| + - value: Water | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 12 | |
| + slot_group: JGI-Metagenomics | |
| + range: dna_sample_format_enum | |
| + required: false | |
| + recommended: true | |
| + dna_sample_name: | |
| + name: dna_sample_name | |
| + description: Give the DNA sample a name that is meaningful to you. Sample names | |
| + must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. | |
| + title: DNA sample name | |
| + examples: | |
| + - value: JGI_pond_041618 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 4 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_seq_project: | |
| + name: dna_seq_project | |
| + title: DNA seq project ID | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '1191234' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 1 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_seq_project_PI: | |
| + name: dna_seq_project_PI | |
| + title: DNA seq project PI | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: Jane Johnson | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 17 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_seq_project_name: | |
| + name: dna_seq_project_name | |
| + title: DNA seq project name | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: JGI Pond metagenomics | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 2 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + dna_volume: | |
| + name: dna_volume | |
| + title: DNA volume in ul | |
| + comments: | |
| + - Units must be in uL. Enter the numerical part only. Value must 0-1000. Values | |
| + <25 by special permission only. | |
| + examples: | |
| + - value: '25' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 6 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| + minimum_value: 0 | |
| + maximum_value: 1000 | |
| + proposal_dna: | |
| + name: proposal_dna | |
| + title: DNA proposal ID | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '504000' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 19 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metagenomics | |
| + required: false | |
| + recommended: true | |
| diff --git a/src/schema/portal/jgi_metatranscriptomics.yaml b/src/schema/portal/jgi_metatranscriptomics.yaml | |
| new file mode 100644 | |
| index 0000000..c0174d0 | |
| --- /dev/null | |
| +++ b/src/schema/portal/jgi_metatranscriptomics.yaml | |
| @@ -0,0 +1,316 @@ | |
| +name: jgi_metatranscriptomics | |
| +description: This file defines terms that appear in the 'JGI-Metatranscriptomics' | |
| + section of the NMDC sample metadata submission portal, which is implemented with | |
| + DataHarmonizer as of Spring 2022 | |
| +title: 'NMDC Schema supplement for Submission Portal: JGI-Metatranscriptomics' | |
| +id: https://microbiomedata/schema/jgi_metatranscriptomics | |
| +imports: | |
| +- linkml:types | |
| +license: 'license: https://creativecommons.org/publicdomain/zero/1.0/' | |
| +prefixes: | |
| +- prefix_prefix: linkml | |
| + prefix_reference: https://w3id.org/linkml/ | |
| +- prefix_prefix: nmdc | |
| + prefix_reference: https://microbiomedata/meta/ | |
| +default_prefix: nmdc | |
| +default_range: string | |
| +enums: | |
| + dnase_rna_enum: | |
| + name: dnase_rna_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + 'no': | |
| + text: 'no' | |
| + 'yes': | |
| + text: 'yes' | |
| + rna_cont_type_enum: | |
| + name: rna_cont_type_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + plate: | |
| + text: plate | |
| + tube: | |
| + text: tube | |
| + rna_sample_format_enum: | |
| + name: rna_sample_format_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + 10 mM Tris-HCl: | |
| + text: 10 mM Tris-HCl | |
| + DNAStable: | |
| + text: DNAStable | |
| + Ethanol: | |
| + text: Ethanol | |
| + Low EDTA TE: | |
| + text: Low EDTA TE | |
| + MDA reaction buffer: | |
| + text: MDA reaction buffer | |
| + PBS: | |
| + text: PBS | |
| + Pellet: | |
| + text: Pellet | |
| + RNAStable: | |
| + text: RNAStable | |
| + TE: | |
| + text: TE | |
| + Water: | |
| + text: Water | |
| +slots: | |
| + dnase_rna: | |
| + name: dnase_rna | |
| + title: DNase treated | |
| + comments: | |
| + - Note DNAse treatment is required for all RNA samples. | |
| + examples: | |
| + - value: 'no' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 13 | |
| + slot_group: JGI-Metatranscriptomics | |
| + range: dnase_rna_enum | |
| + required: false | |
| + recommended: true | |
| + proposal_rna: | |
| + name: proposal_rna | |
| + title: RNA proposal ID | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '504000' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 19 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_absorb1: | |
| + name: rna_absorb1 | |
| + description: 260/280 measurement of RNA sample purity | |
| + title: RNA absorbance 260/280 | |
| + comments: | |
| + - Recommended value is between 1 and 3. | |
| + examples: | |
| + - value: '2.02' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 7 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + recommended: true | |
| + rna_absorb2: | |
| + name: rna_absorb2 | |
| + description: 260/230 measurement of RNA sample purity | |
| + title: RNA absorbance 260/230 | |
| + comments: | |
| + - Recommended value is between 1 and 3. | |
| + examples: | |
| + - value: '2.02' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 8 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + recommended: true | |
| + rna_collect_site: | |
| + name: rna_collect_site | |
| + description: Provide information on the site your RNA sample was collected from | |
| + title: RNA collection site | |
| + examples: | |
| + - value: untreated pond water | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 15 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_concentration: | |
| + name: rna_concentration | |
| + title: RNA concentration in ng/ul | |
| + comments: | |
| + - Units must be in ng/uL. Enter the numerical part only. Must be calculated using | |
| + a fluorometric method. Acceptable values are 0-2000. | |
| + examples: | |
| + - value: '100' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 5 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + minimum_value: 0 | |
| + maximum_value: 1000 | |
| + rna_cont_type: | |
| + name: rna_cont_type | |
| + description: Tube or plate (96-well) | |
| + title: RNA container type | |
| + examples: | |
| + - value: plate | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 10 | |
| + slot_group: JGI-Metatranscriptomics | |
| + range: rna_cont_type_enum | |
| + required: false | |
| + recommended: true | |
| + rna_cont_well: | |
| + name: rna_cont_well | |
| + title: RNA well number | |
| + comments: | |
| + - Required when 'plate' is selected for container type. Corner wells must be blank. | |
| + For partial plates, fill by columns. Leave blank if the sample will be shipped | |
| + in a tube. | |
| + examples: | |
| + - value: B2 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 11 | |
| + string_serialization: '{96 well plate pos}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_container_ID: | |
| + name: rna_container_ID | |
| + title: RNA container label | |
| + comments: | |
| + - Must be unique across all tubes and plates, and <20 characters. All samples | |
| + in a plate should have the same plate label. | |
| + examples: | |
| + - value: Pond_MT_041618 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 9 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_isolate_meth: | |
| + name: rna_isolate_meth | |
| + description: Describe the method/protocol/kit used to extract DNA/RNA. | |
| + title: RNA isolation method | |
| + examples: | |
| + - value: phenol/chloroform extraction | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 16 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_organisms: | |
| + name: rna_organisms | |
| + description: List any organisms known or suspected to grow in co-culture, as well | |
| + as estimated % of the organism in that culture. | |
| + title: RNA expected organisms | |
| + examples: | |
| + - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles | |
| + (1%) | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 14 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + recommended: true | |
| + rna_project_contact: | |
| + name: rna_project_contact | |
| + title: RNA seq project contact | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: John Jones | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 18 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_samp_ID: | |
| + name: rna_samp_ID | |
| + title: RNA sample ID | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '187654' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 3 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_sample_format: | |
| + name: rna_sample_format | |
| + description: Solution in which the RNA sample has been suspended | |
| + title: RNA sample format | |
| + examples: | |
| + - value: Water | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 12 | |
| + slot_group: JGI-Metatranscriptomics | |
| + range: rna_sample_format_enum | |
| + required: false | |
| + recommended: true | |
| + rna_sample_name: | |
| + name: rna_sample_name | |
| + description: Give the RNA sample a name that is meaningful to you. Sample names | |
| + must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. | |
| + title: RNA sample name | |
| + examples: | |
| + - value: JGI_pond_041618 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 4 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + minimum_value: 0 | |
| + maximum_value: 2000 | |
| + rna_seq_project: | |
| + name: rna_seq_project | |
| + title: RNA seq project ID | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: '1191234' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 1 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_seq_project_PI: | |
| + name: rna_seq_project_PI | |
| + title: RNA seq project PI | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: Jane Johnson | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 17 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_seq_project_name: | |
| + name: rna_seq_project_name | |
| + title: RNA seq project name | |
| + comments: | |
| + - Do not edit these values. A template will be provided by NMDC in which these | |
| + values have been pre-filled. | |
| + examples: | |
| + - value: JGI Pond metatranscriptomics | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 2 | |
| + string_serialization: '{text}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| + rna_volume: | |
| + name: rna_volume | |
| + title: RNA volume in ul | |
| + comments: | |
| + - Units must be in uL. Enter the numerical part only. Value must 0-1000. Values | |
| + <25 by special permission only. | |
| + examples: | |
| + - value: '25' | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 6 | |
| + string_serialization: '{float}' | |
| + slot_group: JGI-Metatranscriptomics | |
| + required: false | |
| + recommended: true | |
| diff --git a/src/schema/portal/mixs_inspired.yaml b/src/schema/portal/mixs_inspired.yaml | |
| new file mode 100644 | |
| index 0000000..56d2d82 | |
| --- /dev/null | |
| +++ b/src/schema/portal/mixs_inspired.yaml | |
| @@ -0,0 +1,240 @@ | |
| +name: mixs_inspired | |
| +description: This file defines terms that appear in the 'MIxS Inspired' section of | |
| + the NMDC sample metadata submission portal, which is implemented with DataHarmonizer | |
| + as of Spring 2022 | |
| +title: 'NMDC Schema supplement for Submission Portal: MIxS Inspired' | |
| +id: https://microbiomedata/schema/mixs_inspired | |
| +imports: | |
| +- linkml:types | |
| +license: 'license: https://creativecommons.org/publicdomain/zero/1.0/' | |
| +prefixes: | |
| +- prefix_prefix: linkml | |
| + prefix_reference: https://w3id.org/linkml/ | |
| +- prefix_prefix: nmdc | |
| + prefix_reference: https://microbiomedata/meta/ | |
| +default_prefix: nmdc | |
| +default_range: string | |
| +slots: | |
| + collection_date_inc: | |
| + name: collection_date_inc | |
| + description: Date the incubation was harvested/collected/ended. Only relevant | |
| + for incubation samples. | |
| + title: incubation collection date | |
| + notes: | |
| + - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only | |
| + comments: | |
| + - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 | |
| + are all acceptable. | |
| + examples: | |
| + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:collection_date | |
| + rank: 2 | |
| + string_serialization: '{date, arbitrary precision}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + collection_time: | |
| + name: collection_time | |
| + description: The time of sampling, either as an instance (single point) or interval. | |
| + title: collection time, GMT | |
| + notes: | |
| + - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional | |
| + time only | |
| + comments: | |
| + - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' | |
| + examples: | |
| + - value: 13:33 or 13:33:55 | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:collection_date | |
| + rank: 1 | |
| + string_serialization: '{time, seconds optional}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + collection_time_inc: | |
| + name: collection_time_inc | |
| + description: Time the incubation was harvested/collected/ended. Only relevant | |
| + for incubation samples. | |
| + title: incubation collection time, GMT | |
| + notes: | |
| + - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional | |
| + time only | |
| + comments: | |
| + - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' | |
| + examples: | |
| + - value: 13:33 or 13:33:55 | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:collection_date | |
| + rank: 3 | |
| + string_serialization: '{time, seconds optional}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + experimental_factor_other: | |
| + name: experimental_factor_other | |
| + description: Other details about your sample that you feel can't be accurately | |
| + represented in the available columns. | |
| + title: experimental factor- other | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:experimental_factor|additional_info | |
| + rank: 7 | |
| + string_serialization: '{text}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + filter_method: | |
| + name: filter_method | |
| + description: Type of filter used or how the sample was filtered | |
| + title: filter method | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:filter_type | |
| + rank: 6 | |
| + string_serialization: '{text}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + isotope_exposure: | |
| + name: isotope_exposure | |
| + description: List isotope exposure or addition applied to your sample. | |
| + title: isotope exposure/addition | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:chem_administration | |
| + rank: 16 | |
| + string_serialization: '{termLabel} {[termID]}; {timestamp}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + micro_biomass_C_meth: | |
| + name: micro_biomass_C_meth | |
| + description: Reference or method used in determining microbial biomass | |
| + title: microbial biomass carbon method | |
| + comments: | |
| + - required if "microbial_biomass_C" is provided | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:micro_biomass_meth | |
| + rank: 11 | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + micro_biomass_N_meth: | |
| + name: micro_biomass_N_meth | |
| + description: Reference or method used in determining microbial biomass nitrogen | |
| + title: microbial biomass nitrogen method | |
| + comments: | |
| + - required if "microbial_biomass_N" is provided | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:micro_biomass_meth | |
| + rank: 13 | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_group: MIxS Inspired | |
| + microbial_biomass_C: | |
| + name: microbial_biomass_C | |
| + description: The part of the organic matter in the soil that constitutes living | |
| + microorganisms smaller than 5-10 micrometer. If you keep this, you would need | |
| + to have correction factors used for conversion to the final units | |
| + title: microbial biomass carbon | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:microbial_biomass | |
| + rank: 10 | |
| + string_serialization: '{float} {unit}' | |
| + slot_group: MIxS Inspired | |
| + microbial_biomass_N: | |
| + name: microbial_biomass_N | |
| + description: The part of the organic matter in the soil that constitutes living | |
| + microorganisms smaller than 5-10 micrometer. If you keep this, you would need | |
| + to have correction factors used for conversion to the final units | |
| + title: microbial biomass nitrogen | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:microbial_biomass | |
| + rank: 12 | |
| + string_serialization: '{float} {unit}' | |
| + slot_group: MIxS Inspired | |
| + non_microb_biomass: | |
| + name: non_microb_biomass | |
| + description: Amount of biomass; should include the name for the part of biomass | |
| + measured, e.g.insect, plant, total. Can include multiple measurements separated | |
| + by ; | |
| + title: non-microbial biomass | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:biomass|microbial_biomass | |
| + rank: 8 | |
| + string_serialization: '{text};{float} {unit}' | |
| + slot_group: MIxS Inspired | |
| + non_microb_biomass_method: | |
| + name: non_microb_biomass_method | |
| + description: Reference or method used in determining biomass | |
| + title: non-microbial biomass method | |
| + comments: | |
| + - required if "non-microbial biomass" is provided | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:microbial_biomass | |
| + rank: 9 | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_group: MIxS Inspired | |
| + org_nitro_method: | |
| + name: org_nitro_method | |
| + description: Method used for obtaining organic nitrogen | |
| + title: organic nitrogen method | |
| + comments: | |
| + - required if "org_nitro" is provided | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:org_nitro|tot_nitro_cont_meth | |
| + rank: 14 | |
| + string_serialization: '{PMID}|{DOI}|{URL}' | |
| + slot_group: MIxS Inspired | |
| + other_treatment: | |
| + name: other_treatment | |
| + description: Other treatments applied to your samples that are not applicable | |
| + to the provided fields | |
| + title: other treatments | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:additional_info | |
| + rank: 15 | |
| + string_serialization: '{text}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + start_date_inc: | |
| + name: start_date_inc | |
| + description: Date the incubation was started. Only relevant for incubation samples. | |
| + title: incubation start date | |
| + notes: | |
| + - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only | |
| + comments: | |
| + - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 | |
| + are all acceptable. | |
| + examples: | |
| + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:collection_date | |
| + rank: 4 | |
| + string_serialization: '{date, arbitrary precision}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| + start_time_inc: | |
| + name: start_time_inc | |
| + description: Time the incubation was started. Only relevant for incubation samples. | |
| + title: incubation start time, GMT | |
| + notes: | |
| + - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional | |
| + time only | |
| + comments: | |
| + - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' | |
| + examples: | |
| + - value: 13:33 or 13:33:55 | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:collection_date | |
| + rank: 5 | |
| + string_serialization: '{time, seconds optional}' | |
| + slot_group: MIxS Inspired | |
| + recommended: true | |
| diff --git a/src/schema/portal/sample_id.yaml b/src/schema/portal/sample_id.yaml | |
| new file mode 100644 | |
| index 0000000..d2fd947 | |
| --- /dev/null | |
| +++ b/src/schema/portal/sample_id.yaml | |
| @@ -0,0 +1,66 @@ | |
| +name: sample_id | |
| +description: This file defines terms that appear in the 'Sample ID' section of the | |
| + NMDC sample metadata submission portal, which is implemented with DataHarmonizer | |
| + as of Spring 2022 | |
| +title: 'NMDC Schema supplement for Submission Portal: Sample ID' | |
| +id: https://microbiomedata/schema/sample_id | |
| +imports: | |
| +- linkml:types | |
| +license: 'license: https://creativecommons.org/publicdomain/zero/1.0/' | |
| +prefixes: | |
| +- prefix_prefix: linkml | |
| + prefix_reference: https://w3id.org/linkml/ | |
| +- prefix_prefix: nmdc | |
| + prefix_reference: https://microbiomedata/meta/ | |
| +default_prefix: nmdc | |
| +default_range: string | |
| +enums: | |
| + analysis_type_enum: | |
| + name: analysis_type_enum | |
| + from_schema: https://example.com/nmdc_dh | |
| + permissible_values: | |
| + metabolomics: | |
| + text: metabolomics | |
| + metagenomics: | |
| + text: metagenomics | |
| + metaproteomics: | |
| + text: metaproteomics | |
| + metatranscriptomics: | |
| + text: metatranscriptomics | |
| + natural organic matter: | |
| + text: natural organic matter | |
| +slots: | |
| + analysis_type: | |
| + name: analysis_type | |
| + description: Select all the data types associated or available for this biosample | |
| + title: analysis/data type | |
| + examples: | |
| + - value: metagenomics; metabolomics; proteomics | |
| + from_schema: https://example.com/nmdc_dh | |
| + see_also: | |
| + - MIxS:investigation_type | |
| + rank: 3 | |
| + multivalued: true | |
| + slot_group: Sample ID | |
| + range: analysis_type_enum | |
| + required: false | |
| + recommended: true | |
| + sample_link: | |
| + name: sample_link | |
| + description: A unique identifier to assign parent-child, subsample, or sibling | |
| + samples. This is relevant when a sample or other material was used to generate | |
| + the new sample. | |
| + title: sample linkage | |
| + comments: | |
| + - 'This field allows multiple entries separated by ; (Examples: Soil collected | |
| + from the field will link with the soil used in an incubation. The soil a plant | |
| + was grown in links to the plant sample. An original culture sample was transferred | |
| + to a new vial and generated a new sample)' | |
| + examples: | |
| + - value: IGSN:DSJ0284 | |
| + from_schema: https://example.com/nmdc_dh | |
| + rank: 5 | |
| + string_serialization: '{text}:{text}' | |
| + slot_group: Sample ID | |
| + recommended: true | |
| + multivalued: true | |
| diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml | |
| index 055942f..40e0209 100644 | |
| --- a/src/schema/workflow_execution_activity.yaml | |
| +++ b/src/schema/workflow_execution_activity.yaml | |
| @@ -18,7 +18,7 @@ imports: | |
| subsets: | |
| workflow subset: | |
| description: >- | |
| - Subset consisting of just the workflow exectution activities | |
| + Subset consisting of just the workflow execution activities | |
| classes: | |
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