@prefix nmdc: <https://w3id.org/nmdc/> .
nmdc:nmdc a owl:Ontology ;
rdfs:label "NMDC" ;
dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
dcterms:title "NMDC Schema" ;
pav:version "0.0.0" ;
skos:definition """Schema for National Microbiome Data Collaborative (NMDC).
This schema is organized into multiple modules, such as:
* a set of core types for representing data values
* a subset of the mixs schema
* an annotation schema
* the NMDC schema itself, into which the other modules are imported""" ;
skos:editorialNote "not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1" .
<https://w3id.org/mixs/env_broad_scale> a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "env_broad_scale" ;
dcterms:title "broad-scale environmental context" ;
rdfs:range nmdc:ControlledIdentifiedTermValue ;
rdfs:subPropertyOf <https://w3id.org/mixs/environment_field> ;
skos:altLabel "broad-scale environmental context" ;
skos:definition "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" ;
skos:inScheme <https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml> ;
nmdc:expected_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." .see also src/scripts/date_created_blank_node.py
gold:Gb0110681 a nmdc:Biosample ;
dcterms:description "Grasslands soil microbial communities from the Angelo Coastal Reserve, plot 2. There is a duplicate submission for this entry in NCBI. The NCBI identifiers for a duplicate are PRJNA449266 and SAMN08902829" ;
dcterms:isPartOf gold:Gs0110119 ;
MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ;
nmdc:has_raw_value "grassland biome [ENVO:01000177]" ;
nmdc:term ENVO:01000177 ] ;
MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ;
nmdc:has_raw_value "biosphere reserve [ENVO:00000376]" ;
nmdc:term ENVO:00000376 ] ;
MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ;
nmdc:has_raw_value "grassland soil [ENVO:00005750]" ;
nmdc:term ENVO:00005750 ] ;
[ ] <https://schema.org/dateCreated> "2024-04-11T14:51:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
<http://www.w3.org/2000/01/rdf-schema#comment> "https://api.microbiomedata.org" . local/nmdc-no-use-native-uris.owl.ttl: src/schema/nmdc.yaml
$(RUN) gen-owl --no-use-native-uris $< > $@
local/nmdc_materialized.ttl: src/schema/nmdc.yaml
$(RUN) python src/scripts/schema_view_relation_graph.py \
--schema $< \
--output $@nmdc:nmdc.owl.ttl a owl:Ontology ;
rdfs:label "NMDC" ;
dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
dcterms:title "NMDC Schema" ;
pav:version "0.0.0" ;
skos:definition """Schema for National Microbiome Data Collaborative (NMDC).
This schema is organized into multiple modules, such as:
* a set of core types for representing data values
* a subset of the mixs schema
* an annotation schema
* the NMDC schema itself, into which the other modules are imported""" ;
skos:editorialNote "not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1" .
<https://w3id.org/mixs/0000012> a owl:ObjectProperty ;
rdfs:label "env_broad_scale" ;
dcterms:title "broad-scale environmental context" ;
rdfs:range nmdc:ControlledIdentifiedTermValue ;
rdfs:subPropertyOf <https://w3id.org/mixs/environment_field> ;
skos:altLabel "broad-scale environmental context" ;
skos:definition "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" ;
skos:inScheme <https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml> ;
nmdc:expected_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." .
nmdc:Biosample a owl:Class ;
dcterms:description xsd:string ;
dcterms:isPartOf nmdc:Study ;
MIXS:0000001 nmdc:QuantityValue ;
MIXS:0000002 xsd:string ;
MIXS:0000008 nmdc:ControlledTermValue ;
MIXS:0000009 nmdc:GeolocationValue ;
MIXS:0000010 nmdc:TextValue ;
MIXS:0000011 nmdc:TimestampValue ;
MIXS:0000012 nmdc:ControlledIdentifiedTermValue ;
MIXS:0000013 nmdc:ControlledIdentifiedTermValue ;
MIXS:0000014 nmdc:ControlledIdentifiedTermValue ;http://3.236.215.220/repository
This is not super efficient because some class/slot definitions are repeated
- The default graph: EMPTY?
- https://w3id.org/nmdc/nmdc: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/project/owl/nmdc.owl.ttl
- https://w3id.org/nmdc/nmdc_relation_graph: local/nmdc_materialized.ttl
- https://w3id.org/linkml/meta: https://raw.githubusercontent.com/linkml/linkml-model/main/linkml_model/owl/meta.owl.ttl
- http://purl.obolibrary.org/obo/nmdco.owl: https://raw.githubusercontent.com/microbiomedata/nmdc-ontology/main/nmdco.owl
- https://w3id.org/mixs: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/project/owl/mixs.owl.ttl
- https://api.microbiomedata.org: local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl (~175 MB)
- https://w3id.org/nmdc/nmdc-no-use-native-uris: local/nmdc-no-use-native-uris.owl.ttl
@prefix MIXS: <https://w3id.org/mixs/> .
<https://w3id.org/mixs> a owl:Ontology ;
rdfs:label "mixs" ;
dcterms:source <https://github.com/GenomicsStandardsConsortium/mixs/raw/issue-610-temp-mixs-xlsx-home/mixs/excel/mixs_v6.xlsx> ;
pav:version "v6.2.0" ;
skos:note "slot titles that are associated with more than one slot name/SCN: host sex" .
MIXS:env_broad_scale a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "env_broad_scale" ;
dcterms:title "broad-scale environmental context" ;
schema1:keywords "context",
"environmental" ;
rdfs:range [ a rdfs:Datatype ;
owl:intersectionOf ( MIXS:string [ a rdfs:Datatype ;
owl:onDatatype xsd:string ;
owl:withRestrictions ( [ xsd:pattern "^([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+) \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\d+\\]$" ] ) ] ) ] ;
skos:definition "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" ;
skos:inScheme <https://w3id.org/mixs> .
