dwinston

%%{ init: { 'flowchart': { 'curve': 'monotoneX' } } }%%
flowchart LR 
    Concept["skos:Concept"]
    Issue["ibis:Issue"]
    Agent["prov:Agent"]
    Position["ibis:Position"]

    %% <ibis>

dwinston

%%{ init: { 'flowchart': { 'curve': 'monotoneX' } } }%%
flowchart LR 
    Concept["skos:Concept"]
    Issue["ibis:Issue"]
    Agent["prov:Agent"]
    Position["ibis:Position"]

    State["pm:State"]
    Goal["pm:Goal"]

dwinston

%%{ init: { 'flowchart': { 'curve': 'monotoneX' } } }%%
flowchart LR
    Concept["skos:Concept"]
    Issue["ibis:Issue"]
    Agent["prov:Agent"]
    Position["ibis:Position"]
    
    ConceptScheme["skos:ConceptScheme"]
 Argument["ibis:Argument"] 

dwinston

erDiagram
  Process ||--|| Material : outputs
  Material ||--o{ Measurement : subjectTo
  Ingredient }o--|| Material : from
  Ingredient }o--|| Process : inputTo
  Record }o--|| RecordType : has
  RecordType }o--o| Template : mayBe
  RecordType }o--o| Spec : mayBe
 RecordType }o--o| Run : mayBe

dwinston

flowchart TD
    %% t1(["terminator (process start/end)"])
    %% s1["(process) step"]
    %% d1{decision}
    %% b1[("(data)base")]
    %% m1[\manual step/]
    %% o1[/"(input/output) object"/]
    %% p1[[predefined step]]
    classDef literal fill:#dff;,stroke:#bbb

dwinston

{
  "access_methods": [{"access_url": {"url": "https://gist.githubusercontent.com/dwinston/05a176b69744a3dfc52a1c8b07590867/raw/c58d8039544378d7ca20b9a80c87abcc983e4f76/readsqc-in-example.json"}}],
  "checksums": [{"type": "sha256", "checksum": "9e1d75d48d3e90bfec0b4608b8c1755eab88e51e69003dd1329b46086bbd3f68"}],
  "created_time": "2022-09-27T14:16:00-04:00",
  "size": 1009
}

dwinston

{"data_object_set": [{
    "id" : "jgi:534819030d87850d7aea2a16",
    "name" : "7846.2.85463.CGTACG.fastq.gz",
    "description" : "Raw sequencer read data",
    "file_size_bytes" : 11031180705,
    "type" : "nmdc:DataObject"
}
],
 "read_QC_analysis_activity_set": [{
    "id" : "nmdc:498a1b67f0b35bc4f059a5de7d5ddb49",

dwinston

My intended identifier design was nmdc:<shoulder><generated_id> where shoulder is an opaque namespace granted to a minting (sub)organization to avoid ID clashes in case they are bringing existing (not generated) IDs into the mix, and it helps keep IDs short for a minting org that doesn't mint a lot.

Unfortunately, it seems folks really really want to infer semantics from an ID rather than the discipline of resolving it and fetching metadata. So we've had a mushy compromise where the shoulders are kinda memorable, like "mga0" is for metagenome annotations.

I propose, given insistence on the desire for by-eye ID typing, we re-set the scheme as nmdc: , where type_code is an alphabetical code that is part of a recognized and controlled set, like how "Gb" is "GOLD biosample" (e.g., https://identifiers.org/gold:Gb0110680) and "Gs" is "GOLD study" (e.g., [https://identifiers.org/gold:Gs0103573](https://identifiers.org/gold:Gs0103573

dwinston

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

dwinston

diff --git a/jsonschema/nmdc.schema.json b/jsonschema/nmdc.schema.json
index 3a18b59..1efa788 100644
--- a/jsonschema/nmdc.schema.json
+++ b/jsonschema/nmdc.schema.json
@@ -53,6 +53,28 @@
          "title": "Agent",
          "type": "object"
       },
+      "AnalysisTypeEnum": {
+         "description": "",