Duplicated has_output and downstream_activity in YAML for 663d668500002178

[kimrutherford]

In the YAML for 663d668500002178 from the API this looks like a duplicate has_output:

- id: gomodel:663d668500002178/663d668500002179
  enabled_by:
    type: EnabledByGeneProductAssociation
    evidence:
    - term: ECO:0000315...
    - term: ECO:0000316...
    - term: ECO:0000318...
    provenances:
    - contributor:...
    term: PomBase:SPAC20G8.03
...
  has_output:
  - type: MoleculeAssociation
    evidence:
    - term: ECO:0000315...
    - term: ECO:0000316...
    - term: ECO:0000318...
    provenances:
    - contributor:...
    term: CHEBI:17268
  - type: MoleculeAssociation
    evidence:
    - term: ECO:0000315...
    - term: ECO:0000316...
    - term: ECO:0000318...
    provenances:
    - contributor:...
    term: CHEBI:17268

And the downstream_activity CausalAssociation for that activity occurs twice, but with different evidence codes?

  causal_associations:
  - type: CausalAssociation
    evidence:
    - term: ECO:0000315...
    - term: ECO:0000316...
    - term: ECO:0000318...
    - term: ECO:0000316...
    provenances:
    - contributor:...
    predicate: RO:0002413
    downstream_activity: gomodel:663d668500002178/663d668500002281
  - type: CausalAssociation
    evidence:
    - term: ECO:0000315...
    - term: ECO:0000318...
    provenances:
    - contributor:...
    predicate: RO:0002413
    downstream_activity: gomodel:663d668500002178/663d668500002281

https://live-go-cam.geneontology.io/product/yaml/go-cam/663d668500002178.yaml

[kimrutherford]

See also:

• Produce high-level gocam-py YAML files for consumption pipeline-raw-go-cam#4 (comment)

and:

• Produce high-level gocam-py YAML files for consumption pipeline-raw-go-cam#4 (comment)

[pgaudet]

My guess is that comes from the redundant relations output + provides input for:

Provides input for has these 2 evidences:

Output has these 3 evidences:

Which matches what you show.

[pkalita-lbl]

I think the issue is upstream of gocam-py.

The Minerva model translation code in gocam-py is faithfully recreating some duplication that exists in the Minerva JSON file. In particular this file: https://go-public.s3.amazonaws.com/files/go-cam/663d668500002178.json contains two facts objects with the same subject-object-predicate combo and three evidence pointers:

{
  "id": "gomodel:663d668500002178",
  "individuals": [ ... ],
  "facts": [
    ...
    {
      "subject": "gomodel:663d668500002178/663d668500002179",  // myo-inositol:proton symporter activity
      "property": "RO:0002234",                                // has output
      "property-label": "RO:0002234",
      "object": "gomodel:663d668500002178/67b1629100003514",  // myo-inositol
      "annotations": [
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003518",
          "value-type": "IRI"
        },
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003519",
          "value-type": "IRI"
        },
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003520",
          "value-type": "IRI"
        },
        {
          "key": "contributor",
          "value": "https://orcid.org/0000-0001-6330-7526"
        },
        {
          "key": "date",
          "value": "2025-02-26"
        },
        {
          "key": "providedBy",
          "value": "http://www.pombase.org"
        }
      ]
    },
    ...
    {
      "subject": "gomodel:663d668500002178/663d668500002179",
      "property": "RO:0002234", 
      "property-label": "RO:0002234",
      "object": "gomodel:663d668500002178/67b1629100003514",
      "annotations": [
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003515",
          "value-type": "IRI"
        },
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003516",
          "value-type": "IRI"
        },
        {
          "key": "evidence",
          "value": "gomodel:663d668500002178/67b1629100003517",
          "value-type": "IRI"
        },
        {
          "key": "contributor",
          "value": "https://orcid.org/0000-0001-6330-7526"
        },
        {
          "key": "date",
          "value": "2025-02-26"
        },
        {
          "key": "providedBy",
          "value": "http://www.pombase.org"
        }
      ]
    },

I started a conversation with @kltm and @balhoff on Slack to help track down the source of the duplication, but ultimately I'm not sure that the gocam-py codebase is going to do anything other than raise a warning if it encounters something like this.

[kimrutherford]

I think the issue is upstream of gocam-py.

@pkalita-lbl Thanks for investigating that. I think this issue can be closed since it's not gocam-py related.

[pkalita-lbl]

@balhoff pointed out that the duplication is present in the OWL files too:

• https://github.com/geneontology/noctua-models/blob/8ff6af591560bce07d2059a44a2d09036ade3b4e/models/663d668500002178.ttl#L1035-L1042
• https://github.com/geneontology/noctua-models/blob/8ff6af591560bce07d2059a44a2d09036ade3b4e/models/663d668500002178.ttl#L1104-L1111

I'll leave this issue open for now while we continue to track down the source of the issue in the off chance there is something we end up wanting to do in gocam-py.