Alignment of the Biolink Model edge annotation to GO-CAM ingest semantics

[RichardBruskiewich]

Synopsis:

We would like to enhance the Biolink Model to better capture GO-CAM annotation.

Working group (or team) originating this issue:

DINGO

Objective

This issue is a discussion issue to review how GO-CAM currently maps onto Biolink Model Association types to identify gaps in the (mostly edge qualifier slot annotation?) representation of the data. Specific ideas and recommendations are not noted here, but will be iteratively compiled below this issue introduction.

Some comments from @sierra-moxon about this (referring to the sample GO-CAM json data and legacy sample modelling noted below):

We don't need all of these...but we do need some set of generic qualifiers whose range is a GOTerm:ID, that can hold things like "target_gene_molecular_function" ... maybe something like biolink:subject_molecular_function_qualifier and biolink:object_molecular_function_qualifier would be easy, but not very applicable to other data sources beyond GO.

it could be we have the qualifiers we need already... I have a feel, though, that "aspect" range is currently an enumeration rather than a slot that takes identifiers.... I want to evaluate if the coverage of our current generic qualifiers can be used to hold GO terms...  for example, is a biological process always an "aspect" or is a molecular function always an "aspect"

Additional Information:

Sample data for modeling purposes:

Here is a sample of how the GO edge data looks like:

{
  "directed": true,
  "multigraph": false,
  "graph": {
    "model_info": {
      "id": "gomodel:6870555700001150",
      "title": "Perlecan interaction with post-translationally modified dystroglycan is required for acetylcholinesterase localization and accumulation at the neuromuscular junction(Human)",
      "taxon": "NCBITaxon:9606",
      "status": "production"
    }
  },
  "nodes": [
    {
      "id": "UniProtKB:P22303",
      "gene_product": "UniProtKB:P22303",
      "model_id": "gomodel:6870555700001150",
      "label": "ACHE Hsap"
    },
    {
      "id": "UniProtKB:O95461",
      "gene_product": "UniProtKB:O95461",
      "model_id": "gomodel:6870555700001150",
      "label": "LARGE1 Hsap"
    },
    {
      "id": "UniProtKB:Q9Y215",
      "gene_product": "UniProtKB:Q9Y215",
      "model_id": "gomodel:6870555700001150",
      "label": "COLQ Hsap"
    },
    {
      "id": "UniProtKB:P98160",
      "gene_product": "UniProtKB:P98160",
      "model_id": "gomodel:6870555700001150",
      "label": "HSPG2 Hsap"
    }
  ],
  "edges": [
    {
      "source": "UniProtKB:O95461",
      "target": "UniProtKB:P98160",
      "source_gene": "UniProtKB:O95461",
      "target_gene": "UniProtKB:P98160",
      "model_id": "gomodel:6870555700001150",
      "causal_predicate": "RO:0002413",
      "causal_predicate_has_reference": [
        "PMID:22223806"
      ],
      "causal_predicate_assessed_by": [
        "ECO:0000314"
      ],
      "causal_predicate_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_molecular_function": "GO:0015020",
      "source_gene_biological_process": "GO:0035269",
      "source_gene_biological_process_has_reference": [
        "PMID:22223806"
      ],
      "source_gene_biological_process_assessed_by": [
        "ECO:0000314"
      ],
      "source_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_occurs_in": "GO:0005794",
      "source_gene_occurs_in_has_reference": [
        "PMID:25279699"
      ],
      "source_gene_occurs_in_assessed_by": [
        "ECO:0000314"
      ],
      "source_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_product": "UniProtKB:O95461",
      "source_gene_product_has_reference": [
        "PMID:22223806"
      ],
      "source_gene_product_assessed_by": [
        "ECO:0000314"
      ],
      "source_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_molecular_function": "GO:0060090",
      "target_gene_biological_process": "GO:0035418",
      "target_gene_biological_process_has_reference": [
        "GO_REF:0000024"
      ],
      "target_gene_biological_process_assessed_by": [
        "ECO:0000250"
      ],
      "target_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_occurs_in": "GO:0031594",
      "target_gene_occurs_in_has_reference": [
        "PMID:14702351"
      ],
      "target_gene_occurs_in_assessed_by": [
        "ECO:0000305"
      ],
      "target_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_product": "UniProtKB:P98160",
      "target_gene_product_has_reference": [
        "GO_REF:0000024"
      ],
      "target_gene_product_assessed_by": [
        "ECO:0000250"
      ],
      "target_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ]
    },
    {
      "source": "UniProtKB:Q9Y215",
      "target": "UniProtKB:P22303",
      "source_gene": "UniProtKB:Q9Y215",
      "target_gene": "UniProtKB:P22303",
      "model_id": "gomodel:6870555700001150",
      "causal_predicate": "RO:0012009",
      "causal_predicate_has_reference": [
        "PMID:14702351"
      ],
      "causal_predicate_assessed_by": [
        "ECO:0000305"
      ],
      "causal_predicate_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_molecular_function": "GO:0060090",
      "source_gene_biological_process": "GO:0035418",
      "source_gene_biological_process_has_reference": [
        "PMID:14702351"
      ],
      "source_gene_biological_process_assessed_by": [
        "ECO:0000315"
      ],
      "source_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_occurs_in": "GO:0031594",
      "source_gene_occurs_in_has_reference": [
        "PMID:14702351"
      ],
      "source_gene_occurs_in_assessed_by": [
        "ECO:0000314"
      ],
      "source_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_product": "UniProtKB:Q9Y215",
      "source_gene_product_has_reference": [
        "PMID:14702351"
      ],
      "source_gene_product_assessed_by": [
        "ECO:0000314"
      ],
      "source_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_molecular_function": "GO:0003990",
      "target_gene_biological_process": "GO:0001507",
      "target_gene_biological_process_has_reference": [
        "PMID:1517212"
      ],
      "target_gene_biological_process_assessed_by": [
        "ECO:0000305"
      ],
      "target_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_occurs_in": "GO:0031594",
      "target_gene_occurs_in_has_reference": [
        "PMID:14702351"
      ],
      "target_gene_occurs_in_assessed_by": [
        "ECO:0000314"
      ],
      "target_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_product": "UniProtKB:P22303",
      "target_gene_product_has_reference": [
        "PMID:1517212"
      ],
      "target_gene_product_assessed_by": [
        "ECO:0000315"
      ],
      "target_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ]
    },
    {
      "source": "UniProtKB:P98160",
      "target": "UniProtKB:Q9Y215",
      "source_gene": "UniProtKB:P98160",
      "target_gene": "UniProtKB:Q9Y215",
      "model_id": "gomodel:6870555700001150",
      "causal_predicate": "RO:0002629",
      "causal_predicate_has_reference": [
        "GO_REF:0000024",
        "GO_REF:0000024"
      ],
      "causal_predicate_assessed_by": [
        "ECO:0000250",
        "ECO:0000250"
      ],
      "causal_predicate_contributors": [
        "https://orcid.org/0000-0002-5283-6593",
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_molecular_function": "GO:0060090",
      "source_gene_biological_process": "GO:0035418",
      "source_gene_biological_process_has_reference": [
        "GO_REF:0000024"
      ],
      "source_gene_biological_process_assessed_by": [
        "ECO:0000250"
      ],
      "source_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_occurs_in": "GO:0031594",
      "source_gene_occurs_in_has_reference": [
        "PMID:14702351"
      ],
      "source_gene_occurs_in_assessed_by": [
        "ECO:0000305"
      ],
      "source_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "source_gene_product": "UniProtKB:P98160",
      "source_gene_product_has_reference": [
        "GO_REF:0000024"
      ],
      "source_gene_product_assessed_by": [
        "ECO:0000250"
      ],
      "source_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_molecular_function": "GO:0060090",
      "target_gene_biological_process": "GO:0035418",
      "target_gene_biological_process_has_reference": [
        "PMID:14702351"
      ],
      "target_gene_biological_process_assessed_by": [
        "ECO:0000315"
      ],
      "target_gene_biological_process_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_occurs_in": "GO:0031594",
      "target_gene_occurs_in_has_reference": [
        "PMID:14702351"
      ],
      "target_gene_occurs_in_assessed_by": [
        "ECO:0000314"
      ],
      "target_gene_occurs_in_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ],
      "target_gene_product": "UniProtKB:Q9Y215",
      "target_gene_product_has_reference": [
        "PMID:14702351"
      ],
      "target_gene_product_assessed_by": [
        "ECO:0000314"
      ],
      "target_gene_product_contributors": [
        "https://orcid.org/0000-0002-5283-6593"
      ]
    }
  ]
}

Previous team Biolink Model brainstorming about GO-CAM:

# The protein ser/thr kinase activator activity of Ras85D in the plasma membrane directly positively regulates # MAPKKK activity of Raf in the cytoplasm within the EGFR signaling pathway"
# Very complicated GO-CAM example . . .
 
subject: Dmel Ras85D
subject_aspect: protein ser/thr kinase activator activity
subject_specialization: plasma membrane
predicate: affects > regulates   
qualified_predicate: causes* 
object: Dmel Raf
object_aspect: MAPKKK activity
object_specialization: cytoplasm
object_direction: increased
pathway_context_qualifier: EGFR signaling pathway
that was one of our old examples...

See also legacy 4-7-22 Qualifier Based Association Proposal.

Relevant members for discussion:

@sierra-moxon, @mbrush, @kevinschaper