gocam.yaml

id: http://w3id.org/ontogpt/gocam
name: gocam-template
title: GO-CAM Template
description: >-
  A template for GO-CAMs
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  linkml: https://w3id.org/linkml/
  gocam: http://w3id.org/ontogpt/gocam/
  GO: http://purl.obolibrary.org/obo/GO_
  CL: http://purl.obolibrary.org/obo/CL_

default_prefix: gocam
default_range: string

imports:
  - linkml:types
  - core

classes:
  GoCamAnnotations:
    tree_root: true
    attributes:
      genes:
        description: semicolon-separated list of genes
        multivalued: true
        range: Gene
      organisms:
        description: semicolon-separated list of organism taxons
        multivalued: true
        range: Organism
      gene_organisms:
        annotations:
          prompt: semicolon-separated list of asterisk separated gene to organism relationships
        multivalued: true
        range: GeneOrganismRelationship
      activities:
        description: semicolon-separated list of molecular activities
        multivalued: true
        range: MolecularActivity
      gene_functions:
        description: semicolon-separated list of gene to molecular activity relationships
        multivalued: true
        range: GeneMolecularActivityRelationship
      cellular_processes:
        description: semicolon-separated list of cellular processes
        multivalued: true
        range: CellularProcess
      pathways:
        description: semicolon-separated list of pathways
        multivalued: true
        range: Pathway
      gene_gene_interactions:
        description: semicolon-separated list of gene to gene interactions
        multivalued: true
        range: GeneGeneInteraction
      gene_localizations:
        description: >-
          semicolon-separated list of genes plus their location in the cell;
          for example, "gene1 / cytoplasm; gene2 / mitochondrion"
        multivalued: true
        range: GeneSubcellularLocalizationRelationship

  Gene:
    is_a: NamedEntity
    id_prefixes:
      - HGNC
      - PR
      - UniProtKB
    annotations:
      annotators: gilda:, bioportal:hgnc-nr
  Pathway:
    is_a: NamedEntity
    id_prefixes:
      - GO
      - PW
    annotations:
      annotators: sqlite:obo:go, sqlite:obo:pw
  CellularProcess:
    is_a: NamedEntity
    id_prefixes:
      - GO
    annotations:
      annotators: sqlite:obo:go
  MolecularActivity:
    is_a: NamedEntity
    id_prefixes:
      - GO
    annotations:
      annotators: sqlite:obo:go
  GeneLocation:
    is_a: NamedEntity
    id_prefixes:
      - GO
      - CL
      - UBERON
    annotations:
      annotators: "sqlite:obo:go, sqlite:obo:cl"
    slot_usage:
      id:
        values_from:
          - GOCellComponentType
          - CellType
  Organism:
    is_a: NamedEntity
    id_prefixes:
      - NCBITaxon
      - EFO
    annotations:
      annotators: gilda:, sqlite:obo:ncbitaxon
  Molecule:
    is_a: NamedEntity
    id_prefixes:
      - CHEBI
      - PR
    annotations:
      annotators: gilda:, sqlite:obo:chebi

  GeneOrganismRelationship:
    is_a: CompoundExpression
    attributes:
      gene:
        range: Gene
      organism:
        range: Organism

  GeneMolecularActivityRelationship:
    is_a:   CompoundExpression
    attributes:
      gene:
        range: Gene
        annotations:
          prompt: the name of the gene in the pair. This comes first.
      molecular_activity:
        range: MolecularActivity
        annotations:
          prompt: the name of the molecular function in the pair. This comes second. May be a GO term.
    annotations:
      prompt.example: |-
        TODO
        
        gene: HGNC:1234
        molecular_activity: GO:0003674

  GeneMolecularActivityRelationship2:
    is_a:   CompoundExpression
    attributes:
      gene:
        range: Gene
        annotations:
          prompt: the name of the gene.
      molecular_activity:
        range: MolecularActivity
        annotations:
          prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term.
      target:
        range: Molecule
        annotations:
          prompt: the name of the molecular entity that is the target of the molecular activity.

  GeneSubcellularLocalizationRelationship:
    is_a:   CompoundExpression
    attributes:
      gene:
        range: Gene
      location:
        range: GeneLocation

  GeneGeneInteraction:
    is_a:   CompoundExpression
    attributes:
      gene1:
        range: Gene
      gene2:
        range: Gene

enums:

  GeneLocationEnum:
    inherits:
      - GOCellComponent
      - CellType

  GOCellComponentType:
    reachable_from:
      source_ontology: obo:go
      source_nodes:
        - GO:0005575 ## cellular_component
  CellType:
    reachable_from:
      source_ontology: obo:cl
      source_nodes:
        - CL:0000000 ## cell