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geneontology / go-shapes

Schema for Gene Ontology Causal Activity Models defined using RDF Shapes
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Add Root MF Shape #287

Open tmushayahama opened 1 year ago

tmushayahama commented 1 year ago

RootMF Shape will be useful for BP Only annotations. Currently, the relations allowed are

image

Something like this

<RootMolecularFunction> @<GoCamEntity> AND EXTRA a {
  a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
  occurs_in: @<AnatomicalEntity> {0,1};
  causally_upstream_of_or_within: ( @<MolecularFunction> OR @<MolecularEvent> OR @<BiologicalProcess> ) *;
  causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> *;
  causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> *;
  causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
  causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
  causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
} // rdfs:comment  "A root molecular function"

<MolecularFunction> @<GoCamEntity> AND EXTRA a {
  a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
  enabled_by:  ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {0,1} // <exclude_from_extensions> true ;
  part_of: @<BiologicalProcess> * // <exclude_from_extensions> true ;
  has_part: @<MolecularFunction> *;
  occurs_in: @<AnatomicalEntity> {0,1};
  has_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
  has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
  directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
  regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  directly_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  directly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  directly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  causally_upstream_of_or_within: ( @<MolecularFunction> OR @<MolecularEvent> OR @<BiologicalProcess> ) *; // <exclude_from_extensions> true ;
  causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> *; // <exclude_from_extensions> true ;
  causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> *; // <exclude_from_extensions> true ;
  causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true ;
  happens_during: ( @<BiologicalPhase> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *; // <exclude_from_extensions> true ;
} // rdfs:comment  "A molecular function"

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