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Issue noctua standard annotations 14 kva draft #315

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May 30, 2024
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Issue noctua standard annotations 14 kva draft #315

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3bab2e7
Update go-cam-shapes.shex
vanaukenk May 1, 2024
363464c
Merge pull request #312 from geneontology/vanaukenk-patch-16
vanaukenk May 1, 2024
3320990
Update WIP_standard_annot_ShEx
vanaukenk May 2, 2024
6d7897b
Merge pull request #313 from geneontology/vanaukenk-patch-16
vanaukenk May 2, 2024
675934d
Update README.md
vanaukenk May 9, 2024
7a87fd5
Update go-cam-shapes.shex
vanaukenk May 9, 2024
3734d2e
Update go-cam-shapes.shex
vanaukenk May 10, 2024
967a11e
Update go-cam-shapes.shex
vanaukenk May 10, 2024
f54cfdb
Update go-cam-shapes.shex
vanaukenk May 13, 2024
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1 change: 0 additions & 1 deletion README.md
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Expand Up @@ -4,7 +4,6 @@

Using RDF Shapes to define the schema of Gene Ontology Causal Activity Models


# Schema

See [shapes/go-cam-shapes.shex](shapes/go-cam-shapes.shex)
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12 changes: 7 additions & 5 deletions shapes/WIP_standard_annot_ShEx
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Expand Up @@ -172,6 +172,8 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
part_of: @<BiologicalProcess> *;
has_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
has_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
has_primary_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
occurs_in: @<AnatomicalEntity> {0,1};
has_target_end_location: @<AnatomicalEntity> {0,1};
has_target_start_location: @<AnatomicalEntity> {0,1};
Expand Down Expand Up @@ -457,18 +459,18 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
<ProteinContainingComplex> @<GoCamEntity> AND EXTRA a {
a @<ProteinContainingComplexClass>;
enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
contributes_to: @<MolecularFunction> {0,1};
located_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> ) {0,1};
is_active_in: ( @<CellularAnatomicalEntity> OR @<RootCellularComponent> OR @VirionComponent> ) {0,1};
part_of: @<ProteinContainingComplex> *;
has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
involved_in: ( @<BiologicalProcess> OR @<RootBiologicalProcess> ) {0,1};
acts_upstream_of_negative_effect: @<BiologicalProcess> {0,1};
acts_upstream_of_positive_effect: @<BiologicalProcess> {0,1};
acts_upstream_of_or_within_negative_effect: @<BiologicalProcess> {0,1};
acts_upstream_of_or_within_positive_effect: @<BiologicalProcess> {0,1};
acts_upstream_of_or_within_positive_effect: @<BiologicalProcess> {0,1};
has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;

} // rdfs:comment "a protein complex"

<ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
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40 changes: 23 additions & 17 deletions shapes/go-cam-shapes.shex
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Expand Up @@ -129,6 +129,7 @@ PREFIX results_in_growth_of: <http://purl.obolibrary.org/obo/RO_0002343>
PREFIX results_in_movement_of: <http://purl.obolibrary.org/obo/RO_0002565>
PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>


<GoCamModel> {
a [owl:Ontology] + ;
contributor: xsd:string +; #TODO would be better as an IRI
Expand Down Expand Up @@ -193,6 +194,8 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
part_of: @<BiologicalProcess> *;
has_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
has_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_input: @<ChemicalEntity> *;
has_primary_output: @<ChemicalEntity> *;
occurs_in: @<AnatomicalEntity> {0,1};
transports_or_maintains_localization_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
has_target_end_location: @<AnatomicalEntity> {0,1};
Expand Down Expand Up @@ -405,32 +408,32 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>

<MolecularFunction> @<GoCamEntity> AND EXTRA a {
a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
enabled_by: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
enabled_by: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) * // <exclude_from_extensions> true;
part_of: @<BiologicalProcess> *;
has_part: @<MolecularFunction> *;
has_part: @<MolecularFunction> * // <exclude_from_extensions> true;
occurs_in: @<AnatomicalEntity> {0,1};
has_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) * // <exclude_from_extensions> true;
regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
indirectly_regulates: ( @<MolecularFunction> OR @<MolecularEvent>) *;
indirectly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
indirectly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
constitutively_upstream_of: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
removes_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
has_small_molecule_regulator: @<ChemicalEntity> *;
has_small_molecule_activator: @<ChemicalEntity> *;
has_small_molecule_inhibitor: @<ChemicalEntity> *;
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> *;
indirectly_regulates: ( @<MolecularFunction> OR @<MolecularEvent>) * // <exclude_from_extensions> true;
indirectly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) * // <exclude_from_extensions> true;
indirectly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) * // <exclude_from_extensions> true;
constitutively_upstream_of: ( @<MolecularFunction> OR @<MolecularEvent> ) * // <exclude_from_extensions> true;
removes_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) * // <exclude_from_extensions> true;
has_small_molecule_regulator: @<ChemicalEntity> * // <exclude_from_extensions> true;
has_small_molecule_activator: @<ChemicalEntity> * // <exclude_from_extensions> true;
has_small_molecule_inhibitor: @<ChemicalEntity> * // <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> ) *;
causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
Expand Down Expand Up @@ -521,11 +524,14 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>

<ProteinContainingComplex> @<GoCamEntity> AND EXTRA a {
a @<ProteinContainingComplexClass>;
located_in: @<AnatomicalEntity> {0,1};
is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1};
has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex>) *;
located_in: @<AnatomicalEntity> {0,1} // <exclude_from_extensions> true;
is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1} // <exclude_from_extensions> true;
part_of: @<AnatomicalEntity> {0,1};
adjacent_to: @<AnatomicalEntity> *;
overlaps: @<AnatomicalEntity> *;
existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex>) * // <exclude_from_extensions> true;
} // rdfs:comment "a protein complex"

<ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
Expand Down
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