Comments (6)
balhoff
commented on August 15, 2024
@tmushayahama do you need to convert the ShEx to JSON to use it? Or instead should you use the API/data model provided by Shex.js?
from go-shapes.
goodb
commented on August 15, 2024
@tmushayahama here is the current schema in shex json format. If this is useful to you, we can add the conversion from our default shexc to shexj as part of the build process here. It would be pretty cool if the forms were generated directly from this document.
{
"@context" : "http://www.w3.org/ns/shex.jsonld",
"type" : "Schema",
"shapes" : [ {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntityClass"
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a molecular entity (a gene product, chemical, or complex typically)\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromoleculeClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/CHEBI_33695" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ProvenanceAnnotated",
"type" : "Shape",
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://purl.org/dc/elements/1.1/contributor",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.org/dc/elements/1.1/date",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.org/pav/providedBy",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : -1
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromoleculeClass"
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0001025",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000050",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex",
"min" : 0,
"max" : 1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"an information biomacromolecule - e.g. a protein or RNA product\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/EvidenceClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/ECO_0000000" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/MolecularFunctionClass", "http://purl.obolibrary.org/obo/go/shapes/NegatedMolecularFunctionClass" ]
},
"min" : 1,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002333",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule", "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" ]
},
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000050",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000066",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "http://purl.obolibrary.org/obo/go/shapes/CellularComponent" ]
},
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002234",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002233",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002413",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002211",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002212",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002213",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002578",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002630",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002406",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002418",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0004046",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0004047",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002411",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002305",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002304",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002092",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalPhase", "http://purl.obolibrary.org/obo/go/shapes/LifeCycleStage", "http://purl.obolibrary.org/obo/go/shapes/PlantStructureDevelopmentStage" ]
},
"min" : 0,
"max" : -1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"A molecular function\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntityClass", "http://purl.obolibrary.org/obo/go/shapes/NegatedAnatomicalEntityClass" ]
}
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000050",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity",
"min" : 0,
"max" : 1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"an anatomical entity\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex",
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplexClass"
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0001025",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000051",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule",
"min" : 0,
"max" : -1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a protein complex\""
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/LifeCycleStage",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/LifeCycleStageClass"
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a lifecycle stage\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/NegatedBiologicalProcessClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "bnode"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#complementOf",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcessClass"
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ProteinClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/CHEBI_36080" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/MacromolecularMachine",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/Protein", "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" ]
}, {
"type" : "Shape"
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunctionClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/GO_0003674" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcessClass", "http://purl.obolibrary.org/obo/go/shapes/NegatedBiologicalProcessClass" ]
},
"min" : 1,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000050",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002233",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002234",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000066",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "http://purl.obolibrary.org/obo/go/shapes/CellularComponent" ]
},
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002313",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002339",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002338",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002411",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002305",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002304",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction" ]
},
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002211",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002212",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002213",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess",
"min" : 0,
"max" : -1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"A biological process\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalPhaseClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/GO_0044848" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/PlantStructureDevelopmentStage",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/PlantStructureDevelopmentStageClass"
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a plant structure developmental stage\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/ProvenanceAnnotated" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://www.w3.org/2002/07/owl#NamedIndividual" ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"Every entity we care about is a named individual\""
}
} ],
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#label",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2004/02/skos/core#exactMatch",
"min" : 0,
"max" : -1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"Default allowable metadata for GO-CAM entities\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponentClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/GO_0005575" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcessClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/GO_0008150" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntityClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/NegatedMolecularFunctionClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "bnode"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#complementOf",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/MolecularFunctionClass"
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/PlantStructureDevelopmentStageClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/PO_0009012" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplexClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/GO_0032991" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/NegatedAnatomicalEntityClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "bnode"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#complementOf",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntityClass"
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/OwlClass",
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://www.w3.org/2002/07/owl#Class" ]
},
"min" : 1,
"max" : 1
}
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalPhase",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/BiologicalPhaseClass"
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a biological phase\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/CellularComponentClass", "http://purl.obolibrary.org/obo/go/shapes/NegatedCellularComponentClass" ]
},
"min" : 1,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/BFO_0000050",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity",
"min" : 0,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002220",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity",
"min" : 0,
"max" : -1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0002131",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity",
"min" : 0,
"max" : -1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a cellular component\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/Evidence",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/EvidenceClass",
"min" : 1,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.org/dc/elements/1.1/source",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 1,
"max" : 1
}, {
"type" : "TripleConstraint",
"predicate" : "http://geneontology.org/lego/evidence-with",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : 1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"A kind of evidence\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/AnnotatedEdge",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "bnode"
}, "http://purl.obolibrary.org/obo/go/shapes/ProvenanceAnnotated" ]
}, {
"type" : "Shape",
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://www.w3.org/2002/07/owl#Axiom" ]
}
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#annotatedSource",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity"
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#annotatedProperty",
"valueExpr" : {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}
}, {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#annotatedTarget",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity"
}, {
"type" : "TripleConstraint",
"predicate" : "http://geneontology.org/lego/evidence",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/Evidence",
"min" : 0,
"max" : -1
} ]
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/LifeCycleStageClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/UBERON_0000105" ]
}
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/Gene",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", {
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0001025",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a gene (a piece of DNA with a purpose)\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/NegatedCellularComponentClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "bnode"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2002/07/owl#complementOf",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponentClass"
}
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/Protein",
"type" : "ShapeAnd",
"shapeExprs" : [ "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", {
"type" : "Shape",
"extra" : [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ],
"expression" : {
"type" : "EachOf",
"expressions" : [ {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/ProteinClass"
}, {
"type" : "TripleConstraint",
"predicate" : "http://purl.obolibrary.org/obo/RO_0001025",
"valueExpr" : "http://purl.obolibrary.org/obo/go/shapes/CellularComponent",
"min" : 0,
"max" : 1
} ]
},
"annotations" : [ {
"type" : "Annotation",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#comment",
"object" : {
"value" : "\"a protein\""
}
} ]
} ]
}, {
"id" : "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntityClass",
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "ShapeAnd",
"shapeExprs" : [ {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}, "http://purl.obolibrary.org/obo/go/shapes/OwlClass" ]
}, {
"type" : "Shape",
"extra" : [ "http://www.w3.org/2000/01/rdf-schema#subClassOf" ],
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://www.w3.org/2000/01/rdf-schema#subClassOf",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [ "http://purl.obolibrary.org/obo/CHEBI_24431" ]
}
}
} ]
} ]
}
from go-shapes.
goodb
commented on August 15, 2024
@tmushayahama if you start working with this, let me know. Assuming you want the json representation, we will want to establish a way for you to generate it from the shexc representation we use here in the project - so that you can keep up to date.
from go-shapes.
tmushayahama
commented on August 15, 2024
@goodb I totally forgot to respond on the earlier. Thank you for that schema, I am already using the idea of the schema representation found here in Noctua Form https://github.com/geneontology/noctua-form-base/blob/master/src/%40noctua.form/data/config/insert-entity-definition.ts . In that config folder you can also see I used it to define combined units like bp only, cc only and activity unit
It is actually more of the same structure. Few exception are
- wording,
- form labels, human things
- hard coded constant values. (resolved urls to using id value).
- cardinality, instead of min and max values, I just used oneToOne, oneToMany enums.
- removed all things I don't need :)
But yes, this would be cool if generated because now the form is now very dynamic. Using cardinality, Noctua Form can even determine what you can insert as your object by looking at subject and its triples and possible future triples (predicate and object combination). like below All this I used the json example idea.
However the only catch will be I am using the same schema for autocomplete. i.e. instead of CARO, it is autocompleting on CL:000003 and UBERON: xxx @vanaukenk can explain on this part.
Thanx for the update comment
from go-shapes.
ericprud
commented on August 15, 2024
Y'all may have already run across these ways to change ShExC to ShExJ:
shex-simple webapp
Load a schema, make sure the Query Map is empty, hit [Validate]
shex-cli node module
There's a command-line node script you can install or run via npx.
shex-to-json foo.shex # parse ShExC to ShExJ and send to stdout
echo "<S1> { <p> . }" | shex-to-json - # - to read from stdinno install
echo "<S1> { <p> . }" | npx -p @shexjs/cli -p @shexjs/parser shex-to-json -local install
Make a directory and use npm to install the script:
cd $_ &&
npm init -y > /dev/null &&
npm install @shexjs/{cli,parser} > /dev/null &&
echo "<S1> { <p> . }" | ./node_modules/.bin/shex-to-json -This leaves you with something you can run quickly without hitting the network.
global install
Install the script "globally", meaning it gets installed in the user's path (assuming proper/lucky npm installation).
npm install -g @shexjs/{cli,parser} > /dev/null && echo "<S1> { <p> . }" | shex-to-json -The default linux npm package installation may require you to sudo to write into /usr/lib.
Node wisdom says that you should only install -g (globally) if you're installing a command-line script, as in this case. It's safe to experiment because you can always
npm uninstall -g @shexjs/{cli,parser}If you ever wonder how much global cruft you've accumulated, you can
npm list -g --depth 0Stability
ShExJ is very stable and the CG has a commitment to maintain backward compatibility. The script is dead-simple and shouldn't change. The package will change the next time I publish. After that, you won't need to include @shexjs/parser (which should have been listed as a dependency already).
from go-shapes.
vanaukenk
commented on August 15, 2024
Should we leave this ticket open?
from go-shapes.
Related Issues (20)
- Add two new model level annotations: “maximal-causal-chain-length” and “display-as-pathway-override”
- Update ShEX rules for transporter activity HOT 1
- Explore adding comments to ShEx, to aid extracting information from the schema into secondary data products
- Add GitHub actions to convert GO ShEx to necessary secondary data products
- Create example LinkML schema from JSON HOT 4
- Discuss the JSON schema HOT 4
- Separate out application and shape metadata
- Update ShEx for new MF-MF relations
- Add has_primary_input/output to BP shapes? HOT 2
- Change contributor and provider values to IRIs HOT 1
- Add Root MF Shape
- Separate branches for dev and for production server HOT 3
- LinkML Typescript with array
- Error in gen-project-linkml.yaml on dev branch(?)
- Add has_primary_input to transporters/transport
- Remove 'directly activates' after all MF-MF relations are updated in existing models
- Add 'small molecule regulator' relations to the MF shape HOT 2
- Negation in Shapes for CC and Small Molecules HOT 2
- Experiment with minimal/"GPAD" ShEx HOT 7
- Update ShEx to use primary input and primary output HOT 1
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