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SRI Ontology Service
karafecho edited this page Sep 14, 2023
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The SRI Ontology Service (aka, "SRI Ontology KP" or "SRI Ontology KG") provides a Translator Reasoner API (TRAPI) service interface to an integrated collection of bio-ontologies. Inter-concept relations have been precomputed using an OWL reasoner and stored in the UberGraph RDF triplestore. Mappings from the Biolink Model to ontology classes and properties are used to query ontology relations as TRAPI edges.
The Ontology-KP exposes a standard TRAPI service interface.
Query example (find parts of the hand):
{
"message": {
"query_graph": {
"nodes": {
"n0": {
"category": "biolink:AnatomicalEntity"
},
"n1": {
"category": "biolink:AnatomicalEntity",
"id": "UBERON:0002398"
}
},
"edges": {
"e0": {
"subject": "n0",
"object": "n1",
"predicate": "biolink:part_of"
}
}
}
}
}cURL command:
curl -X POST "https://stars-app.renci.org/sparql-kp/query" -H "accept: application/json" -H "Content-Type: application/json" -d "{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"category\":\"biolink:AnatomicalEntity\"},\"n1\":{\"category\":\"biolink:AnatomicalEntity\",\"id\":\"UBERON:0002398\"}},\"edges\":{\"e0\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicate\":\"biolink:part_of\"}}}}}"
Query result:
{
"message": {
"query_graph": {
"nodes": {
"n0": {
"category": "biolink:AnatomicalEntity"
},
"n1": {
"category": "biolink:AnatomicalEntity",
"id": "UBERON:0002398"
}
},
"edges": {
"e0": {
"predicate": "biolink:part_of",
"subject": "n0",
"object": "n1"
}
}
},
"knowledge_graph": {
"nodes": {
"UBERON:5011982": {
"name": "manual digit 7 plus metapodial segment",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004312": {
"name": "distal phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0008465": {
"name": "abductor pollicis brevis muscle",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003865": {
"name": "distal phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010688": {
"name": "skeleton of manual acropodium",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001463": {
"name": "manual digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010678": {
"name": "manual digit 4 phalanx cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010677": {
"name": "manual digit 3 phalanx cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001431": {
"name": "distal carpal bone 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200179": {
"name": "manual claw",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003639": {
"name": "manual digit 5 phalanx",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004409": {
"name": "distal epiphysis of phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001412": {
"name": "common palmar digital vein",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004392": {
"name": "epiphysis of second metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014884": {
"name": "distal epiphysis of distal phalanx of manual digit 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006213": {
"name": "carpus cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009588": {
"name": "mesenchyme of interdigital region between manual digits 3 and 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003597": {
"name": "manual digit connective tissue",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5003623": {
"name": "manual digit 3 plus metapodial segment",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015045": {
"name": "manual digit 3 metacarpus endochondral element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004423": {
"name": "proximal epiphysis of second metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010570": {
"name": "manual digit 1 metacarpus cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0019246": {
"name": "palmar skin crease",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5101463": {
"name": "manual digit 1 digitopodial skeleton",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200108": {
"name": "outer digit of hand",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007735": {
"name": "metacarpophalangeal joint of manual digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015025": {
"name": "manual digit 1 phalanx endochondral element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015091": {
"name": "distal carpal bone 3 cartilage",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0013622": {
"name": "manual autopod pad",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015097": {
"name": "distal carpal bone 5 cartilage",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006167": {
"name": "forelimb proper dorsal digital arteries",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003648": {
"name": "metacarpal bone of digit 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010568": {
"name": "manual digit 4 metacarpus pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015044": {
"name": "manual digit 2 metacarpus endochondral element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200041": {
"name": "aponeurosis palmaris",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014886": {
"name": "distal epiphysis of distal phalanx of manual digit",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014885": {
"name": "distal epiphysis of distal phalanx of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004489": {
"name": "musculature of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0012268": {
"name": "equine forelimb splint bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004331": {
"name": "proximal phalanx of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200180": {
"name": "semilunate carpal",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004453": {
"name": "metacarpus region",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:3010193": {
"name": "prepollical protuberances",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009589": {
"name": "mesenchyme of interdigital region between manual digits 4 and 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5103625": {
"name": "manual digit 5 digitopodial skeleton",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003649": {
"name": "metacarpal bone of digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015098": {
"name": "distal carpal bone 5 pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006165": {
"name": "median dorsal digital artery for digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011978": {
"name": "epiphysis of middle phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0016426": {
"name": "proximal interphalangeal joint of little finger",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005451": {
"name": "segment of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003230": {
"name": "epithelium of carpal region",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011982": {
"name": "manual digit 7",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010726": {
"name": "os vesalianum manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005880": {
"name": "prepollex",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001435": {
"name": "carpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004424": {
"name": "proximal epiphysis of third metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015079": {
"name": "proximal carpal cartilage",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006141": {
"name": "palmar digital artery",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004422": {
"name": "proximal epiphysis of first metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004440": {
"name": "proximal epiphysis of proximal phalanx of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010679": {
"name": "manual digit 5 phalanx cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001501": {
"name": "lumbrical muscle of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5003622": {
"name": "manual digit 2 plus metapodial segment",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0036173": {
"name": "abductor digiti minimi of hand",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004437": {
"name": "proximal epiphysis of middle phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004416": {
"name": "proximal epiphysis of metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004338": {
"name": "proximal phalanx of manual digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015027": {
"name": "manual digit 3 phalanx endochondral element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015095": {
"name": "distal carpal bone 4 pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003623": {
"name": "manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010572": {
"name": "manual digit 3 metacarpus cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005257": {
"name": "manual digit mesenchyme",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0002988": {
"name": "first dorsal interosseous of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004432": {
"name": "proximal epiphysis of distal phalanx of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001430": {
"name": "distal carpal bone 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015024": {
"name": "manual digit phalanx endochondral element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004561": {
"name": "proper palmar digital vein",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5103623": {
"name": "manual digit 3 digitopodial skeleton",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003636": {
"name": "manual digit 2 phalanx",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:3010060": {
"name": "centrale (fore)",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004553": {
"name": "forelimb digital artery",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005645": {
"name": "manual digit 2 epithelium",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015146": {
"name": "manus hair",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004443": {
"name": "proximal epiphysis of proximal phalanx of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006140": {
"name": "palmar digital vein",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003646": {
"name": "metacarpal bone of digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014671": {
"name": "distal interphalangeal joint of manural digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010686": {
"name": "manual digit phalanx cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001518": {
"name": "skin of wrist",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004330": {
"name": "proximal phalanx of manual digit 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005693": {
"name": "manual digit 3 mesenchyme",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004321": {
"name": "middle phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014668": {
"name": "distal interphalangeal joint of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010574": {
"name": "manual digit 5 metacarpus cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004320": {
"name": "middle phalanx of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011132": {
"name": "intercarpal joint",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011977": {
"name": "epiphysis of proximal phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009880": {
"name": "carpal skeleton",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0015069": {
"name": "distal carpal cartilage element",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0003533": {
"name": "manual digit skin",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004444": {
"name": "proximal epiphysis of distal phalanx of manual digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005648": {
"name": "manual digit 5 epithelium",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001428": {
"name": "intermedium",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:5103624": {
"name": "manual digit 4 digitopodial skeleton",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007731": {
"name": "interphalangeal joint of manual digit 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006013": {
"name": "interdigital region between manual digits",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0012124": {
"name": "avian scapholunar bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0013753": {
"name": "distal epiphysis of metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009552": {
"name": "distal segment of manual digit",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011868": {
"name": "midcarpal joint",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006026": {
"name": "interdigital region between manual digits 1 and 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0008438": {
"name": "webbed interdigital region between manual digits",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014883": {
"name": "distal epiphysis of distal phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004414": {
"name": "proximal epiphysis of phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0012261": {
"name": "manual major digit (Aves)",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:3010127": {
"name": "fringe on postaxial edge of finger IV",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011104": {
"name": "epiphysis of fifth metacarpal bone",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007722": {
"name": "interphalangeal joint of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011273": {
"name": "nail of manual digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0014882": {
"name": "distal epiphysis of distal phalanx of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010569": {
"name": "manual digit 5 metacarpus pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200188": {
"name": "manual toe disc",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0036172": {
"name": "palmaris brevis",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007732": {
"name": "interphalangeal joint of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0006029": {
"name": "interdigital region between manual digits 2 and 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010566": {
"name": "manual digit 2 metacarpus pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007738": {
"name": "metacarpophalangeal joint of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0002234": {
"name": "proximal phalanx of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004420": {
"name": "proximal epiphysis of phalanx of manual digit 4",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004439": {
"name": "proximal epiphysis of middle phalanx of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010690": {
"name": "manual digit 1 epithelium",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004329": {
"name": "proximal phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200186": {
"name": "distal keel of metacarpal III",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011131": {
"name": "intermetacarpal joint",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:4200104": {
"name": "metacarpal extensor pit",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010567": {
"name": "manual digit 3 metacarpus pre-cartilage condensation",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0011265": {
"name": "carpometacarpal joint of digit 1",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009600": {
"name": "mesenchyme of interdigital region of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0007747": {
"name": "metacarpophalangeal joint of manual digit 5",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:3000856": {
"name": "intercalary element of fore digit",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004418": {
"name": "proximal epiphysis of phalanx of manual digit 2",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005694": {
"name": "manual digit 4 mesenchyme",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0005276": {
"name": "dorsal skin of finger",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0009587": {
"name": "mesenchyme of interdigital region between manual digits 2 and 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0012290": {
"name": "fused carpal bones 2 and 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0001502": {
"name": "interosseous muscle of manus",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0004441": {
"name": "proximal epiphysis of proximal phalanx of manual digit 3",
"category": [
"biolink:AnatomicalEntity"
]
},
"UBERON:0010739": {
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}https://stars-app.renci.org/sparql-kp/docs/index.html?url=docs.yaml
Ontology-KP is registered with Smart API (need to resolve technical issue linking to entry).
Ontology-KP requires a Java virtual machine. Instructions for building and running can be found in the source repository.
Jim Balhoff