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80 lines (80 loc) · 4.15 KB
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{
"ols_lexical": {
"max_results": 20,
"timeout_ms": 60000,
"max_concurrent_requests": 5
},
"ols_embedding": {
"min_similarity": 0.7,
"max_deep_results": 100,
"max_shallow_results": 10,
"timeout_ms": 60000,
"max_concurrent_embedding_requests": 3,
"max_concurrent_similar_requests": 10
},
"oxo": {
"enabled": false
},
"ontology_presets": [
{
"name": "EFO and OBO Foundry",
"ontologies": ["efo","uberon","cl","pcl","go","bspo","pato","oba","hp","mp","fypo","mondo","chebi","ro","ecto","envo","obi","maxo","eco","ncbitaxon","pr","ncit","po","ppo","to","peco","fbbt","foodon","pco","iao","mmo","mi","so","wbbt","wbls","wbphenotype","zfa","apo","mmusdv","hsapdv","vbo","uo"],
"include_obo_ontologies": true
},
{
"name": "Just OBO Foundry",
"ontologies": ["uberon","cl","pcl","go","bspo","pato","oba","hp","mp","fypo","mondo","chebi","ro","ecto","envo","obi","maxo","eco","ncbitaxon","pr","ncit","po","ppo","to","peco","fbbt","foodon","pco","iao","mmo","mi","so","wbbt","wbls","wbphenotype","zfa","apo","mmusdv","hsapdv","vbo","uo"],
"include_obo_ontologies": true
}
],
"prefix_map": {
"owl": "http://www.w3.org/2002/07/owl#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"xml": "http://www.w3.org/XML/1998/namespace",
"swrl": "http://www.w3.org/2003/11/swrl#",
"swrlb": "http://www.w3.org/2003/11/swrlb#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"dc": "http://purl.org/dc/elements/1.1/",
"oac": "http://www.openannotation.org/ns/",
"prov": "http://www.w3.org/TR/prov-o/",
"zooma": "http://www.ebi.ac.uk/fgpt/zooma/",
"zoomaterms": "http://rdf.ebi.ac.uk/terms/zooma/",
"zoomaresource": "http://rdf.ebi.ac.uk/resource/zooma/",
"annotation": "http://rdf.ebi.ac.uk/resource/zooma/annotation/",
"propval": "http://rdf.ebi.ac.uk/resource/zooma/propertyvalue/",
"ebi": "http://www.ebi.ac.uk/",
"ebiresource": "http://rdf.ebi.ac.uk/resource/",
"arrayexpress": "http://www.ebi.ac.uk/arrayexpress/",
"aeresource": "http://rdf.ebi.ac.uk/resource/zooma/arrayexpress/",
"aeannotation": "http://rdf.ebi.ac.uk/resource/zooma/arrayexpress/annotation/",
"aeexperiment": "http://rdf.ebi.ac.uk/resource/zooma/arrayexpress/experiment/",
"aeproperty": "http://rdf.ebi.ac.uk/resource/zooma/arrayexpress/property/",
"gxa": "http://www.ebi.ac.uk/gxa/",
"gxaresource": "http://rdf.ebi.ac.uk/resource/zooma/gxa/",
"gxaannotation": "http://rdf.ebi.ac.uk/resource/zooma/gxa/annotation/",
"gxaexperiment": "http://rdf.ebi.ac.uk/resource/zooma/gxa/experiment/",
"gxaproperty": "http://rdf.ebi.ac.uk/resource/zooma/gxa/property/",
"genome": "http://www.genome.gov/",
"gwas": "http://www.genome.gov/gwastudies/",
"gwasresource": "http://rdf.ebi.ac.uk/resource/zooma/gwas/",
"gwasannotation": "http://rdf.ebi.ac.uk/resource/zooma/gwas/annotation/",
"gwassnp": "http://rdf.ebi.ac.uk/resource/zooma/gwas/snp/",
"gwasproperty": "http://rdf.ebi.ac.uk/resource/zooma/gwas/property/",
"owlresource": "http://rdf.ebi.ac.uk/resource/zooma/owl/",
"owlannotation": "http://rdf.ebi.ac.uk/resource/zooma/owl/annotation/",
"owlproperty": "http://rdf.ebi.ac.uk/resource/zooma/owl/property/",
"efo": "http://www.ebi.ac.uk/efo/",
"snap": "http://www.ifomis.org/bfo/1.1/snap#",
"span": "http://www.ifomis.org/bfo/1.1/span#",
"cl": "http://purl.org/obo/owl/CL#",
"obo": "http://purl.obolibrary.org/obo/",
"oboinowl": "http://www.geneontology.org/formats/oboInOwl#",
"ncbitaxon": "http://purl.org/obo/owl/NCBITaxon#",
"bto": "http://purl.org/obo/owl/BTO#",
"pato": "http://purl.org/obo/owl/PATO#",
"pubmed": "http://europepmc.org/abstract/MED/",
"orpha": "http://www.orphanet.org/rdfns#"
}
}