ontologies.json

{
  "UMLS": {
    "comment": "initial preparation of files extracted from UMLS",
    "execute": "./umls_init/umls_init.py"
  },
  "CCF": {
    "owl_url": "https://data.bioontology.org/ontologies/CCF/submissions/14/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "comment": "Human Reference Atlas Common Coordinate Framework Ontology",
    "sab": "CCF"
  },
  "HGNCNR": {
    "owl_url": "https://data.bioontology.org/ontologies/HGNC-NR/submissions/5/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/HGNC-NR",
    "comment": "Human Reference Atlas Common Coordinate Framework Ontology",
    "sab": "HGNCNR"
  },
  "CCO": {
    "owl_url": "http://brg.ai.sri.com/CCO/downloads/cco.owl",
    "home_url": "http://brg.ai.sri.com/CCO/",
    "comment": "Cell Component Ontology"
  },
  "CHEBI": {
    "owl_url": "http://purl.obolibrary.org/obo/chebi.owl.gz",
    "home_url": "http://www.obofoundry.org/ontology/chebi.html",
    "comment": "Chemical Entities of Biological Interest, zipped"
  },
  "CL": {
    "owl_url": "http://purl.obolibrary.org/obo/cl.owl",
    "home_url": "http://www.obofoundry.org/ontology/cl.html",
    "comment": "Complete cell ontology, plus inter-ontology axioms, and imports modules"
  },
  "CL_BASE": {
    "owl_url": "http://purl.obolibrary.org/obo/cl/cl-base.owl",
    "home_url": "http://www.obofoundry.org/ontology/cl.html",
    "comment": "Complete cell ontology, but with no imports or external axioms",
    "sab": "CL"
  },
  "DOID": {
    "owl_url": "http://purl.obolibrary.org/obo/doid.owl",
    "home_url": "https://disease-ontology.org/",
    "comment": "Human Disease Ontology"
  },
  "EDAM": {
    "owl_url": "http://edamontology.org/EDAM.owl",
    "home_url": "http://edamontology.org/page",
    "comment": "Ontology of bioscientific data analysis and data management"
  },
  "HSAPDV": {
    "owl_url": "http://purl.obolibrary.org/obo/hsapdv.owl",
    "home_url": "https://www.ebi.ac.uk/ols/ontologies/hsapdv",
    "comment": "Life cycle stages for Human"
  },
  "MI": {
    "owl_url": "http://purl.obolibrary.org/obo/mi.owl",
    "home_url": "https://www.ebi.ac.uk/ols/ontologies/mi",
    "comment": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions"
  },
  "MP": {
    "owl_url": "http://purl.obolibrary.org/obo/mp.owl",
    "home_url": "http://obofoundry.org/ontology/mp.html",
    "comment": "Standard terms for annotating mammalian phenotypic data"
  },
  "OBI": {
    "owl_url": "http://purl.obolibrary.org/obo/obi.owl",
    "home_url": "http://obi-ontology.org/",
    "comment": "Ontology for Biomedical Investigations"
  },
  "OGI": {
    "owl_url": "https://data.bioontology.org/ontologies/OGI/submissions/18/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/OGI",
    "comment": "Ontology for Genetic Interval",
    "download_owl_url_to_file_name": "ogi.owl",
    "sab": "OGI"
  },
  "ORDO": {
    "owl_url": "https://data.bioontology.org/ontologies/ORDO/submissions/28/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/ORDO",
    "comment": "Orphanet Rare Disease Ontology",
    "download_owl_url_to_file_name": "ordo.owl",
    "sab": "ORDO"
  },
  "PATO": {
    "owl_url": "http://purl.obolibrary.org/obo/pato.owl",
    "home_url": "http://www.obofoundry.org/ontology/pato.html",
    "comment": "Phenotype And Trait Ontology "
  },
  "PATO_BASE": {
    "owl_url": "http://purl.obolibrary.org/obo/pato/pato-base.owl",
    "home_url": "http://www.obofoundry.org/ontology/pato.html",
    "comment": "Phenotype And Trait Ontology - includes axioms linking to other ontologies, but no imports of those ontologies"
  },
  "PR": {
    "owl_url": "http://purl.obolibrary.org/obo/pr.owl",
    "home_url": "http://www.obofoundry.org/ontology/pr.html",
    "comment": "Protein Ontology. Specify an organism (e.g., human) via the optional -p argument to filter the nodes to a manageable size."
  },
  "RO": {
    "owl_url": "http://purl.obolibrary.org/obo/ro.owl",
    "home_url": "http://www.obofoundry.org/ontology/ro.html",
    "comment": "This Relation Ontology should get relationships and inverses and the RO code where we want the name"
  },
  "SBO": {
    "owl_url": "http://purl.obolibrary.org/obo/sbo.owl",
    "home_url": "https://obofoundry.org/ontology/sbo.html",
    "comment": "Systems Biology Ontology",
    "sab": "SBO"
  },
  "UBERON": {
    "owl_url": "http://purl.obolibrary.org/obo/uberon.owl",
    "home_url": "https://uberon.github.io/downloads.html",
    "comment": "UBER-anatomy ONtology: An integrated cross-species ontology covering anatomical structures in animals. This one contains data without references"
  },
  "UBERON_BASE": {
    "owl_url": "http://purl.obolibrary.org/obo/uberon/uberon-base.owl",
    "home_url": "https://uberon.github.io/downloads.html",
    "comment": "Axioms defined within Uberon and to be used in imports for other ontologies"
  },

  "UNIPROTKB": {
    "home_url": "https://www.uniprot.org/uniprot/?query=facets=reviewed%3Atrue&fil=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22",
    "comment": "Data from UniProtKB exported to OWLNETS format. Supply -s argument to call to use existing UniProtKB data file.",
    "execute": "./uniprotkb/uniprotkb_owlnets.py"
  },
  "VARIO": {
    "owl_url": "http://www.variationontology.org/vario_download/vario.owl",
    "home_url": "http://www.variationontology.org/download.shtml",
    "comment": "A Variation Ontology: for standardized, systematic description of effects, consequences and mechanisms of variations"
  },
  "HUBMAP": {
    "comment": "HubMAP application ontology, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py HUBMAP"
  },
  "SENNET": {
    "comment": "SenNet application ontology, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py SENNET"
  },
  "SWO": {
    "owl_url": "http://purl.obolibrary.org/obo/swo.owl",
    "home_url": "https://github.com/allysonlister/swo",
    "comment": "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation"
  },
  "BAO": {
    "owl_url": "https://data.bioontology.org/ontologies/BAO/submissions/41/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/BAO",
    "comment": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results"
  },
  "UO": {
    "owl_url": "http://purl.obolibrary.org/obo/uo.owl",
    "home_url": "https://obofoundry.org/ontology/uo.html",
    "comment": "Unit Ontology"
  },
  "MONDO": {
    "owl_url": "http://purl.obolibrary.org/obo/mondo.owl",
    "home_url": "https://obofoundry.org/ontology/mondo.html",
    "comment": "The Mondo Disease Ontology (MONDO): a global community effort to harmonize multiple disease resources to yield a coherent merged ontology"
  },
  "EFO": {
    "owl_url": "https://data.bioontology.org/ontologies/EFO/submissions/262/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/EFO",
    "comment": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets."
  },
  "FALDO": {
    "owl_url": "https://data.bioontology.org/ontologies/FALDO/submissions/18/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/FALDO",
    "comment": "FALDO is the Feature Annotation Location Description Ontology. (Part of GlyGen ingestion)"
  },
  "UNIPROT": {
    "owl_url": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl",
    "home_url": "https://ftp.uniprot.org/pub/databases/uniprot/README",
    "comment": "UniProt"
  },
  "GLYCORDF": {
    "owl_url": "https://raw.githubusercontent.com/glycoinfo/GlycoRDF/master/ontology/glycan.rdf",
    "home_url": "https://github.com/glycoinfo/GlycoRDF",
    "comment": "GlycoRDF OWL in RDF/XML"
  },
  "GLYCOCOO": {
    "owl_url": "https://raw.githubusercontent.com/glycoinfo/GlycoCoO/master/ontology/glycocoo.owl",
    "home_url": "https://github.com/glycoinfo/GlycoCoO",
    "comment": "GlycoCoO in Turtle"
  },
  "OBIB": {
    "owl_url": "http://purl.obolibrary.org/obo/obib.owl",
    "home_url": "https://obofoundry.org/ontology/obib.html",
    "comment": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration."
  },
  "XCO": {
    "home_url": "https://bioportal.bioontology.org/ontologies/XCO",
    "comment": "XCO from GZipped CSV",
    "execute": "./gzip_csv/gzip_csv_owlnets.py 'https://data.bioontology.org/ontologies/XCO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv' XCO"
  },
  "HRAVS": {
    "home_url": "https://bioportal.bioontology.org/ontologies/HRAVS",
    "comment": "The value set for the Human Reference Atlas metadata records as part of the Human BioMolecular Atlas Program (HuBMAP)",
    "execute": "./gzip_csv/gzip_csv_owlnets.py 'https://data.bioontology.org/ontologies/HRAVS/download?apikey=4983e1fe-1f54-412e-99bb-74764d659cb0&download_format=csv' HRAVS"
  },
  "NPO": {
    "owl_url": "https://data.bioontology.org/ontologies/NPOKB/submissions/14/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
    "home_url": "https://bioportal.bioontology.org/ontologies/NPOKB?p=summary",
    "comment": "NPO in Turtle"
  },
  "LINCS": {
    "comment": "LINCS data in edges/nodes format",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py LINCS"
  },
  "AZ": {
    "comment": "Azimuth annotations, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py AZ"
  },
  "GTEXEXP": {
    "comment": "GTEXEXP data in edges/nodes format",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py GTEXEXP"
  },
  "GTEXCOEXP": {
    "comment": "GTEXCOEXP data in edges/nodes format",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py GTEXCOEXP"
  },
  "GTEXEQTL": {
    "comment": "GTEXEQTL data in edges/nodes format",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py GTEXEQTL"
  },
  "GENCODE": {
    "comment": "Data from GenCode",
    "execute": "./gencode/gencode.py"
  },
  "NPOSKCAN": {
    "owl_url": "https://github.com/SciCrunch/NIF-Ontology/releases/download/sckan-2023-04-29/npo-simple-sckan-merged.ttl",
    "home_url": "https://github.com/SciCrunch/NIF-Ontology",
    "comment": "NPO-SKCAN in Turtle"
  },
  "PGO": {
    "home_url": "https://bioportal.bioontology.org/ontologies/pseudo/?p=summary",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py PGO",
    "comment": "Pseudogene"
  },
  "GENCODE_VS": {
    "comment": "GenCode application ontology, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py GENCODE_VS"
  },
  "CLINVAR": {
    "home_url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/README.txt",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py CLINVAR",
    "comment": "CLINVAR"
  },
  "CMAP": {
    "home_url": "https://www.broadinstitute.org/connectivity-map-cmap",
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py CMAP",
    "comment": "CMAP"
  },
  "HPOMP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HPOMP",
    "comment": "HPOMP"
  },
  "HGNCHPO": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HGNCHPO",
    "comment": "HGNCHPO - human genotype - phenotype mapping "
  },
  "HCOP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HCOP",
    "comment": "HCOPHGNC - human-mouse orthologs"
  },
  "MPMGI": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py MPMGI",
    "comment": "HCOPMP - mouse_genotype_phenotype"
  },
  "RATHCOP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py RATHCOP",
    "comment": "RATHCOP - human-rat ensemble orthologs"
  },
  "MSIGDB": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py MSIGDB",
    "comment": "MSIGDB"
  },
  "GLYCANS": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py GLYCANS",
    "comment": "GlyGen GLYCANS"
  },
  "PROTEOFORM": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py PROTEOFORM",
    "comment": "GlyGen PROTEOFORM"
  },
  "IDGP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py IDGP",
    "comment": "IDG - compound-protein interactions"
  },
  "IDGD": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py IDGD",
    "comment": "IDG - compound-disease interactions"
  },
  "MW": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py MW",
    "comment": "Metabolic Workbench"
  },
  "ERCCRBS": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py ERCCRBS",
    "comment": "ERCC - Remote Binding Site"
  },
  "HSCLO": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HSCLO",
    "comment": "HSCLO - Chromosome Location Ontology"
  },
  "GENCODEHSCLO": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py GENCODEHSCLO",
    "comment": "GENCODE - HSCLO mapping"
  },
  "4DN": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py 4DN",
    "comment": "4D Nucleome"
  },
  "HRA": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HRA",
    "comment": "Human Reference Atlas"
  },
  "ERCCRBP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py ERCCRBP",
    "comment": "ERCC exRNA Remote Binding Proteins"
  },
  "ERCCREG": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py ERCCREG",
    "comment": "ERCC Regulatory Elements"
  },
  "MOTRPAC": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py MOTRPAC",
    "comment": "MOTRPAC"
  },
  "KF": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py KF",
    "comment": "Gabriella Miller Kids First"
  },
  "HMAZ": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py HMAZ",
    "comment": "HuBMAP Azimuth"
  },
  "CEDAR": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py CEDAR",
    "comment": "CEDAR templates"
  },
  "HMFIELD": {
    "execute": "./hmfields/hmfields.py HMFIELD",
    "comment": "HuBMAP pre-CEDAR metadata"
  },
  "CLINGEN": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py CLINGEN",
    "comment": "CLINGEN"
  },
  "STRING": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py STRING",
    "comment": "StringDB"
  },
  "WP": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py WP",
    "comment": "WikiPathways"
  },
  "CEDAR_ENTITY": {
    "execute": "./cedar_entity/cedar_entity.py",
    "comment": "CEDAR-Provenance Entity mapping"
  },
  "PCL": {
    "owl_url": "https://purl.obolibrary.org/obo/pcl.owl",
    "home_url": "https://github.com/obophenotype/provisional_cell_ontology",
    "comment": "Provisional Cell Ontology"
  },
  "REACTOME_VS": {
    "comment": "Reactome valueset, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py REACTOME_VS"
  },
  "REACTOME": {
    "execute": "./reactome/reactome.py",
    "comment": "Reactome"
  },
  "DGN": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py DGN",
    "comment": "DisGenet"
  },
  "UBKGSOURCE": {
    "comment": "UBKG source ontology, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py UBKGSOURCE"
  },
  "BIOMARKER": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py BIOMARKER",
    "comment": "Biomarker Partnership"
  },
  "OTG": {
    "execute": "./ubkg_edges_nodes/ubkg_edges_nodes.py OTG",
    "comment": "Open Target Genomics"
  },
  "STELLAR": {
    "comment": "STELLAR-CL mappings, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py STELLAR"
  },
  "DCT": {
    "comment": "DeepCellType-CL mappings, obtained from input spreadsheet in SimpleKnowledge format",
    "execute": "./skowlnets/skowlnets.py DCT"
  }
}