--- # GLOBAL_TERMS.yaml # contents in this file are sorted by the value # (i.e. the ontology term after the colon) in {key value} pair !!map { # # these need to be moved to localtts till the terms exist: :!!! "activating_mutation": ":activating", "all_missense_or_inframe": ":all_missense_or_inframe", "biallelic": ":biallelic", "does_not_have_phenotype": ":does_not_have_phenotype", "frequency": ":frequencyOfPhenotype", "has_allelic_requirement": ":has_allelic_requirement", "has_cell_origin": ":has_cell_origin", "has_drug_response": ":has_drug_response", "has_functional_consequence": ":has_functional_consequence", "has_molecular_consequence": ":has_molecular_consequence", "has_sex_specificty": ":has_sex_specificity", "increased_gene_dosage": ":increased_gene_dosage", "monoallelic": ":monoallelic", "mosaic": ":mosaic_genotype", "onset": ":onset", "part_of_contiguous_gene_duplication": ":part_of_contiguous_gene_duplication", # Basic Formal Ontology: "BFO:!!!", "part_of": "BFO:0000050", "has_part": "BFO:0000051", "occurs_in": "BFO:0000066", # "Chemicals of Biological Interest": "CHEBI:!!!", "inchi_key": "CHEBI:InChIKey", # likely incorrect. -> localtt{"inchi_key": "CHEBI"}? "molecular entity": "CHEBI:23367", "gene_product": "CHEBI:33695", # "Citation Typing Ontology": "cito:!!!", "citesAsAuthority": "cito:citesAsAuthority", # "Cell Ontology (cell types)": "CL:!!!", "cell": "CL:0000000", "stem cell": "CL:0000034", "myoblast": "CL:0000056", "fibroblast": "CL:0000057", "epithelial cell": "CL:0000066", "mesothelial": "CL:0000077", "T cell": "CL:0000084", "endothelial cell": "CL:0000115", "melanocyte": "CL:0000148", "smooth muscle cell": "CL:0000192", "B cell": "CL:0000236", "keratinocyte": "CL:0000312", "oncocyte": "CL:0002198", "amniocyte": "CL:0002323", "mesenchymal stem cell of adipose": "CL:0002570", "precursor cell": "CL:0011115", # "Cell Line Ontology": "CLO:!!!", "cell line repository": "CLO:0000008", "cell line": "CLO:0000031", "immortal kidney-derived cell line cell": "CLO:0000220", "Adipose stromal cell": "CLO:0036934", "Amniotic fluid-derived cell line": "CLO:0036935", "Tumor-derived cell line": "CLO:0036938", "Microcell hybrid": "CLO:0036939", "Chorionic villus-derived cell line": "CLO:0036940", # "dublin core entities (metadata)": "dc:!!!", "comment": "dc:comment", "description": "dc:description", "source": "dc:source", "title (dce)": "dc:title", # "Data Catalog Vocabulary": "dcat:!!!" "distribution": "dcat:Distribution", # "dublin core terms": "dcterms:!!!", "identifier": "dcterms:identifier", "title": "dcterms:title", "Source (dct)": "dcterms:source", # N.B. we append ' (dct)' to their label "Publisher": "dcterms:Publisher", "Date Created": "dcterms:created", "creator": "dcterms:creator", "downloadURL": "dcterms:downloadURL", "format": "dcterms:format", "isVersionOf": "dcterms:isVersionOf", "license": "dcterms:license", "rights": "dcterms:rights", # "dublin core metadata types": "dctypes:!!!", "Dataset": "dctypes:Dataset", # "Human Disease Ontology": "DOID:!!!", "disease": "DOID:4", "inherited blood coagulation disease": "DOID:2214", "blood platelet disease": "DOID:2218", # "Evidence Code Ontology": "ECO:!!!", "evidence": "ECO:0000000", "inference from background scientific knowledge": "ECO:0000001", "enzyme assay evidence": "ECO:0000005", "experimental evidence": "ECO:0000006", "expression pattern evidence": "ECO:0000008", "genetic interaction evidence": "ECO:0000011", "functional complementation evidence": "ECO:0000012", "mutant phenotype evidence": "ECO:0000015", "traceable author statement": "ECO:0000033", "no biological data found": "ECO:0000035", "experimental phenotypic evidence": "ECO:0000059", "quantitative trait analysis evidence": "ECO:0000061", "yeast 2-hybrid evidence": "ECO:0000068", "far-Western blotting evidence": "ECO:0000076", "affinity chromatography evidence": "ECO:0000079", "phylogenetic evidence": "ECO:0000080", "immunoprecipitation evidence": "ECO:0000085", "biochemical trait analysis evidence": "ECO:0000172", "genomic context evidence": "ECO:0000177", "clinical study evidence": "ECO:0000180", "sequence alignment evidence": "ECO:0000200", "sequence orthology evidence": "ECO:0000201", "match to sequence model evidence": "ECO:0000202", "combinatorial evidence used in automatic assertion": "ECO:0000213", "biological aspect of descendant evidence": "ECO:0000214", "sequencing assay evidence": "ECO:0000220", "computational combinatorial evidence used in manual assertion": "ECO:0000245", "sequence similarity evidence used in manual assertion": "ECO:0000250", "experimental evidence used in manual assertion": "ECO:0000269", "expression evidence used in manual assertion": "ECO:0000270", "author statement without traceable support used in manual assertion": "ECO:0000303", "author statement supported by traceable reference used in manual assertion": "ECO:0000304", "curator inference used in manual assertion": "ECO:0000305", "inference from background scientific knowledge used in manual assertion": "ECO:0000306", "imported information": "ECO:0000311", "direct assay evidence used in manual assertion": "ECO:0000314", "mutant phenotype evidence used in manual assertion": "ECO:0000315", "genetic interaction evidence used in manual assertion": "ECO:0000316", "biological aspect of ancestor evidence used in manual assertion": "ECO:0000318", "phylogenetic determination of loss of key residues evidence used in manual assertion": "ECO:0000320", "imported manually asserted information used in automatic assertion": "ECO:0000322", "imported automatically asserted information used in automatic assertion": "ECO:0000323", "imaging assay evidence": "ECO:0000324", "physical interaction evidence used in manual assertion": "ECO:0000353", "evidence used in automatic assertion": "ECO:0000501", "blood test evidence": "ECO:0001016", "FRET": "ECO:0001048", "x-ray crystallography evidence": "ECO:0001823", "inference from experimental data evidence": "ECO:0005611", "inference from phenotype manipulation evidence": "ECO:0005612", "inference by association of genotype from phenotype": "ECO:0005613", # "Data and Methods Ontology": "EDAM-DATA:!!!", "gene_family": "EDAM-DATA:3148", # "Experimental Factor Ontology": "EFO:!!!", "age": "EFO:0000246", "sampling_time": "EFO:0000689", "ethnic_group": "EFO:0001799", "African American": "EFO:0003150", "Asian": "EFO:0003152", "Asian Indian": "EFO:0003153", "Asian/Pacific Islander": "EFO:0003154", "Caucasian": "EFO:0003156", "Chinese": "EFO:0003157", "Eastern Indian": "EFO:0003158", "Filipino": "EFO:0003160", "Japanese": "EFO:0003164", "Korean": "EFO:0003165", "Hispanic": "EFO:0003169", "African": "EFO:0004561", # "Environment Ontology": "ENVO:!!!", "environmental_system": "ENVO:01000254", # "Eeagle-i Resource Ontology": "ERO:!!!", "reagent": "ERO:0000006", # to be split into REO terms ...eventually "has_author": "ERO:0000232", "has_url": "ERO:0000480", "Native American": "ERO:0001984", "embryonic stem cell line": "ERO:0002002", "Asian, Vietnamese": "ERO:0002071", "collection": "ERO:0002190", # "Feature Annotation Location Description Ontology": "faldo:!!!" (hacky) "begin": "faldo:begin", "both_strand": "faldo:BothStrandPosition", "end": "faldo:end", "FuzzyPosition": "faldo:FuzzyPosition", "location": "faldo:location", "minus_strand": "faldo:MinusStrandPosition", "plus_strand": "faldo:PlusStrandPosition", "Position": "faldo:Position", # Big P for Position type. little p for confusion "position": "faldo:position", # Little p for position property. big P for confusion. "reference": "faldo:reference", "Region": "faldo:Region", # conflicts with SO!region # "friend of a friend": "foaf:!!!", "depiction": "foaf:depiction", "organization": "foaf:organization", "page": "foaf:page", "person": "foaf:Person", # ??? PATO_0000470: GENO:0000876 # "Genotype Partonomy Ontology": "GENO:!!!", "intrinsic_genotype": "GENO:0000000", "variant_locus": "GENO:0000002", "genomic_variation_complement": "GENO:0000009", "variant single locus complement": "GENO:0000030", "reference_locus": "GENO:0000036", "hemizygous": "GENO:0000134", "heterozygous": "GENO:0000135", "homozygous": "GENO:0000136", "indeterminate": "GENO:0000137", "condition inheritance": "GENO:0000141", "co-dominant inheritance": "GENO:0000143", "complete dominant inheritance": "GENO:0000144", "semi-dominant inheritance": "GENO:0000145", "allosomal dominant inheritance": "GENO:0000146", "autosomal dominant iniheritance": "GENO:0000147", "recessive inheritance": "GENO:0000148", "allosomal recessive inheritance": "GENO:0000149", "autosomal recessive inheritance": "GENO:0000150", "is_allelotype_of": "GENO:0000206", "has_sequence_attribute": "GENO:0000207", "has_genotype": "GENO:0000222", "has_member_with_allelotype": "GENO:0000225", # "": "GENO:0000259" # !!! abandoned term "has_variant_part": "GENO:0000382", "has_reference_part": "GENO:0000385", "compound heterozygous": "GENO:0000402", "is_allele_of": "GENO:0000408", "targets_gene": "GENO:0000414", "has_affected_feature": "GENO:0000418", "is_mutant_of": "GENO:0000440", "is_expression_variant_of": "GENO:0000443", "is_transgene_variant_of": "GENO:0000444", "simple heterozygous": "GENO:0000458", "reagent_targeted_gene": "GENO:0000504", "wildtype": "GENO:0000511", "allele": "GENO:0000512", "extrinsic_genotype": "GENO:0000524", "effective_genotype": "GENO:0000525", "targeted_gene_complement": "GENO:0000527", "targeted_gene_subregion": "GENO:0000534", "has_qualifier": "GENO:0000580", "homoplasmic": "GENO:0000602", "heteroplasmic": "GENO:0000603", "hemizygous-y": "GENO:0000604", "hemizygous-x": "GENO:0000605", "hemizygous insertion-linked": "GENO:0000606", "has_zygosity": "GENO:0000608", "is_reference_allele_of": "GENO:0000610", "genomic_background": "GENO:0000611", "chromosome_region": "GENO:0000614", "chromosome_subband": "GENO:0000616", "band_intensity": "GENO:0000618", "gpos": "GENO:0000619", "gneg": "GENO:0000620", "gvar": "GENO:0000621", "gpos100": "GENO:0000622", "gpos75": "GENO:0000623", "gpos50": "GENO:0000624", "gpos25": "GENO:0000625", "stalk": "GENO:0000628", # was "short_chromosome_arm" may conflict ucscbands/monochrom "long_chromosome_arm": "GENO:0000629", "has_begin_stage_qualifier": "GENO:0000630", "has_end_stage_qualifier": "GENO:0000631", "gpos66": "GENO:0000632", "gpos33": "GENO:0000633", "is_targeted_by": "GENO:0000634", "regulatory_transgene_feature": "GENO:0000637", "coding_transgene_feature": "GENO:0000638", "sequence_derives_from": "GENO:0000639", "has_origin": "GENO:0000643", "karyotype_variation_complement": "GENO:0000644", "sex_qualified_genotype": "GENO:0000645", "male_genotype": "GENO:0000646", "female_genotype": "GENO:0000647", "unspecified_genomic_background": "GENO:0000649", "has_sex_agnostic_part": "GENO:0000650", "has_extent": "GENO:0000678", "unspecified": "GENO:0000772", "pathogenic_for_condition": "GENO:0000840", "likely_pathogenic_for_condition": "GENO:0000841", "benign_for_condition": "GENO:0000843", "likely_benign_for_condition": "GENO:0000844", "has_uncertain_significance_for_condition": "GENO:0000845", "short repeat": "GENO:0000846", "has_quantifier": "GENO:0000866", "probabalistic_quantifier": "GENO:0000867", "somatic": "GENO:0000882", "germline": "GENO:0000900", # "Gene Ontology": "GO:!!!", "signal_transduction": "GO:0007165", "cellular_process": "GO:0009987", "developmental_process": "GO:0032502", # "Human Phenotype": "HP:!!!", "x_linked_dominant": "HP:0001423", "mitochondrial_inheritance": "HP:0001427", "digenic_inheritance": "HP:0010984", "obsolete": "HP:0031859", # "Information Artifact Ontology": "IAO:!!!", "has measurement value": "IAO:0000004", "journal article": "IAO:0000013", "data set": "IAO:0000100", "measurement datum": "IAO:0000109", "definition": "IAO:0000115", "is_about": "IAO:0000136", "mentions": "IAO:0000142", "photograph": "IAO:0000185", "document": "IAO:0000310", "publication": "IAO:0000311", "OBO foundry unique label": "IAO:0000589", "term replaced by": "IAO:0100001", # "Medical Subject Headings": "MESH:!!!", "Dwarfism": "MESH:D004392", # "MONARCH": "MONARCH:!!!" one archive to rule them all "is_anonymous": "MONARCH:anonymous", "clique_leader": "MONARCH:cliqueLeader", # "MONarch Disease Ontology": "MONDO:!!!", "disease or disorder": "MONDO:0000001", "integumentary system disease": "MONDO:0002051", "lysosomal storage disease": "MONDO:0002561", "hereditary retinal dystrophy": "MONDO:0004589", "cancer": "MONDO:0004992", "metabolic disease": "MONDO:0005066", "retinal disease": "MONDO:0005283", "congenital heart disease": "MONDO:0005453", "hematological system disease": "MONDO:0005570", "platelet disorder, undefined": "MONDO:0008254", "Coneā€“rod dystrophy": "MONDO:0015993", "inborn errors of metabolism": "MONDO:0019052", # "DOID:0014667" "disorder of sex development": "MONDO:0019592", "developmental defect of the eye": "MONDO:0020145", "hereditary optic atrophy": "MONDO:0043878", # "Mammalian Phenotype": "MP:!!!", "embryonic lethality": "MP:0008762", # "NCBI Taxon": "NCBITaxon:!!!", # "": "NCBITaxon:", # "": "NCBITaxon:", "Escherichia coli": "NCBITaxon:562", "Arabidopsis thaliana": "NCBITaxon:3702", "Schizosaccharomyces pombe": "NCBITaxon:4896", "Aspergillus": "NCBITaxon:5052", "Dictyostelium": "NCBITaxon:5782", "Caenorhabditis elegans": "NCBITaxon:6239", "Drosophila melanogaster": "NCBITaxon:7227", "Danio rerio": "NCBITaxon:7955", "Oncorhynchus mykiss": "NCBITaxon:8022", "Xenopus (Silurana) tropicalis": "NCBITaxon:8364", "Gallus gallus": "NCBITaxon:9031", "Ornithorhynchus anatinus": "NCBITaxon:9258", "Macropus eugenii": "NCBITaxon:9315", "Erinaceus europaeus": "NCBITaxon:9365", "Saguinus fuscicollis": "NCBITaxon:9487", "Lagothrix lagotricha": "NCBITaxon:9519", "Saimiri sciureus": "NCBITaxon:9521", "Callicebus moloch": "NCBITaxon:9523", "Erythrocebus patas": "NCBITaxon:9538", "Macaca fascicularis": "NCBITaxon:9541", "Macaca mulatta": "NCBITaxon:9544", "Macaca nemestrina": "NCBITaxon:9545", "Papio anubis": "NCBITaxon:9555", "Gorilla gorilla": "NCBITaxon:9593", "Pan paniscus": "NCBITaxon:9597", "Pan troglodytes": "NCBITaxon:9598", "Pongo pygmaeus": "NCBITaxon:9600", "Homo sapiens": "NCBITaxon:9606", "Canis lupus familiaris": "NCBITaxon:9615", "Ailurus fulgens": "NCBITaxon:9649", "Felis catus": "NCBITaxon:9685", "Equus caballus": "NCBITaxon:9796", "Sus scrofa": "NCBITaxon:9823", "Sus scrofa domestica": "NCBITaxon:9825", "Muntiacus muntjak": "NCBITaxon:9888", "Bos taurus": "NCBITaxon:9913", "Capra hircus": "NCBITaxon:9925", "Ovis aries": "NCBITaxon:9940", "Oryctolagus cuniculus": "NCBITaxon:9986", "Cricetulus griseus": "NCBITaxon:10029", "Mesocricetus auratus": "NCBITaxon:10036", "Peromyscus leucopus": "NCBITaxon:10041", "Peromyscus maniculatus": "NCBITaxon:10042", "Mus": "NCBITaxon:10088", # Genus "Mus caroli": "NCBITaxon:10089", "Mus musculus": "NCBITaxon:10090", "Mus musculus castaneus": "NCBITaxon:10091", "Mus musculus domesticus": "NCBITaxon:10092", "Mus pahari": "NCBITaxon:10093", "Mus saxicola": "NCBITaxon:10094", "Mus spretus": "NCBITaxon:10096", "Mus cervicolor": "NCBITaxon:10097", "Mus cookii": "NCBITaxon:10098", "Mus platythrix": "NCBITaxon:10101", "Mus setulosus": "NCBITaxon:10102", "Mus spicilegus": "NCBITaxon:10103", "Mus minutoides": "NCBITaxon:10105", "Mus abbotti": "NCBITaxon:10108", "Rattus": "NCBITaxon:10114", "Rattus norvegicus": "NCBITaxon:10116", "Cavia porcellus": "NCBITaxon:10141", "Monodelphis domestica": "NCBITaxon:13616", "Mus booduga": "NCBITaxon:27681", "Anolis carolinensis": "NCBITaxon:28377", "Microcebus murinus": "NCBITaxon:30608", "Takifugu rubripe": "NCBITaxon:31033", "Mus musculus bactrianus": "NCBITaxon:35531", "hybrid": "NCBITaxon:37965", "Mus musculus musculus": "NCBITaxon:39442", "Mus crociduroides": "NCBITaxon:41269", "Mus mattheyi": "NCBITaxon:41270", "Peromyscus polionotus": "NCBITaxon:42413", "Peromyscus californicus": "NCBITaxon:42520", "Dictyostelium discoideum": "NCBITaxon:44689", "Macaca nigra": "NCBITaxon:54600", "Mus musculus molossinus": "NCBITaxon:57486", "Chelonoidis niger": "NCBITaxon:66189", "Saguinus labiatus": "NCBITaxon:78454", "Mus musculus gentilulus": "NCBITaxon:80274", "Mus famulus": "NCBITaxon:83773", "Mus musculus brevirostris": "NCBITaxon:116058", "Mus cervicolor cervicolor": "NCBITaxon:135827", "Mus cervicolor popaeus": "NCBITaxon:135828", "Mus fragilicauda": "NCBITaxon:186193", "Mus musculus x Mus spretus": "NCBITaxon:186842", "Mus gratus": "NCBITaxon:229288", "Mus terricolor": "NCBITaxon:254704", "Mus macedonicus spretoides": "NCBITaxon:270352", "Mus macedonicus macedonicus": "NCBITaxon:270353", "Mus indutus": "NCBITaxon:273921", "Mus haussa": "NCBITaxon:273922", "Mus lepidoides": "NCBITaxon:390847", "Mus nitidulus": "NCBITaxon:390848", "Mus tenellus": "NCBITaxon:397330", "Mus cypriacus": "NCBITaxon:468371", "Mus triton": "NCBITaxon:473865", "Mus musculus musculus x M. m. domesticus": "NCBITaxon:477815", "Mus musculus musculus x M. m. castaneus": "NCBITaxon:477816", "Mus baoulei": "NCBITaxon:544437", "Saccharomyces cerevisiae S288C": "NCBITaxon:559292", # "Mus": "NCBITaxon:862507", # SubGenus -- name conflicts with Genus name "Nannomys": "NCBITaxon:862510", "Mus emesi": "NCBITaxon:887131", "Mus musculus domesticus x M. m. molossinus": "NCBITaxon:1266728", "Mus musculus gansuensis": "NCBITaxon:1385377", # "National Cancer Institute Thesaurus": "NCIT:!!!", # "monoallelic_mutation": "NCIT:C129829", # "biallelic_mutation": "NCIT:C129830", "Statistical Significance": "NCIT:C61040", "Manual": "NCIT:C63513", # "mosaic_indiviual": "NCIT:C88144", "Suspected": "NCIT:C71458", "Percent Change From Baseline": "NCIT:C96621", # "Ontology of Adverse Events": "OAE:!!!", "proportional_reporting_ratio": "OAE:0001563", # "Open Biomedical Annotation Model": "OBAN:!!!", "association": "OBAN:association", "association has object": "OBAN:association_has_object", "association has predicate": "OBAN:association_has_predicate", "association has subject": "OBAN:association_has_subject", # "Ontology of Biomedical Investigations": "OBI:!!!", "assay": "OBI:0000070", "p-value": "OBI:0000175", "study": "OBI:0000471", "statistical_hypothesis_test": "OBI:0000673", "has specified numeric value": "OBI:0001937", # "obo-specific annotation properties": "oboInOwl:!!!", "consider": "oboInOwl:consider", "database_cross_reference": "oboInOwl:hasDbXref", "has_exact_synonym": "oboInOwl:hasExactSynonym", "has_related_synonym": "oboInOwl:hasRelatedSynonym", # "Web Ontology Language": "owl:!!!", "annotation_property": "owl:AnnotationProperty", "class": "owl:Class", "datatype_property": "owl:DatatypeProperty", "deprecated": "owl:deprecated", "equivalent_class": "owl:equivalentClass", "named_individual": "owl:NamedIndividual", "object_property": "owl:ObjectProperty", "on_property": "owl:onProperty", "ontology": "owl:Ontology", "restriction": "owl:Restriction", "same_as": "owl:sameAs", "some_values_from": "owl:someValuesFrom", "version_info": "owl:versionInfo", "version_iri": "owl:versionIRI", # "Phenotypic Quality Ontology": "PATO:!!!", "female": "PATO:0000383", "male": "PATO:0000384", "abnormal": "PATO:0000460", "normal": "PATO:0000461", # "Provenance, Authoring and Versioning": "pav:!!!", "created_on": "pav:createdOn", "version": "pav:version", "retrieved_on": "pav:retrievedOn", "created_with": "pav:createdWith", # "Population and Community Ontology": "PCO:!!!", "population": "PCO:0000001", "family": "PCO:0000020", # Place holder predicates: predicates # "PathWay ontology": "PW:!!!", "pathway": "PW:0000001", # "Resource Description Framework": "rdf:!!!", "type": "rdf:type", # "Resource Description Framework Schema": "rdfs:!!!", "domain": "rdfs:domain", "label": "rdfs:label", "subclass_of": "rdfs:subClassOf", "subPropertyOf": "rdfs:subPropertyOf", # "REO": "REO:!!!" _NOT_ in Curie_map.yaml (see ERO:6) # "crispr_reagent": "REO:crispr_TBD", # "morpholio_reagent": "REO:0000042", # "talen_reagent": "REO:0001022", # "Relationship Ontology": "RO:!!!", "in paralogy relationship with": "RO:HOM0000011", "in orthology relationship with": "RO:HOM0000017", "in xenology relationship with": "RO:HOM0000018", "in 1 to 1 homology relationship with": "RO:HOM0000019", "in 1 to 1 orthology relationship with": "RO:HOM0000020", "in ohnology relationship with": "RO:HOM0000022", "in in-paralogy relationship with": "RO:HOM0000023", "has_participant": "RO:0000057", "has_quality": "RO:0000086", "has disposition": "RO:0000091", "derives_from": "RO:0001000", "starts during": "RO:0002091", "ends during": "RO:0002093", "in taxon": "RO:0002162", "has phenotype": "RO:0002200", "gene product of": "RO:0002204", "has gene product": "RO:0002205", "expressed in": "RO:0002206", "starts_with": "RO:0002224", "ends_with": "RO:0002230", "has_input": "RO:0002233", "colocalizes with": "RO:0002325", "contributes to": "RO:0002326", "enables": "RO:0002327", "involved in": "RO:0002331", "member of": "RO:0002350", "has member": "RO:0002351", "output_of": "RO:0002353", "causally upstream of or within": "RO:0002418", "interacts with": "RO:0002434", "genetically interacts with": "RO:0002435", "molecularly_interacts_with": "RO:0002436", "regulates": "RO:0002448", "ubiquitinates": "RO:0002480", "existence_starts_during": "RO:0002488", "existence_ends_during": "RO:0002492", "towards": "RO:0002503", "translates_to": "RO:0002513", "has subsequence": "RO:0002524", "is subsequence of": "RO:0002525", "is upstream of sequence of": "RO:0002528", "is downstream of sequence of": "RO:0002529", "has evidence": "RO:0002558", "causally_influences": "RO:0002566", "existence starts at point": "RO:0002583", "existence ends at point": "RO:0002593", "is substance that treats": "RO:0002606", "is marker for": "RO:0002607", "correlates_with": "RO:0002610", "is_evidence_supported_by": "RO:0002614", "negatively_regulates": "RO:0003002", "positively_regulates": "RO:0003003", "is model of": "RO:0003301", "causes_or_contributes": "RO:0003302", "causes condition": "RO:0003303", "contributes to condition": "RO:0003304", "protective_for_condition": "RO:0003307", "is causal gain of function germline mutation of in": "RO:0004011", "is causal loss of function germline mutation of in": "RO:0004012", "is causal germline mutation in": "RO:0004013", "is causal somatic mutation in": "RO:0004014", "is causal susceptibility factor for": "RO:0004015", "is causal germline mutation partially giving rise to": "RO:0004016", # found in sepio_developer.owl: SEPIO:0000019 # is not found in sepio: SEPIO:0000111 -- # "Scientific Evidence and Provenance Information Ontology": "SEPIO:!!!", "assertion": "SEPIO:0000001", "assertion process": "SEPIO:0000003", "has_evidence_line": "SEPIO:0000006", "has_supporting_evidence_line": "SEPIO:0000007", "has_provenance": "SEPIO:0000011", "proposition_asserted_in": "SEPIO:0000015", "has_agent": "SEPIO:0000017", "created_by": "SEPIO:0000018", # "x-created_at_location": "SEPIO:0000019", "date_created": "SEPIO:0000021", "created_with_resource": "SEPIO:0000022", "is_evidence_for": "SEPIO:0000031", "is_supporting_evidence_for": "SEPIO:0000032", "is_refuting_evidence_for": "SEPIO:0000033", "assertion method": "SEPIO:0000037", "is_specified_by": "SEPIO:0000041", "is_evidence_with_support_from": "SEPIO:0000059", "research": "SEPIO:0000066", "clinical testing": "SEPIO:0000067", "case-control": "SEPIO:0000071", "in vitro": "SEPIO:0000073", "in vivo": "SEPIO:0000074", "literature only": "SEPIO:0000080", "curation": "SEPIO:0000081", "has_evidence_item": "SEPIO:0000084", "has_supporting_activity": "SEPIO:0000085", "is_equilavent_to": "SEPIO:0000098", "is_consistent_with": "SEPIO:0000099", "strongly_contradicts": "SEPIO:0000100", "contradicts": "SEPIO:0000101", "reference population": "SEPIO:0000102", "is_assertion_supported_by_evidence": "SEPIO:0000111", # "is_assertion_supported_by": "SEPIO:0000111", "measures_parameter": "SEPIO:0000114", "evidence_has_supporting_reference": "SEPIO:0000124", "is_inconsistent_with": "SEPIO:0000126", "asserted_by": "SEPIO:0000130", "assertion_confidence_level": "SEPIO:0000167", "confidence_score": "SEPIO:0000168", "phenotyping only": "SEPIO:0000186", # "has_evidence_with_item": "SEPIO:0000189", # "no assertion criteria provided": "SEPIO:9999990", # "no assertion provided": "SEPIO:9999991", # "criteria provided, single submitter": "SEPIO:9999992", # "criteria provided, conflicting interpretations": "SEPIO:9999993", # "criteria provided, multiple submitters, no conflicts": "SEPIO:9999994", # "reviewed by expert panel": "SEPIO:9999995", # "practice guideline": "SEPIO:9999996", # "Semanticscience Integrated Ontology": "SIO:!!!", "web page": "SIO:000302", "count": "SIO:000794", "race": "SIO:001015", # "Sequence Onrology": "SO:!!!", "region": "SO:0000001", # conflicts with faldo:Region "small cytoplasmic RNA": "SO:0000013", "processed_pseudogene": "SO:0000043", "antisense": "SO:0000077", "endogenous_retroviral_gene": "SO:0000100", "transposable_element": "SO:0000101", "polypeptide": "SO:0000104", "chromosome_arm": "SO:0000105", "sequence_feature": "SO:0000110", "transposable_element_gene": "SO:0000111", "genomically_imprinted": "SO:0000134", "assembly_component": "SO:0000143", "read": "SO:0000150", "deletion": "SO:0000159", "enhancer": "SO:0000165", "promoter": "SO:0000167", "retrotransposon": "SO:0000180", "translocation": "SO:0000199", "mature_transcript": "SO:0000233", "microsatellite": "SO:0000289", "CpG_island": "SO:0000307", "pseudogene": "SO:0000336", "RNAi_reagent": "SO:0000337", "chromosome": "SO:0000340", "chromosome_band": "SO:0000341", "ribozyme": "SO:0000374", "vault_RNA": "SO:0000404", "Y RNA": "SO:0000405", "binding_site": "SO:0000409", "chromosomal_transposition": "SO:0000453", "vertebrate_immunoglobulin_T_cell_receptor_segment": "SO:0000460", "pseudogenic_region": "SO:0000462", "centromere": "SO:0000577", "telomere": "SO:0000624", "minisatellite": "SO:0000643", "large_subunit_rRNA": "SO:0000651", "ncRNA": "SO:0000655", "insertion": "SO:0000667", "SNP": "SO:0000694", "experimental_result_region": "SO:0000703", "gene": "SO:0000704", "cDNA": "SO:0000756", "QTL": "SO:0000771", "transgenic": "SO:0000781", "transgenic_transposable_element": "SO:0000796", "fusion": "SO:0000806", "wild_type": "SO:0000817", "chromosome_part": "SO:0000830", "stop codon readthrough": "SO:0000883", "transgene": "SO:0000902", # not really used any more "endogenous_retroviral_sequence": "SO:0000903", "integration_excision_site": "SO:0000946", "haplotype": "SO:0001024", "genome": "SO:0001026", "diplotype": "SO:0001028", "transcriptional_cis_regulatory_region": "SO:0001055", "sequence_alteration": "SO:0001059", "sequence_variant": "SO:0001060", "protein_coding_gene": "SO:0001217", "transgenic_insertion": "SO:0001218", "TSS_region": "SO:0001240", "ncRNA_gene": "SO:0001263", "miRNA_gene": "SO:0001265", "scRNA_gene": "SO:0001266", "snoRNA_gene": "SO:0001267", "snRNA_gene": "SO:0001268", "SRP_RNA_gene": "SO:0001269", "tRNA_gene": "SO:0001272", "biological_region": "SO:0001411", "SNV": "SO:0001483", "heritable_phenotypic_marker": "SO:0001500", "processed_transcript": "SO:0001503", "reference_genome": "SO:0001505", "gene_variant": "SO:0001564", "regulatory_region_variant": "SO:0001566", "splice_acceptor_variant": "SO:0001574", "splice_donor_variant": "SO:0001575", "stop_lost": "SO:0001578", "coding_sequence_variant": "SO:0001580", "missense_variant": "SO:0001583", "stop_gained": "SO:0001587", "frameshift_variant": "SO:0001589", "non_coding_transcript_exon_variant": "SO:0001619", "mature_miRNA_variant": "SO:0001620", "UTR_variant": "SO:0001622", "5_prime_UTR_variant": "SO:0001623", "3_prime_UTR_variant": "SO:0001624", "intron_variant": "SO:0001627", "intergenic_variant": "SO:0001628", "splice_region_variant": "SO:0001630", "downstream_gene_variant": "SO:0001634", "upstream_gene_variant": "SO:0001636", "rRNA_gene": "SO:0001637", "piRNA_gene": "SO:0001638", "RNase_P_RNA_gene": "SO:0001639", "RNase_MRP_RNA_gene": "SO:0001640", "lincRNA_gene": "SO:0001641", "telomerase_RNA_gene": "SO:0001643", "genetic_marker": "SO:0001645", "inframe_variant": "SO:0001650", "score": "SO:0001685", # FIXME - score is not a good solution too generic "pseudogenic_gene_segment": "SO:0001741", "copy_number_gain": "SO:0001742", "copy_number_loss": "SO:0001743", "unitary_pseudogene": "SO:0001759", "unprocessed_pseudogene": "SO:0001760", "TF_binding_site_variant": "SO:0001782", "complex_structural_alteration": "SO:0001784", "structural_alteration": "SO:0001785", "non_coding_exon_variant": "SO:0001792", "protein_altering_variant": "SO:0001818", "synonymous_variant": "SO:0001819", "inframe_insertion": "SO:0001821", "inframe_deletion": "SO:0001822", "mobile_element_insertion": "SO:0001837", "novel_sequence_insertion": "SO:0001838", "polymorphic_pseudogene": "SO:0001841", "lnc_RNA": "SO:0001877", "feature_fusion": "SO:0001882", "transposable_element_pseudogene": "SO:0001897", "antisense_lncRNA": "SO:0001904", "MNV": "SO:0002007", "start_lost": "SO:0002012", "vaultRNA_primary_transcript": "SO:0002040", "dominant_negative_variant": "SO:0002052", "gain_of_function_variant": "SO:0002053", "loss_of_function_variant": "SO:0002054", "scaRNA": "SO:0002095", "immunoglobulin_pseudogene": "SO:0002098", "T_cell_receptor_pseudogene": "SO:0002099", "IG_C_pseudogene": "SO:0002100", "IG_J_pseudogene": "SO:0002101", "IG_V_pseudogene": "SO:0002102", "TR_V_pseudogene": "SO:0002103", "TR_J_pseudogene": "SO:0002104", "translated_unprocessed_pseudogene": "SO:0002106", "transcribed_unprocessed_pseudogene": "SO:0002107", "transcribed_unitary_pseudogene": "SO:0002108", "transcribed_processed_pseudogene": "SO:0002109", "3prime_overlapping_ncRNA": "SO:0002120", "immunoglobulin_gene": "SO:0002122", "IG_C_gene": "SO:0002123", "IG_D_gene": "SO:0002124", "IG_J_gene": "SO:0002125", "IG_V_gene": "SO:0002126", "lncRNA_gene": "SO:0002127", "mt_rRNA": "SO:0002128", "mt_tRNA": "SO:0002129", "sense_intronic": "SO:0002131", "sense_overlapping": "SO:0002132", "TR_C_gene": "SO:0002134", "TR_D_gene": "SO:0002135", "TR_J_gene": "SO:0002136", "TR_V_gene": "SO:0002137", "TEC": "SO:0002139", "ribozyme_gene": "SO:0002181", "sense_overlap_ncRNA_gene": "SO:0002183", "sense_intronic_ncRNA_gene": "SO:0002184", "bidirectional_promoter_lncRNA": "SO:0002185", "substitution": "SO:1000002", "complex_substitution": "SO:1000005", "point_mutation": "SO:1000008", "chromosomal_deletion": "SO:1000029", "chromosomal_inversion": "SO:1000030", "indel": "SO:1000032", "duplication": "SO:1000035", "inversion": "SO:1000036", "chromosomal_duplication": "SO:1000037", "direct_tandem_duplication": "SO:1000039", "Robertsonian_fusion": "SO:1000043", "chromosomal_translocation": "SO:1000044", "reciprocal_chromosomal_translocation": "SO:1000048", "sequence_variant_affecting_polypeptide_function": "SO:1000117", "sequence_variant_causing_loss_of_function_of_polypeptide": "SO:1000118", "sequence_variant_causing_inactive_catalytic_site": "SO:1000120", "sequence_variant_causing_gain_of_function_of_polypeptide": "SO:1000125", "tandem_duplication": "SO:1000173", "chromosome_structure_variation": "SO:1000183", "gene_segment": "SO:3000000", # "Statistics Ontology": "STATO:!!!", "Fisher's exact test": "STATO:0000073", "Mann-Whitney U-test": "STATO:0000076", "effect size estimate": "STATO:0000085", "zscore": "STATO:0000104", "statistical model": "STATO:0000107", "has_value": "STATO:0000129", "fold change": "STATO:0000169", "odds_ratio": "STATO:0000182", "mixed_model": "STATO:0000189", "generalized least squares estimation": "STATO:0000372", # "SWO": "SWO:!!!" _NOT_ in curie_map "Similarity score": "SWO:0000425", # "Integrated anatomy ontology (metazoan)": "UBERON:!!!", # "existence_ends_at ": "UBERON:existence_ends_at ", # "existence_starts_at ": "UBERON:existence_starts_at ", # "Integrated phenotype ontology, and normal traits": "UPHENO:!!!", "phenotype": "UPHENO:0001001", # conflicts with FBcv:0001347 # "ontology for representing scholarship": "VIVO:!!!", "project": "VIVO:Project", # "Vocabulary of Interlinked Datasets": "void:!!!", "class (void)": "void:class", "classPartition": "void:classPartition", "distinctObjects": "void:distinctObjects", "distinctSubjects": "void:distinctSubjects", "entities": "void:entities", "properties": "void:properties", "triples": "void:triples", # "Experimental Conditions Ontology": "XCO:!!!", "environmental_condition": "XCO:0000000"} # keep terminal closing brace on last line