---
# 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",
# "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",
# "dublin core terms": "dcterms:!!!",
"identifier": "dcterms:identifier",
"title": "dcterms:title",
# "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",
"short_chromosome_arm": "GENO:0000628",
"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",
"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",
"Cone–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",
# "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",
# "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_evidence_item_output_from": "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",
"phenotyping only": "SEPIO:0000186",
# "has_evidence_with_item": "SEPIO:0000189",
# "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",
# "Experimental Conditions Ontology": "XCO:!!!",
"environmental_condition": "XCO:0000000"}  # keep terminal closing brace on last line
