@prefix rdf: . @prefix : . @prefix dc: . @prefix obo: . @prefix owl: . @prefix xml: . @prefix xsd: . @prefix foaf: . @prefix rdfs: . @prefix terms: . @prefix linkml: . @prefix oboInOwl: . @prefix odes_field: . @prefix temp_import: . obo:IAO_0000115 "A persistent, unique identifier of a molecular sequence database entry."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000412 "EDAM" ; a owl:Class ; rdfs:label "sequence accession"@en ; rdfs:subClassOf obo:GENEPIO_0001800 . obo:IAO_0000115 "The name of a field in a database."@en ; a owl:Class ; rdfs:label "database field name"@en ; rdfs:subClassOf obo:IAO_0000577 . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001247 . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001247 . obo:IAO_0000114 obo:IAO_0000428 ; rdfs:subClassOf obo:GENEPIO_0001568 . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001247 . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001247 . obo:APOLLO_SV_00000016 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000017 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000019 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000020 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000021 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000022 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000031 a owl:Class ; rdfs:subClassOf obo:IAO_0000027 . obo:APOLLO_SV_00000033 rdfs:subClassOf obo:OBI_0000011 . obo:APOLLO_SV_00000098 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000099 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000153 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002148 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:APOLLO_SV_00000240 ] ) ] ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001925 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0000181 ], [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002144 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:STATO_0000047 ] ) ] ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:APOLLO_SV_00000173 a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:APOLLO_SV_00000240 ] . obo:APOLLO_SV_00000194 a owl:Class ; rdfs:subClassOf obo:IAO_0000033 . obo:APOLLO_SV_00000211 a owl:Class ; rdfs:subClassOf obo:IAO_0000027 . obo:APOLLO_SV_00000236 a owl:Class ; rdfs:subClassOf obo:IDO_0000531 . obo:APOLLO_SV_00000240 a owl:Class ; rdfs:subClassOf obo:OBI_0001508 . obo:APOLLO_SV_00000258 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000267 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000280 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000281 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:APOLLO_SV_00000291 a owl:Class ; rdfs:subClassOf . obo:APOLLO_SV_00000498 a owl:Class . obo:APOLLO_SV_00000511 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001272 . obo:ARO_3004299 a owl:Class ; rdfs:subClassOf obo:BFO_0000019, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000581 ] . obo:ARO_3004300 obo:GENEPIO_0000006 "intermediate"@en ; oboInOwl:hasAlternativeId "I"@en . obo:ARO_3004301 obo:GENEPIO_0000006 "resistant"@en ; oboInOwl:hasAlternativeId "R"@en . obo:ARO_3004302 obo:GENEPIO_0000006 "susceptible"@en ; oboInOwl:hasAlternativeId "S"@en ; oboInOwl:hasExactSynonym "sensitive"@en . obo:ARO_3004303 obo:GENEPIO_0000006 "nonsusceptible"@en ; oboInOwl:hasAlternativeId "NS"@en ; oboInOwl:hasExactSynonym "nonsensitive"@en . obo:ARO_3004304 obo:GENEPIO_0000006 "susceptible - dose dependent"@en ; oboInOwl:hasAlternativeId "SSD"@en ; oboInOwl:hasExactSynonym "sensitive - dose dependent"@en . obo:ARO_3004305 a owl:Class ; rdfs:subClassOf obo:ARO_3004299 . obo:ARO_3004360 rdfs:subClassOf obo:IAO_0000033 . obo:ARO_3004365 oboInOwl:hasAlternativeId "BSAC"^^rdfs:Literal . obo:ARO_3004366 oboInOwl:hasAlternativeId "CLSI"^^rdfs:Literal ; oboInOwl:hasExactSynonym "NCCLS"@en, "National Committee on Clinical Laboratory Standards (NCCLS)"@en ; a owl:Class ; rdfs:comment "On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI"@en . obo:ARO_3004367 oboInOwl:hasAlternativeId "DIN"^^rdfs:Literal . obo:ARO_3004368 oboInOwl:hasAlternativeId "EUCAST"^^rdfs:Literal . obo:ARO_3004369 oboInOwl:hasAlternativeId "SFM"^^rdfs:Literal . obo:ARO_3004371 a owl:Class ; rdfs:subClassOf obo:IAO_0000109 . obo:ARO_3004372 a owl:Class ; rdfs:subClassOf obo:IAO_0000109 . obo:ARO_3004388 a owl:Class ; rdfs:subClassOf obo:OBI_0000070 . obo:ARO_3004390 rdfs:subClassOf obo:OBI_0000968 . obo:ARO_3004391 a owl:Class ; rdfs:subClassOf obo:NCIT_C85540 . obo:ARO_3004397 a owl:Class ; rdfs:subClassOf obo:NCIT_C85540 . obo:ARO_3004404 rdfs:subClassOf obo:NCIT_C25392 . obo:ARO_3004430 obo:GENEPIO_0001763 "depth:1"^^rdfs:Literal ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:ARO_3004431 rdfs:subClassOf obo:ARO_3004299 . obo:ARO_3004440 obo:GENEPIO_0001763 """order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant"""^^rdfs:Literal ; rdfs:subClassOf obo:ARO_3004299 . obo:BFO_0000008 rdfs:comment "Damion Dooley's note: this BFO class is incompatible with \"immaterial entity\" \"n-dimensional concept\"."@en . obo:BFO_0000019 oboInOwl:hasDbXref "http://purl.obolibrary.org/obo/PATO_0000001"^^xsd:anyURI . obo:BFO_0000023 oboInOwl:hasDbXref "http://purl.obolibrary.org/obo/CHEBI_50906"^^xsd:anyURI . obo:BFO_0000029 rdfs:comment "Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface."@en . obo:BFO_0000050 a owl:ObjectProperty ; rdfs:label "part of"@en . obo:BFO_0000051 a owl:ObjectProperty ; rdfs:comment "Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions."@en . obo:BFO_0000054 a owl:ObjectProperty ; rdfs:label "realized in"@en . obo:BFO_0000067 a owl:ObjectProperty . obo:BTO_0000003 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0000067 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0000155 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:BTO_0000353 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0000578 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0000711 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0001120 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0001762 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:BTO_0002181 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0002637 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0002886 rdfs:subClassOf obo:CLO_0000031 . obo:BTO_0004755 rdfs:subClassOf obo:CLO_0000031 . obo:CHEBI_124991 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_134742 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_134958 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_135278 obo:IAO_0000118 "Trd" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_16991 a owl:Class ; rdfs:label "deoxyribonucleic acid"@en ; rdfs:subClassOf obo:CHEBI_33696 . obo:CHEBI_17076 obo:IAO_0000118 "STR", "Sm", "Stm" ; rdfs:subClassOf obo:GENEPIO_0001097, obo:GENEPIO_0002071 . obo:CHEBI_17154 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_17334 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_17939 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_209807 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_22582 obo:IAO_0100001 "http://purl.obolibrary.org/obo/CHEBI_33281"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antibiotic"@en ; owl:deprecated true . obo:CHEBI_23066 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_23367 rdfs:subClassOf obo:CHEBI_24431 . obo:CHEBI_24431 rdfs:subClassOf obo:BFO_0000040 . obo:CHEBI_24531 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_25585 rdfs:subClassOf obo:CHEBI_33250 . obo:CHEBI_26144 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_2637 obo:IAO_0000118 "Am", "Amk" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_26513 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_2676 obo:IAO_0000118 "Amx" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_27565 obo:IAO_0000118 "PAS" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_2790 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_27933 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_28077 obo:IAO_0000118 "Rif" ; rdfs:subClassOf obo:GENEPIO_0002071 . obo:CHEBI_281056 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_28368 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_28659 rdfs:subClassOf obo:CHEBI_25585, obo:CHEBI_33300 . obo:CHEBI_29007 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_29673 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_32066 obo:IAO_0000118 "Pto" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_33290 obo:GENEPIO_0000006 "food role"@en . obo:CHEBI_33300 rdfs:subClassOf obo:CHEBI_33560 . obo:CHEBI_33318 rdfs:subClassOf obo:CHEBI_33250 . obo:CHEBI_33560 rdfs:subClassOf obo:CHEBI_33318 . obo:CHEBI_3371 obo:IAO_0000118 "CAP", "Cm" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_35991 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_36420 rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_3716 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_3732 obo:IAO_0000118 "Clr" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_3749 obo:IAO_0000118 "Cfz" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_3907 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_39447 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_40009 obo:IAO_0000118 "CYC", "Cs" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_45285 obo:GENEPIO_0000006 "pyrazinamide"@en ; obo:IAO_0000118 "Pza" ; rdfs:subClassOf obo:GENEPIO_0002071 . obo:CHEBI_45367 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_46633 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_46770 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_471744 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_4877 obo:IAO_0000118 "E", "ETB", "Emb" ; rdfs:subClassOf obo:GENEPIO_0002071 . obo:CHEBI_487869 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_4885 obo:IAO_0000118 "ETH", "Eto" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001097, obo:GENEPIO_0001187 . obo:CHEBI_5195 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_5280 rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_59132 obo:IAO_0000116 "Currently \"K antigen\" is a CHEBI_73772 chemical entity rather than a role."@en ; rdfs:seeAlso "K antigen"@en . obo:CHEBI_599928 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_6030 obo:IAO_0000118 "Inh", "isoniazid"@en ; rdfs:subClassOf obo:GENEPIO_0002071 . obo:CHEBI_60584 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_6104 obo:IAO_0000118 "Kan" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_63598 obo:IAO_0000118 "Lfx" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_63607 obo:IAO_0000118 "Lzd" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001097, obo:GENEPIO_0001187 . obo:CHEBI_63611 obo:IAO_0000118 "MXF", "Mfx" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001097, obo:GENEPIO_0001187 . obo:CHEBI_63845 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_68452 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_7025 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_71415 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_72292 obo:IAO_0000118 "Bdq" ; rdfs:subClassOf obo:GENEPIO_0001097 . obo:CHEBI_73772 obo:IAO_0000116 "Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role."@en ; oboInOwl:hasDbXref "Snomed: Concept 260824002" ; rdfs:seeAlso obo:CHEBI_59132 ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0000087 ; owl:someValuesFrom obo:CHEBI_59132 ] . obo:CHEBI_75246 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_7731 obo:IAO_0000118 "Ofx" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001097, obo:GENEPIO_0001187 . obo:CHEBI_86324 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_86478 rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_87211 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_87228 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_87230 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_9215 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_9321 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_9421 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_9587 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHEBI_9997 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:CHMO_0000993 a owl:Class . obo:CHMO_0002743 obo:GENEPIO_0000006 "specimen extraction matrix"@en ; a owl:Class ; rdfs:comment "\"This observable is important where process of capturing sample can affect dna extraction.\""@en . obo:CLO_0000031 a owl:Class . obo:CVDO_0000597 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001843 . obo:DOID_10690 rdfs:subClassOf obo:ARO_3004430 . obo:DOID_13148 rdfs:subClassOf obo:ARO_3004430 . obo:DOID_1579 rdfs:subClassOf obo:ARO_3004430 . obo:DOID_3044 rdfs:subClassOf obo:GENEPIO_0001205, obo:OBI_1110049 . obo:DOID_37 rdfs:subClassOf obo:ARO_3004430 . obo:DOID_4 oboInOwl:hasDbXref "http://purl.obolibrary.org/obo/OGMS_0000031"^^xsd:anyURI ; rdfs:subClassOf obo:BFO_0000016 . obo:DOID_7 rdfs:subClassOf obo:DOID_4 . obo:DOID_9471 oboInOwl:hasDbXref obo:IAO_0000120 ; rdfs:subClassOf obo:GENEPIO_0001682 . obo:ENVO_00000002 obo:GENEPIO_0000006 "constructed feature"@en . obo:ENVO_00000004 rdfs:subClassOf obo:BFO_0000029 . obo:ENVO_00000005 obo:GENEPIO_0000006 "state / province / territory / region"@en ; obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; a owl:Class ; rdfs:subClassOf , [ a owl:Restriction ; owl:onProperty obo:RO_0001025 ; owl:someValuesFrom obo:NCIT_C25464 ] . obo:ENVO_00000009 oboInOwl:hasExactSynonym "http://purl.obolibrary.org/obo/NCIT_C25464"@en . obo:ENVO_00000014 rdfs:subClassOf obo:ENVO_00000121 . obo:ENVO_00000015 rdfs:subClassOf obo:GENEPIO_0001151 . obo:ENVO_00000020 rdfs:subClassOf obo:GENEPIO_0001151 . obo:ENVO_00000023 rdfs:subClassOf obo:GENEPIO_0001151 . obo:ENVO_00000027 rdfs:subClassOf obo:GENEPIO_0001151 . obo:ENVO_00000042 rdfs:subClassOf obo:ENVO_00000070 . obo:ENVO_00000068 rdfs:subClassOf obo:ENVO_00000191 . obo:ENVO_00000078 rdfs:subClassOf obo:GENEPIO_0001269 . obo:ENVO_00000080 rdfs:subClassOf obo:ENVO_00000478 . obo:ENVO_00000428 a owl:Class . obo:ENVO_00000450 oboInOwl:hasExactSynonym "irrigation pond"@en . obo:ENVO_00000856 oboInOwl:hasExactSynonym "http://purl.obolibrary.org/obo/NCIT_C80234"@en . obo:ENVO_00002003 oboInOwl:hasExactSynonym "stool"@en . obo:ENVO_00002170 rdfs:subClassOf obo:GENEPIO_0002016 . obo:ENVO_00002173 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_00002191 oboInOwl:hasNarrowSynonym "straw bedding"@en ; rdfs:seeAlso "http://opendata.inra.fr/EOL/EOL_0001601#bedding"^^xsd:anyURI . obo:ENVO_00002222 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_00002272 rdfs:subClassOf obo:ENVO_00000070 . obo:ENVO_00003096 rdfs:subClassOf obo:GENEPIO_0001154 . obo:ENVO_00003864 rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_00010483 a owl:Class . obo:ENVO_01000254 a owl:Class . obo:ENVO_01000486 rdfs:subClassOf obo:ENVO_00000070 . obo:ENVO_01000703 a owl:Class . obo:ENVO_01000753 owl:deprecated true . obo:ENVO_01000922 oboInOwl:hasNarrowSynonym "chicken cage"@en . obo:ENVO_01000923 rdfs:subClassOf obo:GENEPIO_0001269, obo:GENEPIO_0001274 . obo:ENVO_01000932 rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_01000934 rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_01000974 rdfs:subClassOf obo:GENEPIO_0001274 . obo:ENVO_01000986 rdfs:subClassOf obo:GENEPIO_0001269 . obo:ENVO_01000987 rdfs:subClassOf obo:GENEPIO_0001274 . obo:EO_0007027 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:EO_0007033 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007034 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007035 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007036 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007037 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007038 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007285 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EO_0007286 a owl:Class ; rdfs:subClassOf obo:EO_0007027 . obo:EPO_0000016 obo:IAO_0000115 "Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water."@en ; a owl:Class ; rdfs:label "common vehicle transmission"@en ; rdfs:subClassOf obo:TRANS_0000002 . obo:ERO_0000833 a owl:Class ; rdfs:subClassOf obo:OBI_0000070 . obo:ERO_0001183 rdfs:subClassOf obo:OBI_0000626 . obo:ERO_0001286 a owl:Class ; rdfs:subClassOf obo:ERO_0000833 . obo:ERO_0001642 oboInOwl:hasDbXref "NCBI SRA: ION_TORRENT" . obo:ERO_0001965 obo:IAO_0000115 "A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)" ; a owl:Class ; rdfs:label "experimental subject role" ; rdfs:subClassOf obo:GENEPIO_0001537 . obo:ExO_0000038 obo:GENEPIO_0001763 "depth:1" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Medical_state"@en ; oboInOwl:hasExactSynonym "condition"@en, "medical condition"@en, "medical state"@en ; a owl:Class ; rdfs:comment "Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed."@en ; rdfs:seeAlso "http://semanticscience.org/resource/SIO_010057"^^xsd:anyURI ; rdfs:subClassOf obo:GENEPIO_0001170, [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001837 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001845 ] . obo:ExO_0000057 obo:IAO_0000115 "The process of drawing in by breathing."@en ; obo:IAO_0000412 "http://purl.obolibrary.org/obo/ExO_0000057"@en ; a owl:Class ; rdfs:label "inhalation"@en ; rdfs:subClassOf obo:EPO_0000016 . obo:FIX_0000278 obo:IAO_0000115 "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"@en ; obo:IAO_0000119 "MIxS"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:FLU_0000976 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "symptom onset date"@en ; rdfs:subClassOf obo:GENEPIO_0001258 . obo:FOODON_00001002 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure."^^xsd:string ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "foodon product type"@en ; rdfs:subClassOf obo:FOODON_03400361 . obo:FOODON_00002381 obo:GENEPIO_0001763 "lookup" ; a owl:Class . obo:FOODON_00002403 a owl:Class ; rdfs:subClassOf obo:ENVO_00010483 . obo:FOODON_03311737 obo:GENEPIO_0001763 "lookup" ; a owl:Class . obo:FOODON_03400361 a owl:Class ; rdfs:subClassOf obo:BFO_0000040 . obo:FOODON_03411297 a owl:Class . obo:FOODON_03411347 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002016 . obo:FOODON_03411564 a owl:Class ; rdfs:subClassOf obo:ENVO_00010483 . obo:FOODON_03412612 oboInOwl:hasSynonym "asian tiger shrimp"@en, "black tiger shrimp"@en . obo:FOODON_03420116 obo:GENEPIO_0001763 "lookup" ; a owl:Class . obo:FOODON_03430113 a owl:Class . obo:FOODON_03440011 a owl:Class . obo:FOODON_03450002 a owl:Class . obo:FOODON_03460111 a owl:Class . obo:FOODON_03470107 a owl:Class . obo:FOODON_03480020 obo:GENEPIO_0000006 "food packing medium"@en ; a owl:Class . obo:FOODON_03490100 a owl:Class . obo:FOODON_03500010 a owl:Class . obo:FOODON_03510032 a owl:Class . obo:FOODON_03510136 a owl:Class . obo:FOODON_03530050 a owl:Class . obo:FOODON_03530146 a owl:Class . obo:FOODON_03530153 oboInOwl:hasSynonym "gathered"@en, "wild"@en . obo:FOODON_03530206 a owl:Class . obo:GAZ_00000013 a owl:Class ; rdfs:subClassOf obo:GAZ_00000448 . obo:GAZ_00000106 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00000448 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001886 . obo:GAZ_00000457 a owl:Class ; rdfs:subClassOf obo:GAZ_00000013 . obo:GAZ_00000458 a owl:Class ; rdfs:subClassOf obo:GAZ_00000013 . obo:GAZ_00000459 a owl:Class ; rdfs:subClassOf obo:GAZ_00000013 . obo:GAZ_00000460 a owl:Class ; rdfs:subClassOf obo:GAZ_00000013 . obo:GAZ_00000462 a owl:Class ; rdfs:subClassOf obo:GAZ_00000013 . obo:GAZ_00000590 obo:GENEPIO_0000006 "[Oceans and Seas]"@en ; rdfs:subClassOf obo:NCIT_C25464 . obo:GAZ_00000641 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00001016 a owl:Class ; rdfs:subClassOf obo:NCIT_C89811 . obo:GAZ_00001018 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_00001066 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00001508 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00002459 rdfs:subClassOf obo:NCIT_C25464 . obo:GAZ_00002547 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00002561 a owl:Class, owl:NamedIndividual ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00002562 a owl:NamedIndividual . obo:GAZ_00002573 a owl:Class ; rdfs:subClassOf obo:NCIT_C89811 . obo:GAZ_00002574 a owl:Class . obo:GAZ_00002575 a owl:Class . obo:GAZ_00002576 a owl:Class . obo:GAZ_00002616 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002648 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002651 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002705 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002718 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002734 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002756 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002784 a owl:Class ; rdfs:subClassOf obo:NCIT_C89811 . obo:GAZ_00002785 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_00002805 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00002810 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00002826 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002831 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002840 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_00002844 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002848 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001742 . obo:GAZ_00002855 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00002857 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_00002896 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003034 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003092 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Census Regions and Divisions are groupings of States that subdivide the United States."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "United States Census Bureau"@en ; a owl:Class ; rdfs:seeAlso "http://www.census.gov/econ/census/help/geography/regions_and_divisions.html" ; rdfs:subClassOf obo:GENEPIO_0001742 . obo:GAZ_00003093 obo:IAO_0000115 "A census region in the United States of America"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GAZ_00003092 . obo:GAZ_00003094 obo:IAO_0000115 "A census region in the United States of America"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GAZ_00003092 . obo:GAZ_00003095 obo:IAO_0000115 "A census region in the United States of America"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GAZ_00003092 . obo:GAZ_00003096 obo:IAO_0000115 "A census region in the United States of America"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GAZ_00003092 . obo:GAZ_00003108 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003138 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003176 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003192 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003194 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003198 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00003199 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003201 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001742 . obo:GAZ_00003204 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00003214 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00003269 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003287 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003382 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003603 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00003626 a owl:Class ; 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rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008577 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008583 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008595 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008622 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008678 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00008796 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00008835 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00009150 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_00009152 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00009238 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009419 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009431 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009433 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009461 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009465 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009509 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009554 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00009573 a owl:Class ; rdfs:subClassOf obo:GAZ_00000448 . obo:GAZ_00009715 a owl:Class ; rdfs:subClassOf obo:GAZ_00000448 . obo:GAZ_00009905 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00009998 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010010 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010069 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010088 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010090 obo:GENEPIO_0000006 "directly governed city (North Korea)"@en ; a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010130 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010365 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010408 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00010410 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00011335 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00012231 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013569 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013579 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013726 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013817 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013864 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013888 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00013955 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00014914 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_00016203 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_00049570 a owl:Class ; rdfs:subClassOf obo:GAZ_00000448 . obo:GAZ_00051448 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_02000609 a owl:Class ; rdfs:subClassOf obo:NCIT_C89811 . obo:GAZ_02000896 a owl:Class ; rdfs:subClassOf obo:NCIT_C87194 . obo:GAZ_03000061 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_04000000 a owl:Class ; rdfs:subClassOf obo:NCIT_C25632 . obo:GAZ_07000033 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GAZ_07000054 a owl:Class ; rdfs:subClassOf obo:NCIT_C80234 . obo:GENEPIO_0000001 a owl:AnnotationProperty ; rdfs:label "metadata section"@en . obo:GENEPIO_0000002 obo:GENEPIO_0000006 "GSCID-BRC standard"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases."@en ; obo:IAO_0000116 """The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards"""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000600 "This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists."@en ; a owl:Class ; rdfs:label "GSCID-BRC Project and Sample Application Standard"@en ; rdfs:subClassOf obo:GENEPIO_0002073 . obo:GENEPIO_0000003 obo:GENEPIO_0000006 "MIxS standard"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "Minimum Information about any (x) Sequence (MIxS)"@en ; rdfs:subClassOf obo:GENEPIO_0002075 . obo:GENEPIO_0000004 a owl:AnnotationProperty ; rdfs:label "term as in existing standard"@en . obo:GENEPIO_0000005 a owl:AnnotationProperty ; rdfs:label "term source"@en . obo:GENEPIO_0000006 obo:IAO_0000115 "The user interface label is the label that should be placed on a datum when presented on a form or report"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:AnnotationProperty ; rdfs:label "user interface label"@en . obo:GENEPIO_0000008 obo:GENEPIO_0000006 "MIMARKS standard"@en ; obo:IAO_0000115 "The \"minimum information about a marker gene sequence\" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences."@en ; obo:IAO_0000119 "http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html"^^xsd:anyURI ; a owl:Class ; rdfs:label "Minimum information about a marker gene sequence"@en ; rdfs:subClassOf obo:GENEPIO_0002075 . obo:GENEPIO_0000009 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "\"other (metadata choice)\" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed."@en ; obo:IAO_0000116 "This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "other (metadata value)"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0000010 a owl:Class ; rdfs:label "other relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0000011 obo:GENEPIO_0000006 "other"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Other: specify the sample scope that was used."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/" ; a owl:Class ; rdfs:label "other specimen scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0000012 obo:GENEPIO_0000006 "other material"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Other: specify the material that was used."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "other material derived from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0000013 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "\"other capture type\" is a free text description provided to indicate a target capture specification not covered by the other types."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "other capture type"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0000014 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Specify the project method"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "other project method"@en ; rdfs:subClassOf obo:OBI_0001896 . obo:GENEPIO_0000015 obo:IAO_0000115 "This is an organizational category for grouping parameters relevant to a biomedical sample."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 obo:GENEPIO_0002083 ; a owl:Class ; rdfs:label "obsolete: draft GenEpiO BioSample standard"@en ; owl:deprecated true . obo:GENEPIO_0000016 obo:IAO_0000115 "An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 obo:GENEPIO_0001007 ; a owl:Class ; rdfs:label "obsolete: NCBI antibiogram data item"@en ; owl:deprecated true . obo:GENEPIO_0000017 obo:GENEPIO_0000006 "HIPPA PHI guideline"@en ; obo:IAO_0000115 """The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above.\""""@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act"^^xsd:anyURI ; a owl:Class ; rdfs:label "American HIPPA Protected Health Information (PHI) guidelines"@en ; rdfs:subClassOf obo:GENEPIO_0001743 . obo:GENEPIO_0000018 obo:IAO_0000115 "The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001567"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: subject species"@en ; owl:deprecated true . obo:GENEPIO_0000019 obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C45908"^^xsd:anyURI ; oboInOwl:hasDbXref "NCBI BioSample: intersex"@en ; a owl:Class ; rdfs:label "obsolete: intersex"@en ; owl:deprecated true . obo:GENEPIO_0000020 obo:GENEPIO_0000004 "Isolation date" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000115 "date the strain was isolated" ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000021"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: isolation date"@en ; owl:deprecated true . obo:GENEPIO_0000021 obo:GENEPIO_0000001 "Collection" ; obo:GENEPIO_0000004 "Culture isolation date" ; obo:GENEPIO_0000005 "suggested in metadata feedback" ; obo:IAO_0000112 "year/month/day" ; obo:IAO_0000115 "A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Morag)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "culture isolation date"@en ; rdfs:subClassOf obo:GENEPIO_0001491 . obo:GENEPIO_0000022 obo:GENEPIO_0000001 "Collection" ; obo:GENEPIO_0000004 "Frozen date" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "year/month/day"@en ; obo:IAO_0000115 "A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "culture frozen date"@en ; rdfs:subClassOf obo:GENEPIO_0001491 . obo:GENEPIO_0000023 obo:GENEPIO_0000001 "Collection" ; obo:GENEPIO_0000004 "Received date" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "year/month/day" ; obo:IAO_0000115 "date lab received isolate" ; obo:IAO_0000119 "NML LIMS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "isolate received date"@en ; rdfs:subClassOf obo:GENEPIO_0001491 . obo:GENEPIO_0000024 obo:GENEPIO_0000001 "Collection" ; obo:GENEPIO_0000004 "Upload date" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "month/day/year" ; obo:IAO_0000115 "date the isolate was entered into the database" ; obo:IAO_0000119 "NML LIMS" ; oboInOwl:hasDbXref "PulseNet: UploadDate" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "isolate upload date"@en ; rdfs:subClassOf obo:GENEPIO_0001491 . obo:GENEPIO_0000025 obo:GENEPIO_0000001 "Pathogen Isolate" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000112 "gut, spine, tongue, lung"@en ; obo:IAO_0000115 "Name of body site where the specimen was obtained from, such as a specific organ or tissue."@en ; obo:IAO_0000116 "Damion Dooley's note: Although term mentions \"site\" in label, this cannot be placed under \"site\" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise."@en ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "subject anatomical site"@en ; rdfs:seeAlso "http://gensc.org/ns/mixs/host_body_site"^^xsd:anyURI ; rdfs:subClassOf obo:CHMO_0000993, [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:GENEPIO_0002077 ] . obo:GENEPIO_0000026 obo:GENEPIO_0001763 "depth:1"@en, """order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased"""@en ; obo:IAO_0000112 "diseased" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Health or disease status of a given subject at time of specimen collection."@en ; obo:IAO_0000116 "Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject health status at time of specimen collection"@en ; rdfs:subClassOf obo:GENEPIO_0001222 . obo:GENEPIO_0000027 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:IAO_0000112 "sediment, chicken feces, cheese" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived." ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NCBI Biosample" ; a owl:Class ; rdfs:label "specimen source context"@en ; rdfs:subClassOf obo:GENEPIO_0001790, [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0002174 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001297 ] ) ] ; owl:onProperty obo:RO_0002180 ] . obo:GENEPIO_0000028 obo:GENEPIO_0000001 "Pathogen Isolate" ; obo:IAO_0000112 "feces, cerebral spinal fluid (CSF)" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject body product"@en ; rdfs:subClassOf obo:CHMO_0000993, [ a owl:Restriction ; owl:onProperty obo:RO_0003001 ; owl:someValuesFrom obo:GENEPIO_0002077 ] . obo:GENEPIO_0000029 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Geographic location depth" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "value (5m)" ; obo:IAO_0000115 "Please refer to the definitions of depth in the environmental packages" ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "collection depth datum"@en ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000030 obo:IAO_0000115 "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_00010483"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: specimen source environmental material"@en ; owl:deprecated true . obo:GENEPIO_0000031 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "Gender is not used because it is a term referencing human social and cultural convention."@en ; rdfs:label "subject sex specification"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:PATO_0001894 ] . obo:GENEPIO_0000032 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Land use where sample was taken" ; obo:GENEPIO_0000005 "Environment Canada Metadata" ; obo:IAO_0000112 "descriptive; type of human use (park, farm, urban)" ; obo:IAO_0000115 "Human use of land involving the management and modification of natural environment or wilderness into built environment." ; obo:IAO_0000119 "URI: http://en.wikipedia.org/wiki/Land_use" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "specimen collection site land use"@en ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000033 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Fecal Indicator Bacteria Number" ; obo:GENEPIO_0000005 "Environment Canada Metadata" ; obo:IAO_0000112 "12,456 cfu" ; obo:IAO_0000115 "Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens."@en ; obo:IAO_0000119 "URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "fecal indicator bacteria count"@en ; rdfs:subClassOf obo:STATO_0000047, [ a owl:Restriction ; owl:onProperty obo:IAO_0000039 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:UO_0000210 obo:UO_0000212 ) ] ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0002232 ] . obo:GENEPIO_0000034 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Conductivity" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "milliSiemens per centimeter" ; obo:IAO_0000115 "electrical conductivity of water" ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "conductivity measurement datum" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000035 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Dissolved oxygen" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "micromole per kilogram" ; obo:IAO_0000115 "concentration of dissolved oxygen" ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "dissolved oxygen concentration" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000036 obo:GENEPIO_0000006 "GMI MDM standard"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The Global Microbial Identifier \"Minimum data for Matching\" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "the Global Microbial Identifier Minimum Data for Matching (MDM) Standard"@en ; rdfs:seeAlso "http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da"^^xsd:anyURI ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0000037 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Soluble inorganic material" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "soluble organic material name;measurement value" ; obo:IAO_0000115 "concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc." ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "soluble inorganic material"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0000038 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Soluble inorganic material" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "soluble inorganic material concentration"@en ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000039 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Nitrite" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "micromole per liter" ; obo:IAO_0000115 "concentration of nitrite" ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "nitrite concentration" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000040 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Nitrate" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "micromole per liter" ; obo:IAO_0000115 "concentration of nitrate" ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "nitrate concentration" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000041 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Total phosphorous" ; obo:GENEPIO_0000005 "GROUP: MIxS" ; obo:IAO_0000112 "micromole per liter" ; obo:IAO_0000115 "total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus" ; obo:IAO_0000119 "GROUP: MIxS enviro package" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "total phosphorous concentration" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000042 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Stream order" ; obo:GENEPIO_0000005 "Environment Canada Metadata" ; obo:IAO_0000112 "value, 1-12" ; obo:IAO_0000115 "Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway)." ; obo:IAO_0000119 "GROUP: Environment Canada Metadata" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "stream order categorical measurement datum" ; rdfs:subClassOf obo:GENEPIO_0001626, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:unsignedInt ; owl:withRestrictions ([ xsd:maxInclusive "12"^^xsd:unsignedInt ] ) ] ] . obo:GENEPIO_0000043 obo:GENEPIO_0000001 "Environmental Isolate" ; obo:GENEPIO_0000004 "Density of bacteria in sample" ; obo:GENEPIO_0000005 "Environment Canada Metadata" ; obo:IAO_0000112 "OD reading or cfu's or cells per millilitre" ; obo:IAO_0000115 "number of bacteria in sample" ; obo:IAO_0000119 "GROUP: Environment Canada Metadata" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "bacteria density" ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0000044 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Host Primary Enzyme" ; obo:GENEPIO_0000005 "PulseNet Data Capture" ; obo:IAO_0000112 "pick list (XbaI, BlnI)" ; obo:IAO_0000115 "Restriction enzyme for first characterization" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; a owl:Class ; rdfs:label "primary enzyme (LMAAI)"@en ; rdfs:subClassOf obo:GENEPIO_0001709 . obo:GENEPIO_0000045 obo:IAO_0000114 obo:IAO_0000428 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "PFGE test specification"@en ; rdfs:subClassOf obo:GENEPIO_0001688, [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0000046 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0000048 ; owl:onProperty obo:RO_0002180 ] . obo:GENEPIO_0000046 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Host Primary PFGE Pattern" ; obo:GENEPIO_0000005 "NML LIMS" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "First PFGE pattern from given diagnostic restriction enzyme" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "PFGE primary test"@en ; rdfs:subClassOf obo:GENEPIO_0000045 . obo:GENEPIO_0000047 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Host Secondary Enzyme" ; obo:GENEPIO_0000005 "PulseNet Data Capture" ; obo:IAO_0000112 "pick list (XbaI, BlnI)" ; obo:IAO_0000115 "Restriction enzyme for second characterization" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "secondary enzyme (LMACI)"@en ; rdfs:subClassOf obo:GENEPIO_0001709 . obo:GENEPIO_0000048 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Host Secondary PFGE Pattern" ; obo:GENEPIO_0000005 "NML LIMS" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Second PFGE pattern from given diagnostic restriction enzyme" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "PFGE secondary test"@en ; rdfs:subClassOf obo:GENEPIO_0000045 . obo:GENEPIO_0000049 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "MLST Clonal Complex" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews and Bionumerics" ; obo:IAO_0000112 "pick list?" ; obo:IAO_0000115 "Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7" ; obo:IAO_0000119 "URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "MLST clonal complex" ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0000050 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "MLST Sequence Type" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews and Bionumerics" ; obo:IAO_0000112 "pick list?" ; obo:IAO_0000115 "Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST)." ; obo:IAO_0000119 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "MLST sequence typing" ; rdfs:subClassOf obo:GENEPIO_0001420 . obo:GENEPIO_0000051 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The process of fingerprinting the core genome of a bacteria."@en ; obo:IAO_0000116 "Add under upcomming OBI \"DNA fingerprinting assay\"."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000600 "Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains."@en ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "core genome fingerprinting assay" ; rdfs:subClassOf obo:OBI_0000070 . obo:GENEPIO_0000052 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "CGF type" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000112 "pick list" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "output of CGF" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "CGF type" ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0000053 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "16S rRNA sequencing" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000115 "16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study."@en ; obo:IAO_0000119 "URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "16S rRNA sequencing" ; rdfs:subClassOf obo:OBI_0001177 . obo:GENEPIO_0000054 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx toxin type" ; obo:GENEPIO_0000005 "metadata feedback" ; obo:IAO_0000112 "Stx1 or Stx2" ; obo:IAO_0000115 "pathogenic shiga toxin produced by STEC E. coli" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx toxin type datum"@en ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C1225 ] . obo:GENEPIO_0000055 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx toxin subtype" ; obo:GENEPIO_0000005 "metadata feedback" ; obo:IAO_0000112 "stx1a, stx1c" ; obo:IAO_0000115 "shiga toxin variant" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx toxin subtype datum"@en ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C1225 ] . obo:GENEPIO_0000056 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx1 Toxin PCR result" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "CT value?" ; obo:IAO_0000115 "qPCR result of Stx1 gene amplification" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx1 Toxin PCR result" ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OMIT_0020917 ] . obo:GENEPIO_0000057 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx1 Cell Culture" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000115 "level of Stx1 toxin derived tissue culture toxicity" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx1 cell culture level" ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OMIT_0020917 ] . obo:GENEPIO_0000058 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx2 Toxin PCR result" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "CT value?" ; obo:IAO_0000115 "qPCR result of Stx2 gene amplification" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx2 Toxin PCR result" ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OMIT_0020918 ] . obo:GENEPIO_0000059 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Stx2 Cell Culture" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "value?" ; obo:IAO_0000115 "level of Stx2 toxin derived tissue culture toxicity" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Stx2 cell culture level" ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OMIT_0020918 ] . obo:GENEPIO_0000060 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000600 "Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result."@en ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "AccuProbe culture identification assay"@en ; rdfs:subClassOf obo:OBI_0000070, [ a owl:Restriction ; owl:onProperty obo:RO_0002234 ; owl:someValuesFrom obo:GENEPIO_0000062 ] . obo:GENEPIO_0000061 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An AccuProbe reagent kit for identifying Listeria monocytogenes."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "AccuProbe Listeria monocytogenes culture identification reagent kit"@en ; rdfs:subClassOf obo:OBI_0001879 . obo:GENEPIO_0000062 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "positive, negative, not done" ; obo:IAO_0000115 "A categorical diagnostic result of an AccuProbe test."@en ; obo:IAO_0000119 "NML LIMS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "AccuProbe test result" ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:onProperty obo:RO_0002353 ; owl:someValuesFrom obo:GENEPIO_0000060 ] . obo:GENEPIO_0000063 obo:IAO_0000115 "Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product." ; obo:IAO_0000119 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "ribotyping" ; rdfs:subClassOf obo:GENEPIO_0001420 . obo:GENEPIO_0000064 obo:IAO_0000115 "This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria" ; obo:IAO_0000119 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "riboprinting" ; rdfs:subClassOf obo:GENEPIO_0001420 . obo:GENEPIO_0000065 obo:IAO_0000115 "an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species." ; obo:IAO_0000119 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "Qualicon (DuPont) RiboPrinter Microbial Characterization System" ; rdfs:subClassOf obo:OBI_0000968 . obo:GENEPIO_0000066 obo:IAO_0000115 "a library of RiboPrinter recognised patterns" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "DuPont identification pattern library" ; rdfs:subClassOf obo:IAO_0000100 . obo:GENEPIO_0000067 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Riboprinter DUP Number" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "DUP-PST1-1211" ; obo:IAO_0000115 "DuPont identification number from the DuPont identification library" ; obo:IAO_0000119 "NML LIMS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "RiboPrinter DUP Number" ; rdfs:subClassOf obo:IAO_0000109 . obo:GENEPIO_0000068 obo:GENEPIO_0000001 "Lab Analytic" ; obo:GENEPIO_0000004 "Riboprinter DUP similarity" ; obo:GENEPIO_0000005 "NML Labware LIMS" ; obo:IAO_0000112 "The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup." ; obo:IAO_0000115 "Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter" ; obo:IAO_0000119 ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "RiboPrinter DUP similarity" ; rdfs:subClassOf obo:IAO_0000109 . obo:GENEPIO_0000069 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Sequencing Run Date" ; obo:GENEPIO_0000005 "NML NGS Archive" ; obo:IAO_0000112 "yyyy/mm/dd" ; obo:IAO_0000115 "Date the sequencing run was performed"@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing run date"@en ; rdfs:subClassOf obo:GENEPIO_0001491, obo:GENEPIO_0001681, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0000021 ] . obo:GENEPIO_0000070 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Sequencing Location" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000115 "location the sequencing run was performed" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing location" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000071 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Platform" ; obo:GENEPIO_0000005 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/" ; obo:IAO_0000112 "Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A sequencing plaform (brand) is a name of a company that produces sequencer equipment."@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing platform (brand)"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0000072 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Workflow" ; obo:GENEPIO_0000005 "Derived from Sample Sheet" ; obo:IAO_0000112 "Resequencing, FastQ only" ; obo:IAO_0000115 "the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline." ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing workflow" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000073 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Application" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "amplicon sequencing, WGS" ; obo:IAO_0000115 "the sequencing application is the use or purpose of the sequencing" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing application"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000074 obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000115 "the sequencing conditions and the analyte being measured" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; obo:IAO_0100001 obo:OBI_0600047 ; a owl:Class ; rdfs:label "obsolete: sequencing assay"@en ; owl:deprecated true . obo:GENEPIO_0000075 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Chemistry" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "amplicon, resequencing (WGS)" ; obo:IAO_0000115 "lab method to determine the order of nucleotides in a DNA molecule" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing chemistry"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000076 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Read Length" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "151, 251" ; obo:IAO_0000115 "number of base pairs per read" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "read length" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000077 obo:IAO_0000115 "A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete: GSCID-BRC data item"@en ; owl:deprecated true . obo:GENEPIO_0000078 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Multiplex identifiers" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "S017" ; obo:IAO_0000115 "Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters" ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing run multiplex identifiers"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000079 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Sample Name" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf"@en ; obo:IAO_0000112 "1,2,3, AX234, etc."@en, "Control1, Tank1, Froglet1" ; obo:IAO_0000115 "A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis."@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:hasDbXref "Illumina SampleSheet: Sample_ID", "PulseNet: SubmittedNumber"@en ; oboInOwl:hasExactSynonym "sample name"@en, "sample title"@en ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing run sample identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0000080 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Number of cycles" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "500" ; obo:IAO_0000115 "Number of sequencing chemistry cycles"@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing count of chemistry cycles"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000081 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Sequencing Kit" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "MiSeq reagent kit" ; obo:IAO_0000115 "Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications." ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing kit"@en ; rdfs:subClassOf obo:OBI_0000047 . obo:GENEPIO_0000082 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Sequencing Kit version" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "v2, v3" ; obo:IAO_0000115 "A string datum which is the version/configuration of the reagent cartidge."@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "sequencing kit version" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000083 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Adapters" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000112 "adapter A and B sequence" ; obo:IAO_0000115 "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters" ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "adapter sequence"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000084 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Adapter Trimming" ; obo:GENEPIO_0000005 "Derived from Illumina Sample Sheet" ; obo:IAO_0000115 "The removal of adapter sequences from demultiplexed data reads"@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "read adapter trimming"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000085 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000112 "Illumina metagenomic protocol (part 15044223), with Nextera" ; obo:IAO_0000115 "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids." ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html" ; a owl:Class ; rdfs:label "library preparation kit" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000086 obo:GENEPIO_0000001 "Sequencing" ; obo:GENEPIO_0000004 "Number of base pairs" ; obo:GENEPIO_0000005 "inferred from BCCDC interviews" ; obo:IAO_0000112 "300 000" ; obo:IAO_0000115 "The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period." ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "number of expected base pairs per genome" ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0000087 obo:GENEPIO_0000001 "Run QC" ; obo:GENEPIO_0000004 "Number of Reads Passing Filter" ; obo:GENEPIO_0000005 "Output from MiSeq" ; obo:IAO_0000112 "0.92" ; obo:IAO_0000115 """Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.""" ; obo:IAO_0000119 "URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "number of reads passing filter" ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0000088 obo:GENEPIO_0000001 "Run QC" ; obo:GENEPIO_0000004 "Cluster density" ; obo:GENEPIO_0000005 "Output from MiSeq" ; obo:IAO_0000112 "800 k/mm^2" ; obo:IAO_0000115 "Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density." ; obo:IAO_0000119 "URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf" ; a owl:Class ; rdfs:label "sequencer flow cell cluster density" ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000089 obo:GENEPIO_0000001 "Run QC" ; obo:GENEPIO_0000004 "above 30 Qscore" ; obo:GENEPIO_0000005 "Output from MiSeq" ; obo:IAO_0000112 ">75%" ; obo:IAO_0000115 "percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly" ; obo:IAO_0000119 "URI: http://en.wikipedia.org/wiki/Phred_quality_score" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "phred quality score" ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0000090 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Assembly" ; obo:GENEPIO_0000005 "Standard Term" ; obo:IAO_0000112 "the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation" ; obo:IAO_0000115 "Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used." ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "assembly method" ; rdfs:subClassOf obo:GENEPIO_0001425 ; owl:equivalentClass [ a owl:Class ; owl:unionOf (obo:GENEPIO_0001628 obo:GENEPIO_0002028 ) ] . obo:GENEPIO_0000091 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Assembly status" ; obo:GENEPIO_0000005 "from within \"Finishing strategy\" in GROUP: MIxS" ; obo:IAO_0000112 "standard draft or finished" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "\"Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences.\" See subclass choices."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237." ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "assembly status"@en ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0000092 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Coverage" ; obo:GENEPIO_0000005 "from within \"Finishing strategy\" in GROUP: MIxS" ; obo:IAO_0000112 30 ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence." ; obo:IAO_0000119 "URI: http://en.wikipedia.org/wiki/Shotgun_sequencing" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:comment "Damion Dooley's note: Wikipedia defines calculation with: \"the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G\""@en ; rdfs:label "read coverage" ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0000093 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Number of Contigs" ; obo:IAO_0000112 20 ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 "A contig count is the count of contigs that belong to a sequence assembly."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "contig count"@en ; rdfs:subClassOf obo:GENEPIO_0001568, obo:STATO_0000047, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0001462 ] . obo:GENEPIO_0000094 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Assembly name" ; obo:GENEPIO_0000005 "Standard Term" ; obo:IAO_0000112 "name and version of assemby" ; obo:IAO_0000115 "Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community" ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "assembly name (identifier)"@en ; rdfs:subClassOf obo:GENEPIO_0001425, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0000353 ] . obo:GENEPIO_0000095 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Annotation Algorithm" ; obo:GENEPIO_0000005 "Standard Term" ; obo:IAO_0000112 "Prokka" ; obo:IAO_0000115 "Program used for annotation" ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "genome annotation algorithm" ; rdfs:subClassOf obo:GENEPIO_0001423 . obo:GENEPIO_0000096 obo:GENEPIO_0000001 "Assembly QC" ; obo:GENEPIO_0000004 "Annotation Source" ; obo:GENEPIO_0000005 "Standard Term" ; obo:IAO_0000112 "annotation source description" ; obo:IAO_0000115 "For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter" ; obo:IAO_0000119 "GROUP: MIxS" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "genome annotation source" ; rdfs:subClassOf obo:GENEPIO_0001423 . obo:GENEPIO_0000097 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 obo:GENEPIO_0001835 ; a owl:Class ; rdfs:label "obsolete: NCBI BioSample data item"@en ; owl:deprecated true . obo:GENEPIO_0000098 obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0000099 oboInOwl:hasAlternativeId "CDC ID" ; a owl:Class ; rdfs:subClassOf obo:OBI_0001616 . obo:GENEPIO_0000100 a owl:Class ; rdfs:subClassOf . obo:GENEPIO_0000101 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001429 . obo:GENEPIO_0000102 obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001659 . obo:GENEPIO_0000103 obo:IAO_0000115 "An NCBI BioProject data item is a datum within the NCBI BioProject standard collection"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 obo:GENEPIO_0001836 ; a owl:Class ; rdfs:label "obsolete: NCBI BioProject data item"@en ; owl:deprecated true . obo:GENEPIO_0000104 obo:IAO_0000115 "The INDISC consortium \"Minimum data for Matching\" standard aims to define a format to capture reads and minimum metadata. It is developed by the \"Repository and storage of sequence and meta-data\" workgroup 2. It is used in the Global Microbial Identifier platform."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000036"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: INSDC MDM standard"@en ; owl:deprecated true . obo:GENEPIO_0000105 obo:IAO_0000115 "A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:GENEPIO_0000003 ; a owl:Class ; rdfs:label "obsolete: MIxS data item"@en ; owl:deprecated true . obo:GENEPIO_0000106 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft data standard"@en ; rdfs:subClassOf obo:OBI_0000658 . obo:GENEPIO_0000107 obo:IAO_0000231 obo:IAO_0000103 ; obo:IAO_0100001 obo:GENEPIO_0000017 ; a owl:Class ; rdfs:label "obsolete: HIPPA PHI data item"@en ; owl:deprecated true . obo:GENEPIO_0000108 obo:IAO_0000231 obo:IAO_0000103 ; obo:IAO_0100001 obo:GENEPIO_0001839 ; a owl:Class ; rdfs:label "obsolete: PulseNet data item"@en ; owl:deprecated true . obo:GENEPIO_0000109 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf"@en ; a owl:Class ; rdfs:label "I2B2 Data Protection role standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0000110 obo:GENEPIO_0001763 "depth:1"@en, """order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased"""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "CS8" ; a owl:Class ; rdfs:label "subject health status (GSCID-BRC)"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0000111 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample"^^xsd:anyURI ; a owl:Class ; rdfs:label "GSCID-BRC Core Sample standard"@en ; rdfs:subClassOf obo:GENEPIO_0000002, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100051 ] . obo:GENEPIO_0000112 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project" ; a owl:Class ; rdfs:label "GSCID-BRC Core Project standard"@en ; rdfs:subClassOf obo:GENEPIO_0000002 . obo:GENEPIO_0000113 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between \"clinical or host associated\" specimens and \"environmental/food or other pathogen\" specimens."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "specimen category"@en ; rdfs:subClassOf obo:GENEPIO_0001790 . obo:GENEPIO_0000114 obo:IAO_0000112 "day, week, month, year" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Age unit of the age measurement of a subject (individual organism)."@en ; obo:IAO_0000116 "Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "NIAID GSCID-BRC metadata working group" ; a owl:Class ; rdfs:label "subject age - unit"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0000115 obo:IAO_0000115 "The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000118 "National Center for Biotechnology Information standard"@en ; a owl:Class ; rdfs:label "NCBI standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0000116 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a catch-all category for Gazetteer items that have \"located in\" relations but not an imported GAZETTEER class parent in GenEpiO."@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0000117 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "Adapted from NIAID GSCID-BRC metadata working group"@en ; obo:IAO_0000600 "Note that this is expressed in a particular format in some standards."@en ; a owl:Class ; rdfs:label "specimen collection location - city or region"@en ; rdfs:subClassOf obo:GENEPIO_0002162, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:ENVO_00000005 obo:NCIT_C80234 ) ] ] . obo:GENEPIO_0000118 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The country of the site of a given specimen collection event."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "NIAID GSCID-BRC metadata working group"@en ; a owl:Class ; rdfs:label "specimen collection location - country"@en ; rdfs:subClassOf obo:GENEPIO_0002162, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C25464 ] . obo:GENEPIO_0000119 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://tdwg.github.io/dwc/terms/index.htm"^^xsd:anyURI ; a owl:Class ; rdfs:label "Darwin Core Terms"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0000120 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A datetime measurement related to a person's travel with respect to potential epidemilogical implications."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "travel history item"@en ; rdfs:subClassOf obo:GENEPIO_0001041 . obo:GENEPIO_0000121 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "travel start date"@en ; rdfs:subClassOf obo:GENEPIO_0000120 . obo:GENEPIO_0000122 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The date of a person's return to some residence from a journey originating at that residence."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "travel end date"@en ; rdfs:subClassOf obo:GENEPIO_0000120, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0000121 ] . obo:GENEPIO_0000123 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "infection aquired during travel"@en ; rdfs:subClassOf obo:GENEPIO_0001058 . obo:GENEPIO_0000124 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a model of the datums involved in an epidemiology investigation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft pathogenic epidemiology case investigation record"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0000125 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft pathogenic epi case exposure record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000126 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A description of a food item that a case patient has come in contact with."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft pathogenic epi case food record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000127 a owl:Class ; rdfs:label "food brought back from travel"@en ; rdfs:subClassOf obo:GENEPIO_0001058 . obo:GENEPIO_0000128 obo:IAO_0000115 "An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "epidemiology contact network model"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0000129 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "epi contact network model - human"@en ; rdfs:subClassOf obo:GENEPIO_0000128 . obo:GENEPIO_0000130 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "epi contact network model - animal"@en ; rdfs:subClassOf obo:GENEPIO_0000128 . obo:GENEPIO_0000131 obo:IAO_0000115 "A note is text that provides human-readable information on one or more subjects."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "note"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:GENEPIO_0000132 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft pathogenic epi case general information record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000133 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A record of the details around how, when, and from what an isolate was extracted."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft pathogenic epi case isolate detail record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000134 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen source substance"@en ; rdfs:subClassOf obo:BFO_0000040, [ a owl:Restriction ; owl:onProperty obo:RO_0001025 ; owl:someValuesFrom obo:GENEPIO_0002167 ] ; owl:equivalentClass [ a owl:Class ; owl:unionOf (obo:ENVO_00010483 obo:GENEPIO_0001249 obo:GENEPIO_0002077 ) ] . obo:GENEPIO_0000135 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "isolate sequence filename"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000136 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "cluster identifier"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0000137 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft pathogenic epi case test record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000138 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "contact specification - lab test requester"@en ; rdfs:subClassOf obo:GENEPIO_0001606 . obo:GENEPIO_0000139 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A food cultural origin datum indicates the cultural origin of a food product."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "food cultural origin"@en ; rdfs:subClassOf obo:GENEPIO_0001532 . obo:GENEPIO_0000140 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft pathogenic epi case travel record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000141 a owl:Class ; rdfs:label "Region (England) (entry subject to GAZ replacement)"@en ; rdfs:subClassOf obo:GENEPIO_0001742 . obo:GENEPIO_0000142 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "contact specification - epi network contact"@en ; rdfs:subClassOf obo:GENEPIO_0001606 . obo:GENEPIO_0000143 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "public health lab epidemiology contextual data standard"@en ; rdfs:subClassOf obo:GENEPIO_0001743 . obo:GENEPIO_0000144 obo:IAO_0000115 "This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft whole genome sequencing lab test record"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0000145 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft WGS lab bioinformatics process record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000146 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft WGS lab sequencing record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000147 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "NCBI SRA meta information standard"@en ; rdfs:seeAlso "https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_" ; rdfs:subClassOf obo:GENEPIO_0000115 . obo:GENEPIO_0000148 obo:IAO_0000115 "An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay."@en ; a owl:Class ; rdfs:label "isolate raw read filename"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000149 obo:GENEPIO_0000001 "Sequencing" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The version identifier of a packaged kit tailored for specific sequencing workflows."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "library preparation kit version"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000150 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "read trimming and filtering software"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000151 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "bioinformatics pipeline name"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000152 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "bioinformatics pipeline version"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000153 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "bioinformatics pipeline protocol"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0000154 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft WGS lab sequencing quality metrics record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000155 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft WGS lab assembly quality metrics record"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0000156 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects)."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, \"A BioProject record can have multiple project data types\""@en ; rdfs:label "project data type"@en ; rdfs:subClassOf obo:IAO_0000104 . obo:GENEPIO_0000157 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Genome assembly project utilizing already existing sequence data including data that was submitted by a different group"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "assembly project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0000158 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A sequencing project involving clone-ends"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "clone ends project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0000159 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "epigenomics project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0000160 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Exome resequencing project"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "exome resequencing project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0000161 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A whole, or partial, genome sequencing project (with or without a genome assembly)"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "genome sequencing project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0000162 a owl:AnnotationProperty ; rdfs:label "user interface definition"@en . obo:GENEPIO_0001000 obo:IAO_0000115 "The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://platform.reseqtb.org/"^^xsd:anyURI ; a owl:Class ; rdfs:label "draft ReSeq Tuberculosis data platform standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001001 obo:IAO_0000112 "In expressions like: \"<= 8mg/L\""@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "test threshold measurement comparator"@en ; rdfs:subClassOf obo:GENEPIO_0002036 . obo:GENEPIO_0001002 obo:GENEPIO_0000006 "<" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The \"less than\" comparator indicates that a given substance was present at less than a given quantity or concentration."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "<" ; a owl:Class ; rdfs:label "less than"@en ; rdfs:subClassOf obo:GENEPIO_0001001 . obo:GENEPIO_0001003 obo:GENEPIO_0000006 "<="@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The \"less than or equal to\" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "<=" ; a owl:Class ; rdfs:label "less than or equal to"@en ; rdfs:subClassOf obo:GENEPIO_0001001 . obo:GENEPIO_0001004 obo:GENEPIO_0000006 "=="@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The \"equal to\" comparator indicates that a given substance was present at the given quantity or concentration."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "==" ; a owl:Class ; rdfs:label "equal to"@en ; rdfs:subClassOf obo:GENEPIO_0001001 . obo:GENEPIO_0001005 obo:GENEPIO_0000006 ">="@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The \"greater than or equal to\" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId ">=" ; a owl:Class ; rdfs:label "greater than or equal to"@en ; rdfs:subClassOf obo:GENEPIO_0001001 . obo:GENEPIO_0001006 obo:GENEPIO_0000006 ">"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The \"greater than\" comparator indicates that a given substance was present at greater than a given quantity or concentration."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId ">" ; a owl:Class ; rdfs:label "greater than"@en ; rdfs:subClassOf obo:GENEPIO_0001001 . obo:GENEPIO_0001007 obo:GENEPIO_0001763 """order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "NCBI Antibiogram standard"@en ; rdfs:seeAlso "https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/"^^xsd:anyURI ; rdfs:subClassOf obo:GENEPIO_0000115 . obo:GENEPIO_0001008 obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001007" ; a owl:Class ; rdfs:label "obsolete: NCBI isolate AMR testing model"@en ; owl:deprecated true . obo:GENEPIO_0001009 obo:IAO_0000115 "A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Restaurant" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000934"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: restaurant"@en ; owl:deprecated true . obo:GENEPIO_0001010 obo:GENEPIO_0000006 "iPHIS standard"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "Canadian Integrated Public Health Information System (iPHIS) Standard"@en ; rdfs:subClassOf obo:GENEPIO_0001743 . obo:GENEPIO_0001011 obo:IAO_0000112 "254532233433235152213423"^^rdfs:Literal ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci."@en ; obo:IAO_0000600 "The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171"@en ; a owl:Class ; rdfs:label "MIRU24 - international standard"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001012 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000600 "The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156"@en ; a owl:Class ; rdfs:label "MIRU24 - Canadian standard"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001013 a owl:Class ; rdfs:label "spray-wading water"@en ; rdfs:subClassOf obo:GENEPIO_0001154 . obo:GENEPIO_0001014 a owl:Class ; rdfs:label "pool water"@en ; rdfs:subClassOf obo:GENEPIO_0001154 . obo:GENEPIO_0001015 obo:IAO_0100001 obo:ENVO_01000938 ; a owl:Class ; rdfs:label "obsolete: hot tub"@en ; owl:deprecated true . obo:GENEPIO_0001016 obo:IAO_0000115 "A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Cafeteria" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000969"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: cafeteria"@en ; owl:deprecated true . obo:GENEPIO_0001017 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_00003864"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: bakery"@en ; owl:deprecated true . obo:GENEPIO_0001018 obo:IAO_0000115 "A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Delicatessen" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000970"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: delicatessen"@en ; owl:deprecated true . obo:GENEPIO_0001019 obo:IAO_0000115 "A food kiosk is a kiosk (a booth with an open window on one side) that sells food."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000974"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: food kiosk"@en ; owl:deprecated true . obo:GENEPIO_0001020 obo:IAO_0000115 "A grocery store is a retail store that primarily sells food."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000984"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: grocery store"@en ; owl:deprecated true . obo:GENEPIO_0001021 obo:IAO_0000115 "A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000988"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: specialty/ethnic store"@en ; owl:deprecated true . obo:GENEPIO_0001022 obo:IAO_0000115 "A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000987"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: market"@en ; owl:deprecated true . obo:GENEPIO_0001023 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A time measurement datum that pertains to a patient's medical treatment."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "treatment history datum"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001024 obo:IAO_0000115 "A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Take-out"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000972"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: take out restaurant"@en ; owl:deprecated true . obo:GENEPIO_0001025 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "treatment start date"@en ; rdfs:subClassOf obo:GENEPIO_0001023 . obo:GENEPIO_0001026 a owl:Class ; rdfs:label "canoeing / kayaking / boating"@en ; rdfs:subClassOf obo:GENEPIO_0001277 . obo:GENEPIO_0001027 a owl:Class ; rdfs:label "hiking"@en ; rdfs:subClassOf obo:GENEPIO_0001444 . obo:GENEPIO_0001028 a owl:Class ; rdfs:label "camping"@en ; rdfs:subClassOf obo:GENEPIO_0001444 . obo:GENEPIO_0001029 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000033"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: social gathering"@en ; owl:deprecated true . obo:GENEPIO_0001030 obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000035"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: party"@en ; owl:deprecated true . obo:GENEPIO_0001031 obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000038"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: wedding"@en ; owl:deprecated true . obo:GENEPIO_0001032 obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000039"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: baby shower"@en ; owl:deprecated true . obo:GENEPIO_0001033 obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000037"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: potluck"@en ; owl:deprecated true . obo:GENEPIO_0001034 obo:IAO_0100001 "http://purl.obolibrary.org/obo/PCO_0000034"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: community event"@en ; owl:deprecated true . obo:GENEPIO_0001035 obo:IAO_0000115 "A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Nursing_home_care" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000932"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: long term care facility"@en ; owl:deprecated true . obo:GENEPIO_0001036 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "treatment end date"@en ; rdfs:subClassOf obo:GENEPIO_0001023, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001025 ] . obo:GENEPIO_0001037 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "food related exposure event"@en ; rdfs:subClassOf obo:GENEPIO_0001048 . obo:GENEPIO_0001038 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Some bacteria are associated with particular foods. Need relationship"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "infection-specific food detail"@en ; rdfs:subClassOf obo:GENEPIO_0001244 . obo:GENEPIO_0001039 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "tuberculosis treatment drug"@en ; rdfs:seeAlso "“Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf" ; rdfs:subClassOf obo:CHEBI_36357 . obo:GENEPIO_0001040 a owl:Class ; rdfs:label "vegetarian"@en ; rdfs:subClassOf obo:GENEPIO_0001205 . obo:GENEPIO_0001041 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A time measurement datum that pertains to an organism's physical location."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "organism location history datum"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001042 a owl:Class ; rdfs:comment "This will take on a sub-herarchy of food types."@en ; rdfs:label "food avoidance"@en ; rdfs:subClassOf obo:GENEPIO_0001205 . obo:GENEPIO_0001043 a owl:Class ; rdfs:label "special diet"@en ; rdfs:subClassOf obo:GENEPIO_0001205 . obo:GENEPIO_0001044 a owl:Class ; rdfs:label "water related exposure event"@en ; rdfs:subClassOf obo:GENEPIO_0001048 . obo:GENEPIO_0001045 a owl:Class ; rdfs:label "municipal water"@en ; rdfs:subClassOf obo:GENEPIO_0001154 . obo:GENEPIO_0001046 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A time measurement datum indicating the year a person immigrated to a given country."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "immigration year of arrival"@en ; rdfs:subClassOf obo:GENEPIO_0001041 . obo:GENEPIO_0001047 a owl:Class ; rdfs:label "bottled water"@en ; rdfs:subClassOf obo:GENEPIO_0001154 . obo:GENEPIO_0001048 obo:IAO_0000115 "An event (occuring at some location and for some duration of time) where"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "infectious disease exposure event"@en ; rdfs:subClassOf obo:BFO_0000011 . obo:GENEPIO_0001049 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "human related exposure event"@en ; rdfs:subClassOf obo:GENEPIO_0001048 . obo:GENEPIO_0001050 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "animal related exposure event"@en ; rdfs:subClassOf obo:GENEPIO_0001048 . obo:GENEPIO_0001051 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Identification or description of the specific individual from which this sample was obtained"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"^^xsd:anyURI ; a owl:Class ; rdfs:label "NCBI BioSample isolate (human name or description)"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:GENEPIO_0001052 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ENVO_01000923"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: petting zoo"@en ; owl:deprecated true . obo:GENEPIO_0001053 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "agricultural fair"@en ; rdfs:subClassOf obo:PCO_0000033 . obo:GENEPIO_0001054 obo:IAO_0000115 "An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^xsd:anyURI ; a owl:Class ; rdfs:label "isolate passage history datum"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001055 obo:IAO_0000112 "For Eschericia coli: STEC, UPEC"@en ; obo:IAO_0000115 "A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host"@en ; obo:IAO_0000119 "https://en.wiktionary.org/wiki/pathotype"@en ; a owl:Class ; rdfs:label "NCBI pathotype"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:GENEPIO_0001056 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:FOODON_00003357 ; a owl:Class ; rdfs:label "pet treat"@en ; rdfs:subClassOf obo:GENEPIO_0001271 . obo:GENEPIO_0001057 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:FOODON_00003356 ; a owl:Class ; rdfs:label "pet food (raw)"@en ; rdfs:subClassOf obo:GENEPIO_0001271 . obo:GENEPIO_0001058 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "human exposure event - travel datum"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0001059 a owl:Class ; rdfs:label "boat / cruise travel"@en ; rdfs:subClassOf obo:GENEPIO_0001064 . obo:GENEPIO_0001060 a owl:Class ; rdfs:label "train travel"@en ; rdfs:subClassOf obo:GENEPIO_0001064 . obo:GENEPIO_0001061 a owl:Class ; rdfs:label "bus travel"@en ; rdfs:subClassOf obo:GENEPIO_0001064 . obo:GENEPIO_0001062 a owl:Class ; rdfs:label "car travel"@en ; rdfs:subClassOf obo:GENEPIO_0001064 . obo:GENEPIO_0001063 a owl:Class ; rdfs:label "airline travel"@en ; rdfs:subClassOf obo:GENEPIO_0001064 . obo:GENEPIO_0001064 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A travel mode is a type of transportation which a given human has used while travelling on a particular trip."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "travel mode"@en ; rdfs:subClassOf obo:GENEPIO_0001058 . obo:GENEPIO_0001065 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A travel reason is a motivation for traveling on a particular trip expressed by the traveller."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "travel reason"@en ; rdfs:subClassOf obo:GENEPIO_0001058 . obo:GENEPIO_0001066 a owl:Class ; rdfs:label "travel for pleasure"@en ; rdfs:subClassOf obo:GENEPIO_0001065 . obo:GENEPIO_0001067 a owl:Class ; rdfs:label "business activity"@en ; rdfs:subClassOf obo:GENEPIO_0001065 . obo:GENEPIO_0001068 a owl:Class ; rdfs:label "religious missionairy activity"@en ; rdfs:subClassOf obo:GENEPIO_0001065 . obo:GENEPIO_0001069 a owl:Class ; rdfs:label "rural backpacking activity"@en ; rdfs:subClassOf obo:GENEPIO_0001066 . obo:GENEPIO_0001070 a owl:Class ; rdfs:label "visiting relative/friends"@en ; rdfs:subClassOf obo:GENEPIO_0001066 . obo:GENEPIO_0001071 a owl:Class ; rdfs:label "travel tour"@en ; rdfs:subClassOf obo:GENEPIO_0001066 . obo:GENEPIO_0001072 a owl:Class ; rdfs:label "unsure of travel reason"@en ; rdfs:subClassOf obo:GENEPIO_0001065 . obo:GENEPIO_0001073 obo:IAO_0000115 "The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting."@en ; a owl:Class ; rdfs:label "draft tuberculosis - specimen contextual data standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001074 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "behavioural risk factor"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001075 obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001686"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: E. coli serotype part"@en ; owl:deprecated true . obo:GENEPIO_0001076 oboInOwl:hasDbXref "Snomed: Concept 260827009" ; a owl:Class ; rdfs:label "O antigen"@en ; rdfs:subClassOf obo:OBI_1110034 . obo:GENEPIO_0001077 oboInOwl:hasDbXref "Snomed: Concept 260823008" ; a owl:Class ; rdfs:label "H antigen"@en ; rdfs:subClassOf obo:OBI_1110034 . obo:GENEPIO_0001078 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "homeless status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001079 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Serotype"^^xsd:anyURI ; a owl:Class ; rdfs:label "serovar/serotype common name"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001080 a owl:Class ; rdfs:label "Salmonella serovar"@en ; rdfs:subClassOf obo:OMP_0000207, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCBITaxon_590 ] . obo:GENEPIO_0001081 a owl:Class ; rdfs:label "Salmonella serovar name"@en ; rdfs:subClassOf obo:GENEPIO_0001079 . obo:GENEPIO_0001082 a owl:Class ; rdfs:label "Salmonella antigenic formula"@en ; rdfs:subClassOf obo:GENEPIO_0001639, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCBITaxon_590 ] . obo:GENEPIO_0001083 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "drug use status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001084 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "incarceration status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001085 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "HIV status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001086 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "HIV risk status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001087 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "A.I.D.S status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001088 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "drug abuse status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001089 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "injection drug use status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001090 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "recreational drug use status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001091 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "methadone use status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001092 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "" ; a owl:Class ; rdfs:label "substantial alcohol use/abuse status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001093 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "" ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "smoking status"@en ; rdfs:subClassOf obo:GENEPIO_0001074 . obo:GENEPIO_0001094 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A country of birth is the country that a given person (or animal) was born in."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "country of birth"@en ; rdfs:subClassOf obo:GENEPIO_0001170, [ a owl:Restriction ; owl:onProperty obo:BFO_0000067 ; owl:someValuesFrom obo:NCIT_C25155 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C25464 ] . obo:GENEPIO_0001095 obo:IAO_0000112 """Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report)"""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset."@en ; a owl:Class ; rdfs:label "sequence number"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001096 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley", "The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive."@en ; a owl:Class ; rdfs:label "date last seen alive"@en ; rdfs:subClassOf obo:GENEPIO_0001126 . obo:GENEPIO_0001097 a owl:Class ; rdfs:label "second line or reserve tuberculosis drug"@en ; rdfs:subClassOf obo:GENEPIO_0001039 . obo:GENEPIO_0001098 a owl:Class ; rdfs:label "tuberculosis infection anatomical site"@en ; rdfs:subClassOf obo:BFO_0000029 . obo:GENEPIO_0001099 obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001007" ; a owl:Class ; rdfs:label "obsolete: NCBI Antibiogram model"@en ; owl:deprecated true . obo:GENEPIO_0001100 obo:GENEPIO_0001763 """order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the minimal set of parameters for drug test results for a particular antimicrobial agent."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft antibiogram drug test model"@en ; rdfs:seeAlso "http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm", "https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/"^^xsd:anyURI ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001101 obo:IAO_0000115 "A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "predicted exposure start"@en ; rdfs:subClassOf obo:GENEPIO_0001473 . obo:GENEPIO_0001102 obo:IAO_0000115 "A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "predicted exposure end"@en ; rdfs:subClassOf obo:GENEPIO_0001473 . obo:GENEPIO_0001103 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "map project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001104 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Metagenome: sequence analysis of environmental samples"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "metagenome project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001105 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Metagenome assembly: a genome assembly generated from sequenced environmental samples"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "metagenome assembly project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001106 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Other: a free text description is provided to indicate Other data type"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "other project data type"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001107 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Phenotype or Genotype: project correlating phenotype and genotype"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "phenotype or genotype project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001108 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Proteome: large scale proteomics experiment including mass spec. analysis"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "proteome project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001109 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "random survey project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001110 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "targeted locus (loci) project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001111 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "transcriptome or gene expression"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001112 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A sequencing project with a primary goal of identifying large or small sequence variation across populations."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "variation project"@en ; rdfs:subClassOf obo:GENEPIO_0000156 . obo:GENEPIO_0001113 obo:GENEPIO_0001763 "help: Consult the http://www.insdc.org/country.html country list for valid options."@en ; obo:IAO_0000115 "The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: \"Canada:Vancouver\"."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "INSDC country qualifier"@en ; rdfs:subClassOf obo:GENEPIO_0001666, obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C25464 ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "(Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)?" ] ) ] ; owl:onProperty obo:OBI_0002135 ] . obo:GENEPIO_0001114 obo:GENEPIO_0000006 "phenotype"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Phenotype: phenotypic measurements for submission to dbGaP"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "phenotype project objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001115 obo:GENEPIO_0000006 "genome material"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "genome material from specimen"@en ; rdfs:subClassOf obo:OBI_0001882, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0001026 ] . obo:GENEPIO_0001116 a owl:Class ; rdfs:label "TB lineage 7 - Ethiopia"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0001117 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An object aggregate which has as members whole organs or parts of organs, possibly from different organisms."@en ; obo:IAO_0000117 ; dc:date "2021-04-19T23:36:25Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "organs or organ parts"@en ; rdfs:subClassOf obo:BFO_0000027, [ a owl:Class ; owl:intersectionOf ([ a owl:Restriction ; owl:onProperty obo:RO_0002351 ; owl:someValuesFrom [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:UBERON_0000062 ] ] [ a owl:Restriction ; owl:allValuesFrom [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:UBERON_0000062 ] ; owl:onProperty obo:RO_0002351 ] ) ] . obo:GENEPIO_0001118 obo:IAO_0000115 "A travel destination which a given human has travelled to on a particular trip and is outside Canada."@en ; obo:IAO_0000117 ; dc:date "2021-05-27T04:35:17Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "travel outside Canada"@en ; rdfs:subClassOf obo:GENEPIO_0001783 . obo:GENEPIO_0001119 obo:IAO_0000115 "A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest."@en ; obo:IAO_0000117 ; dc:date "2021-05-27T04:36:13Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "travel outside province/territory"@en ; rdfs:subClassOf obo:GENEPIO_0001783 . obo:GENEPIO_0001120 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000115 "A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project DataHarmonizer application, for contextual data (metadata) harmonization and curation across data providers."@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; obo:IAO_0000119 "https://github.com/Public-Health-Bioinformatics/DataHarmonizer/blob/master/template/canada_covid19/SOP.pdf" ; dc:date "2021-04-24T00:18:57Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0001121 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000115 "A field specification used in the Canadian COVID-10 Genomics Network (CanCOGeN) DataHarmonizer application."@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; dc:date "2021-04-24T00:25:28Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field"@en ; rdfs:seeAlso "https://github.com/Public-Health-Bioinformatics/DataHarmonizer/blob/master/template/canada_covid19/SOP.pdf"@en ; rdfs:subClassOf linkml:SlotDefinition . obo:GENEPIO_0001122 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000115 "A CanCOGeN DataHarmonizer field that refers to a database identifier."@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; dc:date "2021-04-24T00:30:02Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - database identifiers"@en ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001123 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:specimen collector sample ID" ; linkml:comments "Guidance: Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab."@en ; linkml:created_on "2021-04-24T00:42:14Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The user-defined name for the sample."@en ; linkml:examples obo:GENEPIO_0002236 ; linkml:identifier true ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001124 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-26T23:49:57Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:NML submitted specimen primary ID example" ; linkml:value "SR20-12345" . obo:GENEPIO_0001125 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:NML submitted specimen primary ID" ; linkml:comments "Guidance: Store the identifier for the specimen submitted through the NML LaSER system."@en ; linkml:created_on "2021-04-27T02:56:23Z" ; linkml:description "The primary ID of the specimen submitted thorough the National Microbiology Laboratory (NML) LaSER."@en ; linkml:examples obo:GENEPIO_0001124 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001126 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A livespan history item is a date-associated event pertaining to the life of a subject."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "lifespan history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001127 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; dc:date "2021-04-27T03:04:06Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:NML related specimen primary ID example" ; linkml:value "SR20-12345" . obo:GENEPIO_0001128 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 "https://orcid.org/0000-0002-9578-0788" ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:NML related specimen primary ID" ; linkml:comments "Guidance: Store the primary ID of the related specimen previously submitted thorough LaSER"@en ; linkml:created_on "2021-04-27T03:10:30Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The primary ID of the related specimen previously submitted thorough the National Microbiology Laboratory (NML) LaSER."@en ; linkml:examples obo:GENEPIO_0001127 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001129 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:14:01Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:IRIDA sample name example" ; linkml:value "prov_rona_99" . obo:GENEPIO_0001130 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:21:11Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:LocalName ; rdfs:label "CanCOGeN:IRIDA sample name local name" ; linkml:local_name_value "http://purl.obolibrary.org/obo/GENEPIO_0001829" . obo:GENEPIO_0001131 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:IRIDA sample name" ; linkml:comments "Guidance: Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)."@en ; linkml:created_on "2021-04-27T03:24:03Z" ; linkml:description "The identifier assigned to a sequenced isolate in IRIDA."@en ; linkml:examples obo:GENEPIO_0001129 ; linkml:local_names obo:GENEPIO_0001130 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001132 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:35:36Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:umbrella bioproject accession example" ; linkml:value "PRJNA623807" . obo:GENEPIO_0001133 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:umbrella bioproject accession" ; linkml:comments "Guidance: Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject."@en ; linkml:created_on "2021-04-27T03:38:14Z" ; linkml:description "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort."@en ; linkml:examples obo:GENEPIO_0001132 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.ncbi.nlm.nih.gov/books/NBK54015/"^^xsd:anyURI ; linkml:type_uri "select" . obo:GENEPIO_0001134 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:44:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:bioproject accession example" ; linkml:value "PRJNA608651" . obo:GENEPIO_0001135 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:46:59Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:LocalName ; rdfs:label "CanCOGeN:bioproject accession local name" ; linkml:local_name_value "http://purl.obolibrary.org/obo/GENEPIO_0001836" . obo:GENEPIO_0001136 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:50:41Z"^^xsd:dateTime ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:bioproject accession" ; linkml:comments "Guidance: Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project."@en ; linkml:description "The INSDC accession number of the BioProject(s) to which the BioSample belongs."@en ; linkml:examples obo:GENEPIO_0001134 ; linkml:local_names obo:GENEPIO_0001135 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.ncbi.nlm.nih.gov/bioproject/"^^xsd:anyURI ; linkml:type_uri "xs:token" . obo:GENEPIO_0001137 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T03:55:21Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:biosample accession example" ; linkml:value "SAMN14180202" . obo:GENEPIO_0001138 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:03:29Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:LocalName ; rdfs:label "CanCOGeN:biosample accession local name" ; linkml:local_name_value "http://purl.obolibrary.org/obo/GENEPIO_0001836" . obo:GENEPIO_0001139 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:biosample accession" ; linkml:comments "Guidance: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN."@en ; linkml:created_on "2021-04-27T04:06:03Z" ; linkml:description "The identifier assigned to a BioSample in INSDC archives."@en ; linkml:examples obo:GENEPIO_0001137 ; linkml:local_names obo:GENEPIO_0001138 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.ncbi.nlm.nih.gov/biosample"^^xsd:anyURI ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001140 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:09:40Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:SRA accession example" ; linkml:value "SRR11177792" . obo:GENEPIO_0001141 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:13:07Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:LocalName ; rdfs:label "CanCOGeN:SRA accession local name" ; linkml:local_name_value "http://purl.obolibrary.org/obo/GENEPIO_0000147" . obo:GENEPIO_0001142 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:19:10Z"^^xsd:dateTime ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:SRA accession" ; linkml:comments "Guidance: Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR."@en ; linkml:created_on "2021-04-27T04:19:10Z" ; linkml:description "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC."@en ; linkml:examples obo:GENEPIO_0001140 ; linkml:local_names obo:GENEPIO_0001141 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.ncbi.nlm.nih.gov/sra"^^xsd:anyURI ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001143 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:22:41Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:GenBank accession example" ; linkml:value "MN908947.3" . obo:GENEPIO_0001144 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:25:46Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:LocalName ; rdfs:label "CanCOGeN:GenBank accession local name" ; linkml:local_name_value "http://purl.obolibrary.org/obo/OBI_0001614" . obo:GENEPIO_0001145 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:GenBank accession" ; linkml:comments "Guidance: Store the accession returned from a GenBank submission (viral genome assembly)."@en ; linkml:created_on "2021-04-27T04:27:48Z" ; linkml:description "The GenBank identifier assigned to the sequence in the INSDC archives."@en ; linkml:examples obo:GENEPIO_0001143 ; linkml:local_names obo:GENEPIO_0001144 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.ncbi.nlm.nih.gov/genbank/"^^xsd:anyURI, "https://www.ncbi.nlm.nih.gov/genbank/acc_prefix/"^^xsd:anyURI ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001146 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-27T04:33:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:GISAID accession example" ; linkml:value "EPI_ISL_436489" . obo:GENEPIO_0001147 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:GISAID accession" ; linkml:comments "Guidance: Store the accession returned from the GISAID submission."@en ; linkml:created_on "2021-04-27T04:36:10Z" ; linkml:description "The GISAID accession number assigned to the sequence."@en ; linkml:examples obo:GENEPIO_0001146 ; linkml:pattern "UPPER" ; linkml:see_also "https://www.gisaid.org/help/publish-with-data-from-gisaid/"^^xsd:anyURI ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001148 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-04-28T18:48:39Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:third party lab sample ID example" ; linkml:value "SHK123456" . obo:GENEPIO_0001149 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:third party lab sample ID" ; linkml:comments "Guidance: Store the identifier supplied by the third party for the sample."@en ; linkml:created_on "2021-04-28T18:51:40Z" ; linkml:description "The identifier assigned to a sample by a third party service provider."@en ; linkml:examples obo:GENEPIO_0001148 ; linkml:see_also "https://www.switchhealth.ca/en/"^^xsd:anyURI ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001150 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000115 "A CanCOGeN DataHarmonizer field that refers to sample collection and processing information."@en ; obo:IAO_0000117 ; dc:date "2021-05-04T04:40:30Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - sample collection and processing"@en ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001151 a owl:Class ; rdfs:label "untreated water"@en ; rdfs:subClassOf obo:GENEPIO_0001276 . obo:GENEPIO_0001152 a owl:NamedIndividual . obo:GENEPIO_0001153 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample collected by" ; linkml:comments "Guidance: The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)."@en ; linkml:created_on "2021-05-04T05:12:55Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the agency that collected the original sample."@en ; linkml:examples obo:GENEPIO_0001152 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001154 a owl:Class ; rdfs:label "treated water - ambient temperature"@en ; rdfs:subClassOf obo:GENEPIO_0001276 . obo:GENEPIO_0001155 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sample collector contact email example" ; linkml:value "RespLab@lab.ca"^^xsd:string . obo:GENEPIO_0001156 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample collector contact email" ; linkml:comments "Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca."@en ; linkml:created_on "2021-05-04T05:19:56Z" ; linkml:description "The email address of the contact responsible for follow-up regarding the sample."@en ; linkml:examples obo:GENEPIO_0001155 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001157 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-04T05:23:14Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sample collector contact address example" ; linkml:value "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" . obo:GENEPIO_0001158 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample collector contact address" ; linkml:comments "Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country."@en ; linkml:created_on "2021-05-04T05:25:17Z" ; linkml:description "The mailing address of the agency submitting the sample."@en ; linkml:examples obo:GENEPIO_0001157 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001159 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequence submitted by" ; linkml:comments "Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"."@en ; linkml:created_on "2021-05-04T05:28:14Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the agency that generated the sequence."@en ; linkml:examples obo:GENEPIO_0001160 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001160 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-04T05:29:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequence submitted by example" ; linkml:value "Public Health Ontario (PHO)" . obo:GENEPIO_0001161 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-04T05:32:32Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequence submitter contact email example" ; linkml:value "RespLab@lab.ca"^^xsd:string . obo:GENEPIO_0001162 a owl:Class ; rdfs:label "epidemiology investigation data item"@en ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:GENEPIO_0001163 obo:IAO_0000231 "Unclear semantics and origin"@en ; a owl:Class ; rdfs:label "obsolete distribution event"@en ; owl:deprecated true . obo:GENEPIO_0001164 a owl:Class ; rdfs:label "obsolete supply point / event"@en ; owl:deprecated true . obo:GENEPIO_0001165 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequence submitter contact email" ; linkml:comments "Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca."@en ; linkml:created_on "2021-05-04T05:33:30Z" ; linkml:description "The email address of the contact responsible for follow-up regarding the sequence."@en ; linkml:examples obo:GENEPIO_0001161 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001166 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-04T05:36:05Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequence submitter contact address example" ; linkml:value "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" . obo:GENEPIO_0001167 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequence submitter contact address" ; linkml:comments "Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country"@en ; linkml:created_on "2021-05-04T05:37:25Z" ; linkml:description "The mailing address of the agency submitting the sequence."@en ; linkml:examples obo:GENEPIO_0001166 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001168 a owl:Class ; rdfs:label "well water - treated"@en ; rdfs:subClassOf obo:ENVO_01000002, obo:GENEPIO_0001154 . obo:GENEPIO_0001169 a owl:Class ; rdfs:label "Well water - untreated" ; rdfs:subClassOf obo:ENVO_01000002, obo:GENEPIO_0001151 . obo:GENEPIO_0001170 a owl:Class ; rdfs:label "organism datum"@en ; rdfs:seeAlso obo:GENEPIO_0000114, obo:GENEPIO_0001183, obo:GENEPIO_0001640, obo:GENEPIO_0002008, obo:GENEPIO_0002130, obo:GENEPIO_0002131, obo:NCIT_C124295, obo:NCIT_C25190, , "http://purl.obolibrary.org/obo/GENEPIO_0001171"^^xsd:anyURI, "http://purl.obolibrary.org/obo/OBI_0100026"^^xsd:anyURI, "http://purl.obolibrary.org/obo/PATO_0000047"^^xsd:anyURI ; rdfs:subClassOf obo:IAO_0000027, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:GENEPIO_0001171 obo:IAO_0000115 "a role which inheres in an organism and is realized by the process of being alive" ; a owl:Class ; rdfs:label "organism role"@en ; rdfs:subClassOf obo:BFO_0000023, [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:GENEPIO_0001172 a owl:Class ; rdfs:label "isolate organism role"@en ; rdfs:subClassOf obo:GENEPIO_0001171 . obo:GENEPIO_0001173 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T05:25:15Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sample collection date example" ; linkml:value "2020-03-16" . obo:GENEPIO_0001174 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample collection date" ; linkml:comments "Guidance: Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-05-05T05:27:36Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date on which the sample was collected."@en ; linkml:examples obo:GENEPIO_0001173 ; linkml:required true ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001175 a owl:Class ; rdfs:label "animal role"@en ; rdfs:subClassOf obo:GENEPIO_0001171 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0001171 [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:NCBITaxon_33213 ] ) ] . obo:GENEPIO_0001176 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T19:49:38Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sample collection date precision example" ; linkml:value "year" . obo:GENEPIO_0001177 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample collection date precision" ; linkml:comments "Guidance: Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"."@en ; linkml:created_on "2021-05-05T19:51:36Z" ; linkml:description "The precision to which the \"sample collection date\" was provided."@en ; linkml:examples obo:GENEPIO_0001176 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001178 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T19:53:46Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sample received date example" ; linkml:value "2020-03-20" . obo:GENEPIO_0001179 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:sample received date" ; linkml:comments "Guidance: ISO 8601 standard \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-05-05T19:55:31Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date on which the sample was received."@en ; linkml:examples obo:GENEPIO_0001178 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001180 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T19:58:50Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:geo_loc_name (country) example" ; linkml:value "Canada" . obo:GENEPIO_0001181 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:geo_loc_name (country)" ; linkml:comments "Guidance: Provide the country name from the controlled vocabulary provided."@en ; linkml:created_on "2021-05-05T20:00:35Z"^^xsd:dateTime ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The country where the sample was collected."@en ; linkml:examples obo:GENEPIO_0001180 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001182 a owl:Class ; rdfs:label "plant role" ; rdfs:subClassOf obo:GENEPIO_0001171 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0001171 [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:NCBITaxon_33090 ] ) ] . obo:GENEPIO_0001183 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "taxonomic datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001184 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:03:26Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:geo_loc_name (state/province/territory) example" ; linkml:value "Saskatchewan"@en . obo:GENEPIO_0001185 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:geo_loc_name (state/province/territory)" ; linkml:comments "Guidance: Provide the province/territory name from the controlled vocabulary provided."@en ; linkml:created_on "2021-05-05T20:05:18Z"^^xsd:dateTime ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The province/territory where the sample was collected."@en ; linkml:examples obo:GENEPIO_0001184 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001186 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A course of treatment designed to resolve an infectious disease"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "infectious disease treatment"@en ; rdfs:subClassOf obo:GENEPIO_0001222 . obo:GENEPIO_0001187 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a collection of drugs used to test antimicrobial resistance."@en ; obo:IAO_0000116 """This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt"""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "antimicrobial resistance test drug"@en ; rdfs:subClassOf obo:CHEBI_36357 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:CHEBI_36357 [ a owl:Restriction ; owl:onProperty obo:RO_0000087 ; owl:someValuesFrom obo:CHEBI_33281 ] ) ] . obo:GENEPIO_0001188 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:07:52Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:geo_loc_name (city) example" ; linkml:value "Medicine Hat" . obo:GENEPIO_0001189 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:geo_loc_name (city)" ; linkml:comments "Guidance: Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz"@en ; linkml:created_on "2021-05-05T20:09:29Z"^^xsd:dateTime ; linkml:description "The city where the sample was collected."@en ; linkml:examples obo:GENEPIO_0001188 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001190 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:11:51Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:organism example" ; linkml:value "Severe acute respiratory syndrome coronavirus 2" . obo:GENEPIO_0001191 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:organism" ; linkml:comments "Guidance: Use \"Severe acute respiratory syndrome coronavirus 2\". This value is provided in the template."@en ; linkml:created_on "2021-05-05T20:13:16Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Taxonomic name of the organism."@en ; linkml:examples obo:GENEPIO_0001190 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001192 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms."@en ; rdfs:label "analytic datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001193 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/DOID_4"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: type of illness"@en ; owl:deprecated true . obo:GENEPIO_0001194 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:17:02Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:isolate example" ; linkml:value "hCov-19/CANADA/prov_rona_99/2020" . obo:GENEPIO_0001195 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:isolate" ; linkml:comments "Guidance: Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/xxxxx/2020”."@en ; linkml:created_on "2021-05-05T20:19:08Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Identifier of the specific isolate."@en ; linkml:examples obo:GENEPIO_0001194 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001196 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen with confirmed presence of disease agent"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0001197 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:21:37Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:purpose of sampling example" ; linkml:value "Diagnostic testing"@en . obo:GENEPIO_0001198 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:purpose of sampling" ; linkml:comments "Guidance: The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field."@en ; linkml:created_on "2021-05-05T20:23:41Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The reason that the sample was collected."@en ; linkml:examples obo:GENEPIO_0001197 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001199 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T20:26:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:purpose of sampling details example" ; linkml:value "The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada."@en . obo:GENEPIO_0001200 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:purpose of sampling details" ; linkml:comments "Guidance: Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value."@en ; linkml:created_on "2021-05-05T20:29:50Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The description of why the sample was collected, providing specific details."@en ; linkml:examples obo:GENEPIO_0001199 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001201 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-05T21:00:14Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:third party lab service provider name example" ; linkml:value "Switch Health" . obo:GENEPIO_0001202 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001122, owl:NamedIndividual ; rdfs:label "CanCOGeN:third party lab service provider name" ; linkml:comments "Guidance: Store the sample identifier supplied by the third party services provider."@en ; linkml:created_on "2021-05-05T21:02:51Z" ; linkml:description "The name of the third party company or laboratory that provided services."@en ; linkml:examples obo:GENEPIO_0001201 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001203 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:27:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:NML submitted specimen type example" ; linkml:value "swab" . obo:GENEPIO_0001204 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:28:44Z"^^xsd:dateTime ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:NML submitted specimen type" ; linkml:comments "Guidance: This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”."@en ; linkml:created_on "2021-05-11T00:28:44Z" ; linkml:description "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing."@en ; linkml:examples obo:GENEPIO_0001203 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001205 a owl:Class ; rdfs:label "dietary restriction"@en ; rdfs:subClassOf obo:BFO_0000016 . obo:GENEPIO_0001206 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A person which has a patient care role."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "patient type"@en ; rdfs:subClassOf obo:NCIT_C25190 . obo:GENEPIO_0001207 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:31:26Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:NML related specimen relationship type example" ; linkml:value "Follow-up" . obo:GENEPIO_0001208 obo:IAO_0100001 obo:NCIT_C25189 ; a owl:Class ; rdfs:label "obsolete: mother"@en ; owl:deprecated true . obo:GENEPIO_0001209 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:NML related specimen relationship type" ; linkml:comments "Guidance: Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system."@en ; linkml:created_on "2021-05-11T00:33:44Z" ; linkml:description "The relationship of the related specimen to the previous National Microbiology Laboratory (NML) submission."@en ; linkml:examples obo:GENEPIO_0001207 ; linkml:type_uri "select" . obo:GENEPIO_0001210 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:35:33Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:anatomical material example" ; linkml:value "Blood" . obo:GENEPIO_0001211 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:anatomical material" ; linkml:comments "Guidance: Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-05-11T00:37:36Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "A substance obtained from an anatomical part of an organism e.g. tissue, blood."@en ; linkml:examples obo:GENEPIO_0001210 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001212 obo:GENEPIO_0000005 "NCBI BioSample" ; obo:GENEPIO_0001763 "depth:1", "lookup" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "Note that this is closely related to OGMS_0000063 \"disease course\" that lists chronic, progressive, transient and accute processes."@en ; rdfs:label "subject disease outcome"@en ; rdfs:subClassOf obo:GENEPIO_0002018 . obo:GENEPIO_0001213 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:39:45Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:anatomical part example" ; linkml:value "Nasopharynx (NP)" . obo:GENEPIO_0001214 obo:IAO_0000114 , "requires discussion"@en ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:anatomical part" ; linkml:comments "Guidance: Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "An anatomical part of an organism e.g. oropharynx."@en ; linkml:examples obo:GENEPIO_0001213 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001215 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-05-11T00:43:38Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:body product example" ; linkml:value "Feces" . obo:GENEPIO_0001216 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:body product" ; linkml:comments "Guidance: Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-05-11T00:45:08Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "A substance excreted/secreted from an organism e.g. feces, urine, sweat."@en ; linkml:examples obo:GENEPIO_0001215 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001217 a owl:Class ; rdfs:label "treated water - warm/hot"@en ; rdfs:subClassOf obo:GENEPIO_0001276 . obo:GENEPIO_0001218 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T04:46:38Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:environmental material example" ; linkml:value "Face mask" . obo:GENEPIO_0001219 a owl:Class ; rdfs:label "jacuzzi water"@en ; rdfs:subClassOf obo:GENEPIO_0001217 . obo:GENEPIO_0001220 a owl:Class ; rdfs:label "spa water" ; rdfs:subClassOf obo:GENEPIO_0001217 . obo:GENEPIO_0001221 a owl:Class ; rdfs:label "whirlpool water"@en ; rdfs:subClassOf obo:GENEPIO_0001217 . obo:GENEPIO_0001222 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "patient as host datum"@en ; rdfs:subClassOf obo:GENEPIO_0002018, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000531 ] . obo:GENEPIO_0001223 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0100001 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:environmental material" ; linkml:comments "Guidance: Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-06-05T04:51:30Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "A substance obtained from the natural or man-made environment e.g. soil, water, sewage."@en ; linkml:examples obo:GENEPIO_0001218 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001224 a owl:Class ; rdfs:label "pregnancy history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001225 a owl:Class ; rdfs:label "date of conception"@en ; rdfs:subClassOf obo:GENEPIO_0001224 . obo:GENEPIO_0001226 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "lifespan history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001227 obo:IAO_0100001 "http://purl.obolibrary.org/obo/FOODON_03450002"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: food cooking method"@en ; owl:deprecated true . obo:GENEPIO_0001228 obo:IAO_0100001 "http://purl.obolibrary.org/obo/FOODON_03470107"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: food preservation method"@en ; owl:deprecated true . obo:GENEPIO_0001229 a owl:Class ; rdfs:label "infectious disease case datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001230 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T04:55:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:environmental site example" ; linkml:value "Production Facility" . obo:GENEPIO_0001231 a owl:Class ; rdfs:label "laboratory data"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001232 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:environmental site" ; linkml:comments "Guidance: Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-06-05T04:57:02Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave."@en ; linkml:examples obo:GENEPIO_0001230 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001233 obo:IAO_0000114 , "requires discussion"@en ; dc:date "2021-06-05T05:00:54Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:collection device example" ; linkml:value "Swab" . obo:GENEPIO_0001234 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:collection device" ; linkml:comments "Guidance: Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-06-05T05:02:28Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The instrument or container used to collect the sample e.g. swab."@en ; linkml:examples obo:GENEPIO_0001233 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001235 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T05:05:06Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:collection method example" ; linkml:value "Bronchoalveolar lavage (BAL)" . obo:GENEPIO_0001236 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "specimen record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001237 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000118 "specimen type (host or environmental context)"@en ; a owl:Class ; rdfs:label "specimen source material category"@en ; rdfs:subClassOf obo:CHMO_0000993 . obo:GENEPIO_0001238 obo:IAO_0000115 "Organism has a symbiotic relationship with host"@en ; a owl:Class ; rdfs:label "symbiotic role"@en ; rdfs:subClassOf obo:GENEPIO_0001172 . obo:GENEPIO_0001239 obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000113"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: NCBI BioSample attribute package"@en ; owl:deprecated true . obo:GENEPIO_0001240 obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000025"^^xsd:anyURI, "http://purl.obolibrary.org/obo/GENEPIO_0000028"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: host sample material"@en ; owl:deprecated true . obo:GENEPIO_0001241 obo:IAO_0000117 , "requires discussion"@en ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:collection method" ; linkml:comments "Guidance: Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value."@en ; linkml:created_on "2021-06-05T05:06:36Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The process used to collect the sample e.g. phlebotamy, necropsy."@en ; linkml:examples obo:GENEPIO_0001235 ; linkml:required true ; linkml:type_uri "select" ; linkml:value "Bronchoalveolar lavage (BAL)" . obo:GENEPIO_0001242 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T05:10:21Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:collection protocol example" ; linkml:value "BCRonaSamplingProtocol v. 1.2" . obo:GENEPIO_0001243 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:collection protocol" ; linkml:comments "Guidance: Free text."@en ; linkml:created_on "2021-06-05T05:12:09Z" ; linkml:description "The name and version of a particular protocol used for sampling."@en ; linkml:examples obo:GENEPIO_0001242 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001244 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "food specimen detail"@en ; rdfs:subClassOf obo:GENEPIO_0001532 . obo:GENEPIO_0001245 a owl:Class ; rdfs:label "patient specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001731 . obo:GENEPIO_0001246 oboInOwl:hasBroadSynonym "environmental"@en ; oboInOwl:hasDbXref "NCBI Biosample: environmental (swab or sampling)"@en ; a owl:Class ; rdfs:label "environmental specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001237 . obo:GENEPIO_0001247 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A specimen extracted from an animal"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "animal specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001237 . obo:GENEPIO_0001248 a owl:Class ; rdfs:label "built environment specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001246 . obo:GENEPIO_0001249 a owl:Class ; rdfs:label "food specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001246 . obo:GENEPIO_0001250 a owl:Class ; rdfs:label "natural environment specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001246 . obo:GENEPIO_0001251 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The type of person a patient had epidemiological (i.e. close proximity) contact with."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "exposure event person"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:GENEPIO_0001252 obo:IAO_0000114 , "requires discussion"@en ; dc:date "2021-06-05T05:14:41Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:specimen processing example" ; linkml:value "Virus passage" . obo:GENEPIO_0001253 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:specimen processing" ; linkml:comments "Guidance: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"."@en ; linkml:created_on "2021-06-05T05:16:02Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Any processing applied to the sample during or after receiving the sample."@en ; linkml:examples obo:GENEPIO_0001252 ; linkml:multivalued true ; linkml:recommended true ; linkml:type_uri "multiple" . obo:GENEPIO_0001254 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T15:59:16Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:lab host example" ; linkml:value "Vero E6 cell line" . obo:GENEPIO_0001255 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:lab host" ; linkml:comments "Guidance: Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put \"not applicable\"."@en ; linkml:created_on "2021-06-05T16:01:34Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained."@en ; linkml:examples obo:GENEPIO_0001254 ; linkml:recommended true ; linkml:type_uri "select" . obo:GENEPIO_0001256 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:passage number example" ; linkml:created_on "2021-06-05T16:04:42Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:examples obo:GENEPIO_0001256 ; linkml:recommended true ; linkml:type_uri "xs:nonNegativeInteger" ; linkml:value 3 . obo:GENEPIO_0001257 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen."@en ; rdfs:label "exposure group statistics record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001258 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "symptom history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001259 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "health state record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001260 obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C17627" ; a owl:Class ; rdfs:label "obsolete: swab"@en ; owl:deprecated true . obo:GENEPIO_0001261 obo:IAO_0000114 , "requires discussion"@en ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:passage number" ; linkml:comments "Guidance: Provide number of known passages. If not passaged, put \"not applicable\"."@en ; linkml:created_on "2021-06-05T16:06:51Z" ; linkml:description "Number of passages."@en ; linkml:type_uri ""^^xsd:nonNegativeInteger . obo:GENEPIO_0001262 obo:IAO_0000115 "[WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:NCIT_C13347 ; a owl:Class ; rdfs:label "obsolete: fluid - aspirate"@en ; owl:deprecated true . obo:GENEPIO_0001263 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T16:13:47Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:passage method example" ; linkml:value "0.25% trypsin + 0.02% EDTA" . obo:GENEPIO_0001264 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:passage method" ; linkml:comments "Guidance: Free text. Provide a very short description (<10 words). If not passaged, put \"not applicable\"."@en ; linkml:created_on "2021-06-05T16:16:51Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Description of how organism was passaged."@en ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001265 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T16:19:49Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:biomaterial extracted example" ; linkml:value "RNA (total)" . obo:GENEPIO_0001266 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001150, owl:NamedIndividual ; rdfs:label "CanCOGeN:biomaterial extracted" ; linkml:comments "Guidance: Provide the biomaterial extracted from the picklist in the template."@en ; linkml:created_on "2021-06-05T16:21:49Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The biomaterial extracted from samples for the purpose of sequencing."@en ; linkml:examples obo:GENEPIO_0001265 ; linkml:type_uri "select" . obo:GENEPIO_0001267 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Plant rinse is a rinse derived from plant material from one or more plants."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "plant rinse"@en ; rdfs:subClassOf obo:GENEPIO_0002749 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002016 obo:GENEPIO_0002749 ) ] . obo:GENEPIO_0001268 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T16:27:25Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - host information" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001269 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "outbreak animal exposure event location"@en ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:GENEPIO_0001270 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "animal exposure process"@en ; rdfs:subClassOf obo:BFO_0000015 . obo:GENEPIO_0001271 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "animal exposure event by material"@en ; rdfs:subClassOf obo:NCIT_C79916 . obo:GENEPIO_0001272 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure by human contact"@en ; rdfs:subClassOf obo:GENEPIO_0001275 . obo:GENEPIO_0001273 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 "unnecessary distinction"@en ; obo:IAO_0100001 obo:GENEPIO_0001275 ; a owl:Class ; rdfs:label "obsolete: human exposure activity type"@en ; owl:deprecated true . obo:GENEPIO_0001274 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "outbreak human exposure event location"@en ; rdfs:subClassOf obo:GENEPIO_0001297 . obo:GENEPIO_0001275 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "human to human exposure process"@en ; rdfs:subClassOf obo:BFO_0000015 . obo:GENEPIO_0001276 a owl:Class ; rdfs:label "water exposure by source"@en ; rdfs:subClassOf obo:NCIT_C79916 . obo:GENEPIO_0001277 a owl:Class ; rdfs:label "human water activity"@en ; rdfs:subClassOf obo:GENEPIO_0001444 . obo:GENEPIO_0001278 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:44:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host (common name) example" ; linkml:value "Human" . obo:GENEPIO_0001279 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:54:18Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host (scientific name) example" ; linkml:value "Homo sapiens" . obo:GENEPIO_0001280 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:55:40Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host health state example" ; linkml:value "Symptomatic" . obo:GENEPIO_0001281 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:56:55Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host health status details example" ; linkml:value "Hospitalized (ICU)" . obo:GENEPIO_0001282 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:58:04Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host health outcome example" ; linkml:value "Recovered" . obo:GENEPIO_0001283 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T20:59:43Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host disease example" ; linkml:value "COVID-19" . obo:GENEPIO_0001284 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:01:00Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host age example" ; linkml:value 79 . obo:GENEPIO_0001285 obo:IAO_0000114 , "requires discussion"@en ; dc:date "2021-06-05T21:03:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host age unit example" ; linkml:value "years" . obo:GENEPIO_0001286 a owl:Class ; rdfs:comment "This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example."@en ; rdfs:label "health authority"@en ; rdfs:subClassOf obo:OBI_0000245 . obo:GENEPIO_0001287 obo:GENEPIO_0001763 """order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "symptom record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001288 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:05:05Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host age bin example" ; linkml:value "60 - 69" . obo:GENEPIO_0001289 obo:IAO_0000115 "A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate."@en ; a owl:Class ; rdfs:label "PFGE pattern"@en ; rdfs:subClassOf obo:GENEPIO_0001688, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C53471 ] . obo:GENEPIO_0001290 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:06:49Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host gender example" ; linkml:value "male" . obo:GENEPIO_0001291 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "phage type salmonella (DT)"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001292 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "phage type e-coli 0157 (PT)"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001293 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "sequence record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001294 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:08:26Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host residence geo_loc name (country) example" ; linkml:value "United Kingdom" . obo:GENEPIO_0001295 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:10:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host residence geo_loc name (state/province/territory) example" ; linkml:value "Quebec" . obo:GENEPIO_0001296 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:16:16Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host subject ID example" ; linkml:value "BCxy123" . obo:GENEPIO_0001297 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A type of built structure that is suspected to be related to an outbreak investigation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "outbreak exposure event location"@en ; rdfs:seeAlso "http://purl.obolibrary.org/obo/ENVO_00000070" ; rdfs:subClassOf obo:NCIT_C79916 . obo:GENEPIO_0001298 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:18:55Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:symptom onset date example" ; linkml:value "2020-03-16" . obo:GENEPIO_0001299 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:20:59Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:signs and symptoms example" ; linkml:value "Chills (sudden cold sensation); Cough; Fever" . obo:GENEPIO_0001300 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:24:06Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:pre-existing conditions and risk factors example" ; linkml:value "Asthma; Pregnancy; Smoking" . obo:GENEPIO_0001301 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:25:55Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:complications example" ; linkml:value "Acute Respiratory Failure; Coma; Septicemia" . obo:GENEPIO_0001302 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "lab test history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001303 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:27:27Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host vaccination status example" ; linkml:value "Fully Vaccinated" . obo:GENEPIO_0001304 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:28:41Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:vaccine name example" ; linkml:value "Pfizer-BioNTech COVID-19 vaccine" . obo:GENEPIO_0001305 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:29:57Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:number of vaccine doses received example" ; linkml:value 2 . obo:GENEPIO_0001306 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:31:07Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:first dose vaccination date example" ; linkml:value "2021-02-26" . obo:GENEPIO_0001307 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:32:48Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:last dose vaccination date example" ; linkml:value "2021-04-09" . obo:GENEPIO_0001308 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:34:28Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:location of exposure geo_loc name (country) example" ; linkml:value "Canada" . obo:GENEPIO_0001309 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:36:18Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:destination of most recent travel (city) example" ; linkml:value "New York City" . obo:GENEPIO_0001310 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:37:37Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:destination of most recent travel (state/province/territory) example" ; linkml:value "California" . obo:GENEPIO_0001311 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:40:27Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:destination of most recent travel (country) example" ; linkml:value "United Kingdom" . obo:GENEPIO_0001312 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T21:42:17Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:most recent travel departure date example" ; linkml:value "2020-03-16" . obo:GENEPIO_0001313 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:49:15Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:most recent travel return date example" ; linkml:value "2020-04-26" . obo:GENEPIO_0001314 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:50:35Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:travel history example" ; linkml:value "Canada, Vancouver; USA, Seattle; Italy, Milan" . obo:GENEPIO_0001315 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:53:15Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:exposure event example" ; linkml:value "Convention" . obo:GENEPIO_0001316 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:54:46Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:exposure contact level example" ; linkml:value "Direct" . obo:GENEPIO_0001317 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:56:00Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:host role example" ; linkml:value "Patient" . obo:GENEPIO_0001318 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:57:05Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:exposure setting example" ; linkml:value "Healthcare Setting" . obo:GENEPIO_0001319 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:58:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:exposure details example" ; linkml:value "Host role - Other: Bus Driver" . obo:GENEPIO_0001320 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T22:59:56Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection example" ; linkml:value "Yes" . obo:GENEPIO_0001321 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:01:11Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection isolate example" ; linkml:value "SARS-CoV-2/human/USA/CA-CDPH-001/2020" . obo:GENEPIO_0001322 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:02:44Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection date example" ; linkml:value "2021-01-23" . obo:GENEPIO_0001323 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:05:15Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment example" ; linkml:value "No prior antiviral treatment" . obo:GENEPIO_0001324 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:06:40Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment agent example" ; linkml:value "Remdesivir" . obo:GENEPIO_0001325 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:08:46Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment date example" ; linkml:value "2021-01-28" . obo:GENEPIO_0001326 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:11:15Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:purpose of sequencing example" ; linkml:value "Diagnostic testing" . obo:GENEPIO_0001327 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:15:01Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:purpose of sequencing details example" ; linkml:value "Screened for S gene target failure (S dropout)" . obo:GENEPIO_0001328 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:15:59Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequencing date example" ; linkml:value "2020-06-22" . obo:GENEPIO_0001329 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:17:34Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:library ID example" ; linkml:value "XYZ_123345" . obo:GENEPIO_0001330 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:19:32Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:amplicon size example" ; linkml:value "300bp" . obo:GENEPIO_0001331 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:21:00Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:library preparation kit example" ; linkml:value "Nextera XT" . obo:GENEPIO_0001332 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:22:27Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:flow cell barcode example" ; linkml:value "FAB06069" . obo:GENEPIO_0001333 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:23:55Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequencing instrument example" ; linkml:value "MinIon" . obo:GENEPIO_0001334 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:25:16Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequencing protocol name example" ; linkml:value "https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann" . obo:GENEPIO_0001335 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:27:00Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequencing protocol example" ; linkml:value "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." . obo:GENEPIO_0001336 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:28:10Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:sequencing kit number example" ; linkml:value "AB456XYZ789" . obo:GENEPIO_0001337 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:29:37Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:amplicon pcr primer scheme example" ; linkml:value "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" . obo:GENEPIO_0001338 obo:IAO_0100001 obo:RBO_00000017 ; a owl:Class ; rdfs:label "obsolete: earth surface"@en ; owl:deprecated true . obo:GENEPIO_0001339 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:31:04Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:raw sequence data processing method example" ; linkml:value "Porechop 0.2.3" . obo:GENEPIO_0001340 a owl:ObjectProperty ; rdfs:label "obsolete has string specification of"@en ; owl:deprecated true . obo:GENEPIO_0001341 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:32:39Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:dehosting method example" ; linkml:value "Nanostripper" . obo:GENEPIO_0001342 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts."@en ; obo:IAO_0000116 "A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "data specification"@en ; rdfs:seeAlso ; rdfs:subClassOf obo:OBI_0000658 . obo:GENEPIO_0001343 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:34:01Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus sequence name example" ; linkml:value "ncov123assembly3" . obo:GENEPIO_0001344 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T04:49:26Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus sequence filename example" ; linkml:value "ncov123assembly.fasta" . obo:GENEPIO_0001345 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:37:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus sequence filepath example" ; linkml:value "/User/Documents/RespLab/Data/ncov123assembly.fasta" . obo:GENEPIO_0001346 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:38:48Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus sequence software name example" ; linkml:value "Ivar" . obo:GENEPIO_0001347 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:40:31Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus sequence software version example" ; linkml:value 1.3 . obo:GENEPIO_0001348 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:41:41Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:breadth of coverage value example" ; linkml:value "95%" . obo:GENEPIO_0001349 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:43:16Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:depth of coverage value example" ; linkml:value "400x" . obo:GENEPIO_0001350 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:44:32Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:depth of coverage threshold example" ; linkml:value "100x" . obo:GENEPIO_0001351 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:46:13Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:r1 fastq filename example" ; linkml:value "ABC123_S1_L001_R1_001.fastq.gz" . obo:GENEPIO_0001352 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:47:22Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:r2 fastq filename example" ; linkml:value "ABC123_S1_L001_R2_001.fastq.gz" . obo:GENEPIO_0001353 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:48:39Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:r1 fastq filepath example" ; linkml:value "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" . obo:GENEPIO_0001354 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:50:10Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:r2 fastq filepath example" ; linkml:value "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" . obo:GENEPIO_0001355 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:51:16Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:fast5 filename example" ; linkml:value "rona123assembly.fast5" . obo:GENEPIO_0001356 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A specimen history item is a time-related datum about a particular specimen"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "specimen history item"@en ; rdfs:subClassOf obo:GENEPIO_0001790, obo:IAO_0000416 . obo:GENEPIO_0001357 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-05T23:52:36Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:fast5 filepath example" ; linkml:value "/User/Documents/RespLab/Data/rona123assembly.fast5" . obo:GENEPIO_0001358 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:32:27Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:number of base pairs sequenced example" ; linkml:value 387566 . obo:GENEPIO_0001359 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:34:38Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:consensus genome length example" ; linkml:value 38677 . obo:GENEPIO_0001360 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:36:03Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:Ns per 100 kbp example" ; linkml:value 330 . obo:GENEPIO_0001361 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:37:23Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:reference genome accession example" ; linkml:value "NC_045512.2" . obo:GENEPIO_0001362 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:38:44Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:bioinformatics protocol example" ; linkml:value "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" . obo:GENEPIO_0001363 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:40:42Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:lineage/clade name example" ; linkml:value "B.1.1.7" . obo:GENEPIO_0001364 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:41:49Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:lineage/clade analysis software name example" ; linkml:value "Pangolin" . obo:GENEPIO_0001365 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:42:59Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:lineage/clade analysis software version example" ; linkml:value "2.1.10" . obo:GENEPIO_0001366 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T15:43:35Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:variant designation example" ; linkml:value "Variant of Concern" . obo:GENEPIO_0001367 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; obo:RO_0001025 obo:GAZ_00002562 ; obo:RO_0002351 obo:GENEPIO_0001368, obo:GENEPIO_0001369, obo:GENEPIO_0001370, obo:GENEPIO_0001372, obo:GENEPIO_0001373 ; a obo:GENEPIO_0001286, owl:NamedIndividual ; rdfs:comment "Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software."@en . obo:GENEPIO_0001368 obo:RO_0002350 obo:GENEPIO_0001367 ; a owl:NamedIndividual . obo:GENEPIO_0001369 obo:RO_0002350 obo:GENEPIO_0001367 ; a owl:NamedIndividual . obo:GENEPIO_0001370 obo:RO_0002350 obo:GENEPIO_0001367 ; a owl:NamedIndividual . obo:GENEPIO_0001371 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:45:38Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:variant evidence example" ; linkml:value "RT-qPCR" . obo:GENEPIO_0001372 obo:RO_0002350 obo:GENEPIO_0001367 ; a owl:NamedIndividual . obo:GENEPIO_0001373 obo:RO_0002350 obo:GENEPIO_0001367 ; a owl:NamedIndividual . obo:GENEPIO_0001374 obo:IAO_0000117 , "requires discussion"@en ; dc:date "2021-06-06T00:46:44Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:variant evidence details example" ; linkml:value "Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." . obo:GENEPIO_0001375 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:48:08Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:gene name 1 example" ; linkml:value "E gene (orf4)" . obo:GENEPIO_0001376 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:49:54Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr protocol 1 example" ; linkml:value "EGenePCRTest 2" . obo:GENEPIO_0001377 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:51:23Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 1 example" ; linkml:value 21 . obo:GENEPIO_0001378 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:53:14Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:gene name 2 example" ; linkml:value "RdRp gene (nsp12)" . obo:GENEPIO_0001379 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:54:49Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr protocol 2 example" ; linkml:value "RdRpGenePCRTest 3" . obo:GENEPIO_0001380 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:56:07Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 2 example" ; linkml:value 36 . obo:GENEPIO_0001381 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:57:23Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:gene name 3 example" ; linkml:value "RdRp gene (nsp12)" . obo:GENEPIO_0001382 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T00:59:09Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr protocol 3 example" ; linkml:value "RdRpGenePCRTest 3" . obo:GENEPIO_0001383 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T01:00:11Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 3 example" ; linkml:value 30 . obo:GENEPIO_0001384 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T01:01:29Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:authors example" ; linkml:value "Tejinder Singh, Fei Hu, Joe Blogs" . obo:GENEPIO_0001385 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T01:02:39Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:DataHarmonizer provenance example" ; linkml:value "DataHarmonizer provenance: v0.13.21" . obo:GENEPIO_0001386 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host (common name)" ; linkml:comments "Guidance: Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put \"not applicable."@en ; linkml:created_on "2021-06-06T01:12:52Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The commonly used name of the host."@en ; linkml:examples obo:GENEPIO_0001278 ; linkml:type_uri "select" . obo:GENEPIO_0001387 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host (scientific name)" ; linkml:comments "Guidance: Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable\"."@en ; linkml:data_collection_state "2021-06-06T01:15:53Z", "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The taxonomic, or scientific name of the host."@en ; linkml:examples obo:GENEPIO_0001279 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001388 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host health state" ; linkml:comments "Guidance: If known, select a descriptor from the pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:19:17Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Health status of the host at the time of sample collection."@en ; linkml:examples obo:GENEPIO_0001280 ; linkml:type_uri "select" . obo:GENEPIO_0001389 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host health status details" ; linkml:comments "Guidance: If known, select a descriptor from the pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:21:56Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Further details pertaining to the health or disease status of the host at time of collection."@en ; linkml:examples obo:GENEPIO_0001281 ; linkml:type_uri "select" . obo:GENEPIO_0001390 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host health outcome" ; linkml:comments "Guidance: If known, select a descriptor from the pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:25:19Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Disease outcome in the host."@en ; linkml:examples obo:GENEPIO_0001282 ; linkml:type_uri "select" . obo:GENEPIO_0001391 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host disease" ; linkml:comments "Guidance: Select \"COVID-19\" from the pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:30:00Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the disease experienced by the host."@en ; linkml:examples obo:GENEPIO_0001283 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001392 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host age" ; linkml:comments "Guidance: Enter the age of the host in years. If not available, provide a null value. If there is not host, put \"Not Applicable\"."@en ; linkml:created_on "2021-06-06T01:33:44Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Age of host at the time of sampling."@en ; linkml:examples obo:GENEPIO_0001284 ; linkml:maximum_value 130 ; linkml:minimum_value 0 ; linkml:required true ; linkml:type_uri ""^^xsd:decimal . obo:GENEPIO_0001393 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host age unit" ; linkml:comments "Guidance: Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin."@en ; linkml:created_on "2021-06-06T01:37:16Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The unit used to measure the host age, in either months or years."@en ; linkml:examples obo:GENEPIO_0001285 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001394 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host age bin" ; linkml:comments "Guidance: Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value."@en ; linkml:created_on "2021-06-06T01:40:27Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Age of host at the time of sampling, expressed as an age group."@en ; linkml:examples obo:GENEPIO_0001288 ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001395 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host gender" ; linkml:comments "Guidance: Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put \"Not Applicable\"."@en ; linkml:created_on "2021-06-06T01:43:06Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The gender of the host at the time of sample collection."@en ; linkml:examples obo:GENEPIO_0001290 ; linkml:pattern "Title" ; linkml:required true ; linkml:type_uri "select" . obo:GENEPIO_0001396 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host residence geo_loc name (country)" ; linkml:comments "Guidance: Select the country name from pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:46:24Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The country of residence of the host."@en ; linkml:examples obo:GENEPIO_0001294 ; linkml:type_uri "select" . obo:GENEPIO_0001397 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host residence geo_loc name (state/province/territory)" ; linkml:comments "Guidance: Select the province/territory name from pick list provided in the template."@en ; linkml:created_on "2021-06-06T01:49:16Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The state/province/territory of residence of the host."@en ; linkml:examples obo:GENEPIO_0001295 ; linkml:type_uri "select" . obo:GENEPIO_0001398 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:host subject ID" ; linkml:comments "Guidance: Provide the host identifier. Should be a unique, user-defined identifier."@en ; linkml:created_on "2021-06-06T01:51:47Z" ; linkml:description "A unique identifier by which each host can be referred to e.g. #131"@en ; linkml:examples obo:GENEPIO_0001296 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001399 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:symptom onset date" ; linkml:comments "Guidance: ISO 8601 standard \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T01:55:32Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date on which the symptoms began or were first noted."@en ; linkml:examples obo:GENEPIO_0001298 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001400 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:signs and symptoms" ; linkml:comments "Guidance: Select all of the symptoms experienced by the host from the pick list."@en ; linkml:created_on "2021-06-06T01:58:29Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician."@en ; linkml:examples obo:GENEPIO_0001299 ; linkml:multivalued true ; linkml:type_uri "multiple" . obo:GENEPIO_0001401 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:pre-existing conditions and risk factors" ; linkml:comments "Guidance: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team."@en ; linkml:created_on "2021-06-06T02:01:27Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description """Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection."""@en ; linkml:examples obo:GENEPIO_0001300 ; linkml:multivalued true ; linkml:type_uri "multiple" . obo:GENEPIO_0001402 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001268, owl:NamedIndividual ; rdfs:label "CanCOGeN:complications" ; linkml:comments "Guidance: Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team."@en ; linkml:created_on "2021-06-06T02:06:19Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Patient medical complications that are believed to have occurred as a result of host disease."@en ; linkml:examples obo:GENEPIO_0001301 ; linkml:multivalued true ; linkml:type_uri "multiple" . obo:GENEPIO_0001403 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T02:10:31Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - host vaccination information" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001404 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001403, owl:NamedIndividual ; rdfs:label "CanCOGeN:host vaccination status" ; linkml:comments "Guidance: Select the vaccination status of the host from the pick list."@en ; linkml:created_on "2021-06-06T02:26:47Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated)."@en ; linkml:examples obo:GENEPIO_0001303 ; linkml:type_uri "select" . obo:GENEPIO_0001405 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001403, owl:NamedIndividual ; rdfs:label "CanCOGeN:vaccine name" ; linkml:comments "Guidance: Free text. Provide the name of the vaccine."@en ; linkml:created_on "2021-06-06T02:29:12Z" ; linkml:description "The name of the vaccine."@en ; linkml:examples obo:GENEPIO_0001304 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001406 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001403, owl:NamedIndividual ; rdfs:label "CanCOGeN:number of vaccine doses received" ; linkml:comments "Guidance: Record how many doses of the vaccine the host has received."@en ; linkml:created_on "2021-06-06T02:31:41Z" ; linkml:description "The number of doses of the vaccine recived by the host."@en ; linkml:examples obo:GENEPIO_0001305 ; linkml:type_uri ""^^xsd:nonNegativeInteger . obo:GENEPIO_0001407 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001403, owl:NamedIndividual ; rdfs:label "CanCOGeN:first dose vaccination date" ; linkml:comments "Guidance: Provide the vaccination date in ISO 8601 standard format \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T02:37:31Z" ; linkml:description "The date the host was first vaccinated."@en ; linkml:examples obo:GENEPIO_0001306 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001408 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001403, owl:NamedIndividual ; rdfs:label "CanCOGeN:last dose vaccination date" ; linkml:comments "Guidance: Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T02:40:02Z" ; linkml:description "The date the host received their last dose of vaccine."@en ; linkml:examples obo:GENEPIO_0001307 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001409 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T02:44:19Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - host exposure information" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001410 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:location of exposure geo_loc name (country)" ; linkml:comments "Guidance: Select the country name from pick list provided in the template."@en ; linkml:created_on "2021-06-06T02:46:05Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The country where the host was likely exposed to the causative agent of the illness."@en ; linkml:examples obo:GENEPIO_0001308 ; linkml:type_uri "select" . obo:GENEPIO_0001411 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:destination of most recent travel (city)" ; linkml:comments "Guidance: Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz"@en ; linkml:description "The name of the city that was the destination of most recent travel."@en ; linkml:examples obo:GENEPIO_0001309 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001412 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:destination of most recent travel (state/province/territory)" ; linkml:comments "Guidance: Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz"@en ; linkml:created_on "2021-06-06T02:53:39Z" ; linkml:description "The name of the province that was the destination of most recent travel."@en ; linkml:examples obo:GENEPIO_0001310 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001413 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:destination of most recent travel (country)" ; linkml:comments "Guidance: Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz"@en ; linkml:created_on "2021-06-06T02:56:11Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the country that was the destination of most recent travel."@en ; linkml:examples obo:GENEPIO_0001311 ; linkml:type_uri "select" . obo:GENEPIO_0001414 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:most recent travel departure date" ; linkml:comments "Guidance: Provide the travel departure date."@en ; linkml:created_on "2021-06-06T02:59:30Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations."@en ; linkml:examples obo:GENEPIO_0001312 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001415 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:most recent travel return date" ; linkml:comments "Guidance: Provide the travel return date."@en ; linkml:created_on "2021-06-06T03:02:03Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date of a person's most recent return to some residence from a journey originating at that residence."@en ; linkml:examples obo:GENEPIO_0001313 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001416 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:travel history" ; linkml:comments "Guidance: Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first."@en ; linkml:created_on "2021-06-06T03:05:00Z" ; linkml:description "Travel history in last six months."@en ; linkml:examples obo:GENEPIO_0001314 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001417 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:exposure event" ; linkml:comments "Guidance: Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team."@en ; linkml:created_on "2021-06-06T03:07:13Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Event leading to exposure."@en ; linkml:examples obo:GENEPIO_0001315 ; linkml:type_uri "select" . obo:GENEPIO_0001418 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:exposure contact level" ; linkml:comments "Guidance: Select direct or indirect exposure from the pick-list."@en ; linkml:created_on "2021-06-06T03:09:35Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The exposure transmission contact type."@en ; linkml:examples obo:GENEPIO_0001316 ; linkml:type_uri "select" . obo:GENEPIO_0001419 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:host role" ; linkml:comments "Guidance: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team."@en ; linkml:created_on "2021-06-06T03:11:55Z" ; linkml:description "The role of the host in relation to the exposure setting."@en ; linkml:examples obo:GENEPIO_0001317 ; linkml:multivalued true ; linkml:type_uri "multiple" . obo:GENEPIO_0001420 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "diagnostic test"@en ; rdfs:subClassOf obo:OBI_0000070 . obo:GENEPIO_0001421 obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "obsolete: sample datum"@en ; owl:deprecated true . obo:GENEPIO_0001422 obo:IAO_0000115 "A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001681"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: laboratory sequencing datum"@en ; owl:deprecated true . obo:GENEPIO_0001423 a owl:Class ; rdfs:label "genomic sequencing annotation datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001424 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "ISSUE: lab test results are appropriate to lab test types. Logic around that?"@en ; rdfs:label "lab test record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001425 a owl:Class ; rdfs:label "sequencing assembly datum"@en ; rdfs:subClassOf obo:GENEPIO_0001681, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C53471 ] . obo:GENEPIO_0001426 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "container record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001427 obo:IAO_0000117 "Damion Dooley"@en, "identifier of a person with the context of a health care system"@en ; a owl:Class ; rdfs:label "health care personal identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001428 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:exposure setting" ; linkml:comments "Guidance: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team."@en ; linkml:created_on "2021-06-06T03:14:25Z" ; linkml:description "The setting leading to exposure."@en ; linkml:examples obo:GENEPIO_0001318 ; linkml:multivalued true ; linkml:type_uri "multiple" . obo:GENEPIO_0001429 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "strain identifier"@en ; rdfs:subClassOf obo:IAO_0000577, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C14419 ] . obo:GENEPIO_0001430 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 """A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient."""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "line list object"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001431 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001409, owl:NamedIndividual ; rdfs:label "CanCOGeN:exposure details" ; linkml:comments "Guidance: Free text description of the exposure."@en ; linkml:created_on "2021-06-06T03:17:19Z" ; linkml:description "Additional host exposure information."@en ; linkml:examples obo:GENEPIO_0001319 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001432 obo:IAO_0000115 "This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "awaiting ontology review"@en ; rdfs:subClassOf owl:Thing . obo:GENEPIO_0001433 obo:IAO_0000115 "The IRIDA user ID is a user account identifier provided by the IRIDA.ca system."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001799 . obo:GENEPIO_0001434 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T03:37:37Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - host reinfection information" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001435 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection" ; linkml:comments "Guidance: If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list."@en ; linkml:created_on "2021-06-06T03:40:19Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Whether there was prior SARS-CoV-2 infection."@en ; linkml:examples obo:GENEPIO_0001320 ; linkml:type_uri "select" . obo:GENEPIO_0001436 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection isolate" ; linkml:comments "Guidance: Provide the isolate name of the most recent prior infection. Structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"SARS-CoV-2/host/country/sampleID/date\"."@en ; linkml:created_on "2021-06-06T03:43:38Z" ; linkml:description "The identifier of the isolate found in the prior SARS-CoV-2 infection."@en ; linkml:examples obo:GENEPIO_0001321 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001437 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 infection date" ; linkml:comments "Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T03:47:22Z" ; linkml:description "The date of diagnosis of the prior SARS-CoV-2 infection."@en ; linkml:examples obo:GENEPIO_0001322 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001438 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment" ; linkml:comments "Guidance: If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list."@en ; linkml:created_on "2021-06-06T03:50:07Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "Whether there was prior SARS-CoV-2 treatment with an antiviral agent."@en ; linkml:examples obo:GENEPIO_0001323 ; linkml:type_uri "select" . obo:GENEPIO_0001439 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment agent" ; linkml:comments "Guidance: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put \"No treatment\". If multiple antiviral agents were administered, list them all separated by commas."@en ; linkml:created_on "2021-06-06T03:52:27Z" ; linkml:description "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection."@en ; linkml:examples obo:GENEPIO_0001324 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001440 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001434, owl:NamedIndividual ; rdfs:label "CanCOGeN:prior SARS-CoV-2 antiviral treatment date" ; linkml:comments "Guidance: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T03:55:02Z" ; linkml:description "The date treatment was first administered during the prior SARS-CoV-2 infection."@en ; linkml:examples obo:GENEPIO_0001325 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001441 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T03:57:41Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - sequencing" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001442 obo:IAO_0000115 "The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure group healthy count"@en ; rdfs:subClassOf obo:STATO_0000047 . obo:GENEPIO_0001443 obo:IAO_0000115 "The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure group ill count"@en ; rdfs:subClassOf obo:STATO_0000047 . obo:GENEPIO_0001444 a owl:Class ; rdfs:label "human general activity"@en ; rdfs:subClassOf obo:BFO_0000015 . obo:GENEPIO_0001445 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:purpose of sequencing" ; linkml:comments "Guidance: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field."@en ; linkml:created_on "2021-06-06T03:59:00Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The reason that the sample was sequenced."@en ; linkml:examples obo:GENEPIO_0001326 ; linkml:multivalued true ; linkml:required true ; linkml:type_uri "multiple" . obo:GENEPIO_0001446 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:purpose of sequencing details" ; linkml:comments "Guidance: Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection."@en ; linkml:created_on "2021-06-06T04:02:15Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The description of why the sample was sequenced providing specific details."@en ; linkml:examples obo:GENEPIO_0001327 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001447 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequencing date" ; linkml:comments "Guidance: ISO 8601 standard \"YYYY-MM-DD\"."@en ; linkml:created_on "2021-06-06T04:05:23Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The date the sample was sequenced."@en ; linkml:examples obo:GENEPIO_0001328 ; linkml:type_uri ""^^xsd:date . obo:GENEPIO_0001448 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:library ID" ; linkml:comments "Guidance: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID."@en ; linkml:created_on "2021-06-06T04:08:07Z" ; linkml:description "The user-specified identifier for the library prepared for sequencing."@en ; linkml:examples obo:GENEPIO_0001329 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001449 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:amplicon size" ; linkml:comments "Guidance: Provide the amplicon size, including the units."@en ; linkml:created_on "2021-06-06T04:10:22Z" ; linkml:description "The length of the amplicon generated by PCR amplification."@en ; linkml:examples obo:GENEPIO_0001330 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001450 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:library preparation kit" ; linkml:comments "Guidance: Provide the name of the library preparation kit used."@en ; linkml:created_on "2021-06-06T04:12:44Z" ; linkml:description "The name of the DNA library preparation kit used to generate the library being sequenced."@en ; linkml:examples obo:GENEPIO_0001331 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001451 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:flow cell barcode" ; linkml:comments "Guidance: Provide the barcode of the flow cell used for sequencing the sample."@en ; linkml:created_on "2021-06-06T04:15:34Z" ; linkml:description "The barcode of the flow cell used for sequencing."@en ; linkml:examples obo:GENEPIO_0001332 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001452 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequencing instrument" ; linkml:comments "Guidance: Select a sequencing instrument from the picklist provided in the template."@en ; linkml:created_on "2021-06-06T04:17:50Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The model of the sequencing instrument used."@en ; linkml:examples obo:GENEPIO_0001333 ; linkml:multivalued true ; linkml:required true ; linkml:type_uri "multiple" . obo:GENEPIO_0001453 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequencing protocol name" ; linkml:comments "Guidance: Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION"@en ; linkml:created_on "2021-06-06T04:21:01Z" ; linkml:description "The name and version number of the sequencing protocol used."@en ; linkml:examples obo:GENEPIO_0001334 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001454 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequencing protocol" ; linkml:comments "Guidance: Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit.\""@en ; linkml:created_on "2021-06-06T04:23:45Z" ; linkml:description "The protocol used to generate the sequence."@en ; linkml:examples obo:GENEPIO_0001335 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001455 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:sequencing kit number" ; linkml:comments "Guidance: Alphanumeric value."@en ; linkml:created_on "2021-06-06T04:26:08Z" ; linkml:description "The manufacturer's kit number."@en ; linkml:examples obo:GENEPIO_0001336 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001456 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001441, owl:NamedIndividual ; rdfs:label "CanCOGeN:amplicon pcr primer scheme" ; linkml:comments "Guidance: Provide the name and version of the primer scheme used to generate the amplicons for sequencing."@en ; linkml:created_on "2021-06-06T04:28:35Z" ; linkml:description "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced."@en ; linkml:examples obo:GENEPIO_0001337 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001457 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T04:32:59Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - bioinformatics and QC metrics" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001458 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:raw sequence data processing method" ; linkml:comments "Guidance: Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3"@en ; linkml:created_on "2021-06-06T04:34:17Z" ; linkml:description "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc."@en ; linkml:examples obo:GENEPIO_0001339 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001459 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:dehosting method" ; linkml:comments "Guidance: Provide the name and version number of the software used to remove host reads."@en ; linkml:created_on "2021-06-06T04:41:47Z2021-06-06T04:41:47Z" ; linkml:description "The method used to remove host reads from the pathogen sequence."@en ; linkml:examples obo:GENEPIO_0001341 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001460 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus sequence name" ; linkml:comments "Guidance: Provide the name and version number of the consensus sequence."@en ; linkml:created_on "2021-06-06T04:44:41Z" ; linkml:description "The name of the consensus sequence."@en ; linkml:examples obo:GENEPIO_0001343 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001461 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus sequence filename" ; linkml:comments "Guidance: Provide the name and version number of the consensus sequence FASTA file."@en ; linkml:created_on "2021-06-06T04:47:05Z" ; linkml:description "The name of the consensus sequence file."@en ; linkml:examples obo:GENEPIO_0001344 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001462 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus sequence filepath" ; linkml:comments "Guidance: Provide the filepath of the consensus sequence FASTA file."@en ; linkml:created_on "2021-06-06T04:49:26Z" ; linkml:description "The filepath of the consesnsus sequence file."@en ; linkml:examples obo:GENEPIO_0001345 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001463 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus sequence software name" ; linkml:comments "Guidance: Provide the name of the software used to generate the consensus sequence."@en ; linkml:created_on "2021-06-06T04:53:51Z" ; linkml:description "The name of software used to generate the consensus sequence.The name of software used to generate the consensus sequence."@en ; linkml:examples obo:GENEPIO_0001346 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001464 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value."@en ; rdfs:label "exposure history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001465 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "isolate history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001466 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet)."@en ; rdfs:label "outbreak history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001467 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Needs to cover the various pregnancy events"@en ; rdfs:label "pregnancy history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001468 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary \"Illness causality\" with respect to a particular case? Requires a relation annotation."@en ; rdfs:label "diagnosis record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001469 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus sequence software version" ; linkml:comments "Guidance: Provide the version of the software used to generate the consensus sequence."@en ; linkml:created_on "2021-06-06T04:56:20Z" ; linkml:description "The version of the software used to generate the consensus sequence."@en ; linkml:examples obo:GENEPIO_0001347 ; linkml:required true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001470 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure event record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001471 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "hospitalization event record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001472 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:breadth of coverage value" ; linkml:comments "Guidance: Provide value as a percent."@en ; linkml:created_on "2021-06-06T04:58:59Z" ; linkml:description "The percentage of the reference genome covered by the sequenced data, to a prescribed depth."@en ; linkml:examples obo:GENEPIO_0001348 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001473 a owl:Class ; rdfs:comment "An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value."@en ; rdfs:label "exposure history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001474 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:depth of coverage value" ; linkml:comments "Guidance: Provide value as a fold of coverage."@en ; linkml:created_on "2021-06-06T05:01:30Z" ; linkml:description "The average number of reads representing a given nucleotide in the reconstructed sequence."@en ; linkml:examples obo:GENEPIO_0001349 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001475 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:depth of coverage threshold" ; linkml:comments "Guidance: Provide the threshold fold coverage."@en ; linkml:created_on "2021-06-06T05:03:32Z" ; linkml:description "The threshold used as a cut-off for the depth of coverage."@en ; linkml:examples obo:GENEPIO_0001350 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001476 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:r1 fastq filename" ; linkml:comments "Guidance: Provide the r1 FASTQ filename."@en ; linkml:created_on "2021-06-06T05:05:51Z" ; linkml:description "The user-specified filename of the r1 FASTQ file."@en ; linkml:examples obo:GENEPIO_0001351 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001477 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:r2 fastq filename" ; linkml:comments "Guidance: Provide the r2 FASTQ filename."@en ; linkml:created_on "2021-06-06T05:09:13Z" ; linkml:description "The user-specified filename of the r2 FASTQ file."@en ; linkml:examples obo:GENEPIO_0001352 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001478 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:r1 fastq filepath" ; linkml:comments "Guidance: Provide the filepath for the r1 FASTQ file. This information aids in data management."@en ; linkml:created_on "2021-06-06T05:11:46Z" ; linkml:description "The location of the r1 FASTQ file within a user's file system."@en ; linkml:examples obo:GENEPIO_0001353 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001479 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:r2 fastq filepath" ; linkml:comments "Guidance: Provide the filepath for the r2 FASTQ file. This information aids in data management."@en ; linkml:created_on "2021-06-06T15:02:08Z" ; linkml:description "The location of the r2 FASTQ file within a user's file system."@en ; linkml:examples obo:GENEPIO_0001354 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001480 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:fast5 filename" ; linkml:comments "Guidance: Provide the FAST5 filename."@en ; linkml:created_on "2021-06-06T15:05:06Z" ; linkml:description "The user-specified filename of the FAST5 file."@en ; linkml:examples obo:GENEPIO_0001355 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001481 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:fast5 filepath" ; linkml:comments "Guidance: Provide the filepath for the FAST5 file. This information aids in data management."@en ; linkml:created_on "2021-06-06T15:07:22Z" ; linkml:description "The location of the FAST5 file within a user's file system."@en ; linkml:examples obo:GENEPIO_0001357 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001482 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:number of base pairs sequenced" ; linkml:comments "Guidance: Provide a numerical value (no need to include units)."@en ; linkml:created_on "2021-06-06T15:10:14Z" ; linkml:description "The number of total base pairs generated by the sequencing process."@en ; linkml:examples obo:GENEPIO_0001358 ; linkml:type_uri ""^^xsd:nonNegativeInteger . obo:GENEPIO_0001483 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:consensus genome length" ; linkml:comments "Guidance: Provide a numerical value (no need to include units)."@en ; linkml:created_on "2021-06-06T15:13:54Z" ; linkml:description "Size of the reconstructed genome described as the number of base pairs."@en ; linkml:examples obo:GENEPIO_0001359 ; linkml:type_uri ""^^xsd:nonNegativeInteger . obo:GENEPIO_0001484 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:Ns per 100 kbp" ; linkml:comments "Guidance: Provide a numerical value (no need to include units)."@en ; linkml:created_on "2021-06-06T15:18:08Z" ; linkml:description "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence."@en ; linkml:examples obo:GENEPIO_0001360 ; linkml:minimum_value 0 ; linkml:type_uri ""^^xsd:decimal . obo:GENEPIO_0001485 obo:IAO_0000114 "requires discussion" ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:reference genome accession" ; linkml:comments "Guidance: Provide the accession number of the reference genome."@en ; linkml:created_on "2021-06-06T15:20:52Z" ; linkml:description "A persistent, unique identifier of a genome database entry."@en ; linkml:examples obo:GENEPIO_0001361 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001486 a owl:Class ; rdfs:label "hospital admission date"@en ; rdfs:subClassOf obo:GENEPIO_0001490 . obo:GENEPIO_0001487 obo:IAO_0000115 "A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure event end"@en ; rdfs:subClassOf obo:GENEPIO_0001473 . obo:GENEPIO_0001488 obo:IAO_0000115 "A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000600 "This datum is NOT predicted as a function of pathogen and first symptom date."@en ; a owl:Class ; rdfs:label "exposure event start"@en ; rdfs:subClassOf obo:GENEPIO_0001473 . obo:GENEPIO_0001489 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001457, owl:NamedIndividual ; rdfs:label "CanCOGeN:bioinformatics protocol" ; linkml:comments "Guidance: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol."@en ; linkml:created_on "2021-06-06T15:23:18Z" ; linkml:description "The name and version number of the bioinformatics protocol used."@en ; linkml:examples obo:GENEPIO_0001362 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001490 a owl:Class ; rdfs:label "hospitalization history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001491 a owl:Class ; rdfs:label "isolate history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001492 a owl:Class ; rdfs:comment "An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet)."@en ; rdfs:label "outbreak history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001493 a owl:Class ; rdfs:label "hospital discharge date"@en ; rdfs:subClassOf obo:GENEPIO_0001490, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001486 ] . obo:GENEPIO_0001494 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "notification date"@en ; rdfs:subClassOf obo:GENEPIO_0001492 . obo:GENEPIO_0001495 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An outbreak date is on which disease onset appears to have occured"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "outbreak date"@en ; rdfs:subClassOf obo:GENEPIO_0001492 . obo:GENEPIO_0001496 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An outbreak over date is the date on which a disease outbreak appears to have abated"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "outbreak over"@en ; rdfs:subClassOf obo:GENEPIO_0001492, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001495 ] . obo:GENEPIO_0001497 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "test history item"@en ; rdfs:subClassOf obo:IAO_0000416 . obo:GENEPIO_0001498 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T15:25:58Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - lineage and variant information" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001499 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "lab test result date"@en ; rdfs:subClassOf obo:GENEPIO_0001497 . obo:GENEPIO_0001500 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:lineage/clade name" ; linkml:comments "Guidance: Provide the Pangolin or Nextstrain lineage/clade name."@en ; linkml:created_on "2021-06-06T15:32:22Z" ; linkml:description "The name of the lineage or clade."@en ; linkml:examples obo:GENEPIO_0001363 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001501 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:lineage/clade analysis software name" ; linkml:comments "Guidance: Provide the name of the software used to determine the lineage/clade."@en ; linkml:created_on "2021-06-06T15:35:38Z" ; linkml:description "The name of the software used to determine the lineage/clade."@en ; linkml:examples obo:GENEPIO_0001364 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001502 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:lineage/clade analysis software version" ; linkml:comments "Guidance: Provide the version of the software used ot determine the lineage/clade."@en ; linkml:created_on "2021-06-06T15:38:00Z" ; linkml:description "The version of the software used to determine the lineage/clade."@en ; linkml:examples obo:GENEPIO_0001365 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001503 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:variant designation" ; linkml:comments "Guidance: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank."@en ; linkml:created_on "2021-06-06T15:40:46Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The variant classification of the lineage/clade i.e. variant, variant of concern."@en ; linkml:examples obo:GENEPIO_0001366 ; linkml:type_uri "select" . obo:GENEPIO_0001504 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:variant evidence" ; linkml:comments "Guidance: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list."@en ; linkml:created_on "2021-06-06T15:43:35Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The evidence used to make the variant determination."@en ; linkml:examples obo:GENEPIO_0001371 ; linkml:type_uri "select" . obo:GENEPIO_0001505 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001498, owl:NamedIndividual ; rdfs:label "CanCOGeN:variant evidence details" ; linkml:comments "Guidance: Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here."@en ; linkml:created_on "2021-06-06T15:47:56Z" ; linkml:description "Details about the evidence used to make the variant determination."@en ; linkml:examples obo:GENEPIO_0001374 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001506 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T15:51:06Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - pathogen diagnostic testing" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001507 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:gene name 1" ; linkml:comments "Guidance: Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"@en ; linkml:created_on "2021-06-06T15:52:42Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the gene used in the diagnostic RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001375 ; linkml:type_uri "select" . obo:GENEPIO_0001508 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr protocol 1" ; linkml:comments "Guidance: The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control."@en ; linkml:created_on "2021-06-06T15:55:20Z" ; linkml:description "The name and version number of the protocol used for diagnostic marker amplification."@en ; linkml:examples obo:GENEPIO_0001376 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001509 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 1" ; linkml:comments "Guidance: Provide the CT value of the sample from the diagnostic RT-PCR test."@en ; linkml:created_on "2021-06-06T15:57:36Z" ; linkml:description "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001377 ; linkml:type_uri "xs:token" . obo:GENEPIO_0001510 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:gene name 2" ; linkml:comments "Guidance: Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"@en ; linkml:created_on "2021-06-06T15:59:50Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the gene used in the diagnostic RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001378 ; linkml:type_uri "select" . obo:GENEPIO_0001511 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr protocol 2" ; linkml:comments "Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control."@en ; linkml:created_on "2021-06-06T16:23:57Z" ; linkml:description "The name and version number of the protocol used for diagnostic marker amplification."@en ; linkml:examples obo:GENEPIO_0001379 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001512 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 2" ; linkml:comments "Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test."@en ; linkml:created_on "2021-06-06T16:26:16Z" ; linkml:description "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001380 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001513 obo:IAO_0000114 "requires discussion" ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:gene name 3" ; linkml:comments "Guidance: Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"@en ; linkml:created_on "2021-06-06T16:28:18Z" ; linkml:data_collection_state "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; linkml:description "The name of the gene used in the diagnostic RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001381 ; linkml:type_uri "select" . obo:GENEPIO_0001514 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr protocol 3" ; linkml:comments "Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control."@en ; linkml:created_on "2021-06-06T16:30:58Z" ; linkml:description "The name and version number of the protocol used for diagnostic marker amplification."@en ; linkml:examples obo:GENEPIO_0001382 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001515 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001506, owl:NamedIndividual ; rdfs:label "CanCOGeN:diagnostic pcr Ct value 3" ; linkml:comments "Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test."@en ; linkml:created_on "2021-06-06T16:33:11Z" ; linkml:description "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test."@en ; linkml:examples obo:GENEPIO_0001383 ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001516 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; dc:date "2021-06-06T16:36:02Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft CanCOGeN DataHarmonizer field - contributor acknowledgement" ; rdfs:subClassOf obo:GENEPIO_0001121 . obo:GENEPIO_0001517 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001516, owl:NamedIndividual ; rdfs:label "CanCOGeN:authors" ; linkml:comments "Guidance: Include the first and last names of all individuals that should be attributed, separated by a comma."@en ; linkml:created_on "2021-06-06T16:37:30Z" ; linkml:description "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission."@en ; linkml:examples obo:GENEPIO_0001384 ; linkml:recommended true ; linkml:type_uri ""^^xsd:token . obo:GENEPIO_0001518 obo:IAO_0000114 "requires discussion"@en ; obo:IAO_0000117 ; a obo:GENEPIO_0001516, owl:NamedIndividual ; rdfs:label "CanCOGeN:DataHarmonizer provenance" ; linkml:comments "Guidance: The current software version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not."@en ; linkml:created_on "2021-06-06T16:39:53Z" ; linkml:description "The DataHarmonizer software version provenance."@en ; linkml:examples obo:GENEPIO_0001385 ; linkml:type_uri "provenance" . obo:GENEPIO_0001532 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A particular attribute (feature, quality or process history) of a food sample."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "The underlying facets will be supplied from the FoodOn food ontology."@en ; rdfs:label "food specimen datum"@en ; rdfs:subClassOf obo:GENEPIO_0001790 . obo:GENEPIO_0001533 obo:GENEPIO_0001763 """order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "food specimen specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0001534 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An agency that has reported a disease cluster."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "disease cluster notification agency"@en ; rdfs:subClassOf obo:OBI_0000245 . obo:GENEPIO_0001535 obo:IAO_0000115 "This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/OBI_0001628" ; a owl:Class ; rdfs:label "obsolete: NCBI BioProject ID"@en ; owl:deprecated true . obo:GENEPIO_0001536 obo:IAO_0000115 "The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure group unknown health status count"@en ; rdfs:subClassOf obo:STATO_0000047 . obo:GENEPIO_0001537 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A role which inheres in a person and is realized by the process of being in the context of civilization"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "person role"@en ; rdfs:subClassOf obo:GENEPIO_0001175 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0001175 [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:NCBITaxon_9606 ] ) ] . obo:GENEPIO_0001538 obo:IAO_0000115 "An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposed person role"@en ; rdfs:subClassOf obo:GENEPIO_0001537 . obo:GENEPIO_0001541 a owl:Class ; rdfs:label "parent-guardian role"@en ; rdfs:subClassOf obo:GENEPIO_0001537 . obo:GENEPIO_0001543 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "illness causality"@en ; rdfs:subClassOf obo:GENEPIO_0001192 . obo:GENEPIO_0001548 a owl:Class ; rdfs:label "pre-existing condition"@en ; rdfs:subClassOf obo:GENEPIO_0001543 . obo:GENEPIO_0001550 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "To restore to the normal state after some pathologic process."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "Dorland's Illustrated Medical Dictionary, 30th ed."@en ; oboInOwl:hasExactSynonym "improving"@en, "recovering"@en ; a owl:Class ; rdfs:label "resolving health trend"@en ; rdfs:subClassOf obo:GENEPIO_0001812, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0002026 ] . obo:GENEPIO_0001551 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "close interpersonal relationship exposure"@en ; rdfs:subClassOf obo:GENEPIO_0001272 . obo:GENEPIO_0001552 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "household exposure"@en ; rdfs:subClassOf obo:GENEPIO_0001275 . obo:GENEPIO_0001553 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure to individual with diarrhea"@en ; rdfs:subClassOf obo:GENEPIO_0001275 . obo:GENEPIO_0001554 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "other human exposure"@en ; rdfs:subClassOf obo:GENEPIO_0001275 . obo:GENEPIO_0001555 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "sexual contact exposure"@en ; rdfs:subClassOf obo:GENEPIO_0001272 . obo:GENEPIO_0001556 obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "exposure via diaper changing (human fecal)"@en ; rdfs:subClassOf obo:GENEPIO_0001275 . obo:GENEPIO_0001558 a owl:Class ; rdfs:label "container identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001559 oboInOwl:hasDbXref "PulseNet: Outbreak" ; a owl:Class ; rdfs:label "outbreak identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001560 oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "reference genome size"@en ; rdfs:subClassOf obo:GENEPIO_0001425, obo:STATO_0000047, [ a owl:Restriction ; owl:onProperty obo:IAO_0000039 ; owl:someValuesFrom obo:UO_0000244 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0001505 ] . obo:GENEPIO_0001561 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The assembly genome size is the sum of all lengths of a sequence assembly's contigs."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:comment "As noted in Quast documentation: \" The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. \""@en ; rdfs:label "assembly genome size"@en ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0001562 obo:IAO_0000115 "Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community"@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "reference genome identifier"@en ; rdfs:subClassOf obo:GENEPIO_0001425, obo:GENEPIO_0001800, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0001505 ] . obo:GENEPIO_0001563 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 """The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample."""@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "genome size delta ratio"@en ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0001564 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 """This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome."""@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "genome size delta ratio QC threshold"@en ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0001565 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428"@en ; obo:IAO_0000115 "The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "contig N50 length QC threshold"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001566 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000112 2000 ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "contig N99 length QC threshold"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001567 obo:GENEPIO_0001763 "lookup" ; obo:IAO_0000112 "Homo sapiens"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, \"Homo sapiens\"."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 obo:GENEPIO_0001835 ; a owl:Class ; rdfs:label "subject organism (host) taxonomic species"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:NCBITaxon_33090 obo:NCBITaxon_33213 obo:NCBITaxon_9606 ) ] ] . obo:GENEPIO_0001568 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 """A single datum having to do with a metric for genomic sequence assembly quality control. A \"quality control measurement\" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A \"quality control metric\" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A \"measure\" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does."""@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "assembly quality control datum"@en ; rdfs:subClassOf obo:GENEPIO_0001425, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0000353 ] . obo:GENEPIO_0001569 obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasAlternativeId "GSCID-BRC:Clinical/host-associated pathogen", "NCBI:Pathogen.cl" ; a owl:Class ; rdfs:label "clinical or host-associated pathogen"@en ; rdfs:subClassOf obo:GENEPIO_0000113, [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000002 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . obo:GENEPIO_0001570 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428"@en ; obo:IAO_0000115 "The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "contig N99"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001571 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 """The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage."""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contig count QC threshold"@en ; rdfs:subClassOf obo:GENEPIO_0000093 . obo:GENEPIO_0001572 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Indicates how the knowledge derived from the project can be applied, and to what field(s)."@en ; obo:IAO_0000116 "Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project"^^xsd:anyURI ; a owl:Class ; rdfs:label "project relevance"@en ; rdfs:subClassOf obo:IAO_0000005 . obo:GENEPIO_0001573 a owl:Class ; rdfs:label "agricultural project relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001574 a owl:Class ; rdfs:label "medical knowledge relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001575 a owl:Class ; rdfs:label "industrial processing relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001576 a owl:Class ; rdfs:label "evolution modelling relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001577 a owl:Class ; rdfs:label "environmental project relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001578 a owl:Class ; rdfs:label "model organism relevance"@en ; rdfs:subClassOf obo:GENEPIO_0001572 . obo:GENEPIO_0001579 obo:IAO_0000115 "The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 obo:GENEPIO_0001836 ; a owl:Class ; rdfs:label "obsolete: NCBI BioProject model"@en ; owl:deprecated true . obo:GENEPIO_0001580 obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000147" ; a owl:Class ; rdfs:label "obsolete: NCBI SRA model"@en ; owl:deprecated true . obo:GENEPIO_0001581 obo:GENEPIO_0000005 "http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"@en, "http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000116 """Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field?"""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected."@en ; rdfs:label "draft NCBI BioSample model - mixed clinical and environmental/food/other"@en ; rdfs:subClassOf obo:GENEPIO_0001611 . obo:GENEPIO_0001582 obo:GENEPIO_0000006 "monoisolate"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/" ; obo:OBI_0001886 "monoisolate" ; a owl:Class ; rdfs:label "monoisolate sample scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001583 obo:GENEPIO_0000006 "multiisolate"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species)."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"@en ; obo:IAO_0000600 "This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated."@en ; a owl:Class ; rdfs:label "multiisolate sample scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001584 obo:GENEPIO_0000006 "multispecies"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A multi-species sample scope involves a sample representing multiple species."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/" ; a owl:Class ; rdfs:label "multispecies sample scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001585 obo:GENEPIO_0000006 "environment"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/" ; a owl:Class ; rdfs:label "environment sample scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001586 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A synthetic sample scope involves a sample synthesized in a laboratory."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/" ; a owl:Class ; rdfs:label "synthetic sample scope"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001587 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "single cell"@en ; rdfs:subClassOf obo:OBI_0001884 . obo:GENEPIO_0001588 obo:GENEPIO_0000006 "other"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Other project objective: specify an objective not listed above"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "other project objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001589 a owl:NamedIndividual ; rdfs:label "United Nations"@en . obo:GENEPIO_0001590 obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasAlternativeId "GSCID-BRC:environmental/food/other", "NCBI:Pathogen.env" ; a owl:Class ; rdfs:label "environmental, food or other pathogen"@en ; rdfs:subClassOf obo:GENEPIO_0000113, [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000002 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . obo:GENEPIO_0001591 obo:GENEPIO_0000006 "whole"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "whole genomic data capture"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0001592 obo:GENEPIO_0000006 "raw sequence reads"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "raw sequence read objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001593 obo:GENEPIO_0000006 "sequence"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies)"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "sequence project objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001594 obo:GENEPIO_0000006 "analysis"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An \"analysis project objective\" indicates there was an other analysis not otherwise indicated, includes submission of BAM files."@en ; obo:IAO_0000116 "This defn. could be a negation of the \"not otherwise indicated\"."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "analysis objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001595 obo:GENEPIO_0000006 "assembly"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Submission of genome assembly (AGP data)"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "assembly objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001596 obo:GENEPIO_0000006 "annotation"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Sequence annotation data"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "sequence annotation objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001597 obo:GENEPIO_0000006 "sequence variation"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Variation: identification of sequence variation data for submission to dbSNP or dbVAR"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "sequence variation project objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001598 obo:GENEPIO_0000006 "epigenetic markers"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "DNA methylation, histone modification, chromatin accessibility datasets"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "epigenetic markers objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001599 obo:GENEPIO_0000006 "expression"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Expression: assays of transcript or protein existence or abundance"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "transcript or protein expression objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001600 obo:GENEPIO_0000006 "maps"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "mapping objective"@en ; rdfs:subClassOf obo:OBI_0001892 . obo:GENEPIO_0001601 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "Phenotypic descriptive data."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "phenotypic observation data from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0001602 obo:GENEPIO_0000006 "select sequence if any sequence data is generated from this project."@en, "sequencing"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "sequencing project method"@en ; rdfs:subClassOf obo:OBI_0001896 . obo:GENEPIO_0001603 obo:GENEPIO_0000006 "array"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Select Array if that is the primary method and no sequence data is submitted"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "array project method"@en ; rdfs:subClassOf obo:OBI_0001896 . obo:GENEPIO_0001604 obo:GENEPIO_0000006 "mass spectrometry"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Select Mass Spectrometry if that is the primary method"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "mass spectrometry project method"@en ; rdfs:subClassOf obo:OBI_0001896 . obo:GENEPIO_0001605 obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 linkml:type_uri ; rdfs:label "obsolete: has primitive data type"@en ; owl:deprecated true . obo:GENEPIO_0001606 obo:GENEPIO_0001763 """order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone""" ; a owl:Class ; rdfs:label "contact specification - person"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0001607 obo:IAO_0000115 "A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "investigation datum"@en ; rdfs:subClassOf obo:IAO_0000109 . obo:GENEPIO_0001608 obo:IAO_0000115 "An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement."@en ; a owl:Class ; rdfs:label "commensal role"@en ; rdfs:subClassOf obo:GENEPIO_0001172 . obo:GENEPIO_0001609 a owl:Class ; rdfs:label "draft isolate details model"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0001610 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject age"@en ; rdfs:subClassOf obo:OBI_0001169 . obo:GENEPIO_0001611 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft NCBI component model"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001612 a owl:Class ; rdfs:label "draft IRIDA BioSample model"@en ; rdfs:subClassOf obo:GENEPIO_0001829 . obo:GENEPIO_0001613 a owl:Class ; rdfs:label "draft GenEpiO epidemiology case record"@en ; rdfs:subClassOf obo:GENEPIO_0001741, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000531 ] . obo:GENEPIO_0001614 obo:IAO_0000115 "A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^xsd:anyURI ; a owl:Class ; rdfs:label "subject description"@en ; rdfs:subClassOf , [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . obo:GENEPIO_0001615 obo:GENEPIO_0000005 "NCBI BioSample"@en ; obo:IAO_0000115 "The host profile or identifiers text is the \"identification or description of the specific individual from which this sample was obtained\"."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref "NCBI BioSample: isolate" ; a owl:Class ; rdfs:label "host profile or identifers"@en ; rdfs:subClassOf . obo:GENEPIO_0001616 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment """This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states \" 'Host' is not the preferred term since some specimens may lack any detectable pathogen\". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral \"host id\""""@en ; rdfs:label "subject identifier"@en ; rdfs:subClassOf obo:OBI_0001141 . obo:GENEPIO_0001617 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Name of disease in a subject that is related to a given investigation, study and/or specimen."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NIAID GSCID-BRC metadata working group"@en ; a owl:Class ; rdfs:comment """Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067"""@en ; rdfs:label "subject disease"@en ; rdfs:subClassOf obo:DOID_4, [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:GENEPIO_0002077 ] . obo:GENEPIO_0001618 obo:GENEPIO_0000005 "INSDC term (top level)"@en ; obo:IAO_0000115 "A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason."@en ; obo:IAO_0000119 ; oboInOwl:hasDbXref obo:GENEPIO_0001666, "NCBI Biosample: missing"@en ; a owl:Class ; rdfs:label "missing"@en ; rdfs:subClassOf obo:GENEPIO_0001850 . obo:GENEPIO_0001619 obo:GENEPIO_0000005 "INSDC term (top level)"@en ; obo:IAO_0000112 "'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A categorical choice recorded when a measurable datum does not apply to a given context."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 ; oboInOwl:hasDbXref obo:GENEPIO_0001666, obo:GENEPIO_0001835 ; a owl:Class ; rdfs:label "not applicable"@en ; rdfs:subClassOf obo:GENEPIO_0001850 . obo:GENEPIO_0001620 obo:GENEPIO_0000005 "INSDC term (lower level)" ; obo:IAO_0000115 "A categorical choice recorded when a datum was not measured with respect to some entity during some process."@en ; obo:IAO_0000119 ; oboInOwl:hasDbXref obo:GENEPIO_0001666, "NCBI Biosample: not collected"@en ; a owl:Class ; rdfs:label "not collected"@en ; rdfs:subClassOf obo:GENEPIO_0001618 . obo:GENEPIO_0001621 a owl:Class ; rdfs:label "draft isolate identifier model"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0001622 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft GenEpiO isolate testing model"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001623 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft NCBI isolate source location model"@en ; rdfs:subClassOf obo:GENEPIO_0001611 . obo:GENEPIO_0001624 a owl:Class ; rdfs:label "draft GenEpiO isolate environment model"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001625 obo:IAO_0000115 "A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://purl.obolibrary.org/obo/GENEPIO_0001835"^^xsd:anyURI ; a owl:Class ; rdfs:label "subject disease stage"@en ; rdfs:subClassOf obo:GENEPIO_0002018 . obo:GENEPIO_0001626 a owl:Class ; rdfs:label "environmental datum"@en ; rdfs:subClassOf obo:IAO_0000109 . obo:GENEPIO_0001627 a owl:Class ; rdfs:label "temperature of sample"@en ; rdfs:subClassOf obo:GENEPIO_0001626, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:PATO_0000146 ] . obo:GENEPIO_0001628 a owl:Class ; rdfs:label "de-novo assembly"@en ; rdfs:subClassOf obo:GENEPIO_0000090 ; owl:disjointWith obo:GENEPIO_0002028 . obo:GENEPIO_0001629 obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0000025"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: sample body source"@en ; owl:deprecated true . obo:GENEPIO_0001630 obo:IAO_0000111 "contig pre-analysis minimum length QC threshold"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://quast.bioinf.spbau.ru/manual.html"@en ; a owl:Class ; rdfs:comment "QUAST specifies which of its report stats are affected by the \"--min-contig\" minimum contig length parameter."@en ; rdfs:label "contig length QC threshold"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001631 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "\"Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic.\" - wikipedia"@en ; rdfs:label "contig NG50"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001632 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A contig length is the count of base pairs in a given sequence assembly contig."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "contig length"@en ; rdfs:subClassOf obo:GENEPIO_0001568, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:SO_0000149 ] . obo:GENEPIO_0001633 obo:GENEPIO_0000001 "Assembly QC" ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 "Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "QUAST manual"@en ; a owl:Class ; rdfs:label "contig L50"@en ; rdfs:subClassOf obo:GENEPIO_0000093 . obo:GENEPIO_0001634 obo:GENEPIO_0000001 "Assembly QC" ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 "The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contig LG99"@en ; rdfs:subClassOf obo:GENEPIO_0000093 . obo:GENEPIO_0001635 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An organism isolate datum is any datum pertaining to an isolate organism"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "obsolete: specimen from subject datum"@en ; owl:deprecated true . obo:GENEPIO_0001636 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "animal body product"@en ; rdfs:subClassOf obo:GENEPIO_0000028, [ a owl:Restriction ; owl:onProperty obo:RO_0003001 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:GENEPIO_0001637 obo:IAO_0000115 "This is the scientific role or category that the subject organism or material has with respect to an investigation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001237"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: specimen source material category"@en ; owl:deprecated true . obo:GENEPIO_0001638 a owl:Class ; rdfs:label "draft GenEpiO general information record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001639 obo:IAO_0000115 "An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "antigenic formula"@en ; rdfs:seeAlso "http://medical-dictionary.thefreedictionary.com/antigen" ; rdfs:subClassOf obo:GENEPIO_0001688, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:CHEBI_59132 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C53471 ] . obo:GENEPIO_0001640 obo:GENEPIO_0001763 "lookup" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen organism taxonomy (species)"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:NCBITaxon_10239 obo:NCBITaxon_2 obo:NCBITaxon_2157 obo:NCBITaxon_2759 ) ] ] . obo:GENEPIO_0001641 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "identifier model"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001642 obo:GENEPIO_0001763 "help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "curator organization name"@en ; rdfs:subClassOf obo:GENEPIO_0001607 . obo:GENEPIO_0001643 oboInOwl:hasDbXref "INSDC:institution_code:BRS"@en, "IRIDA:ACK" ; a owl:Class ; rdfs:label "Agriculture and Agri-Food Canada" ; rdfs:subClassOf obo:OBI_0001893 . obo:GENEPIO_0001644 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "isolate identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001645 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "identifier status"@en ; rdfs:subClassOf obo:GENEPIO_0001607 . obo:GENEPIO_0001646 obo:GENEPIO_0000005 "GenEpiO"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A data protection role is a role (or user permission) that a user has with respect to particular data."@en ; obo:IAO_0000116 "A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "data protection role"@en ; rdfs:seeAlso ; rdfs:subClassOf obo:BFO_0000023 . obo:GENEPIO_0001647 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An identifier used in the initial submission of content to a repository."@en ; a owl:Class ; rdfs:label "original submission"@en ; rdfs:subClassOf obo:GENEPIO_0001645 . obo:GENEPIO_0001648 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000116 "This was created to help define a contributing organization to a repository. However this still needs organizing. The \"collected_by\" field is free text but contact name AND organization could be associated with this in controlled vocabulary."@en ; a owl:Class ; rdfs:label "NCBI Contributing organization / project"@en ; rdfs:subClassOf obo:GENEPIO_0001803 . obo:GENEPIO_0001649 a owl:Class ; rdfs:label "food - liquid"@en ; rdfs:subClassOf obo:GENEPIO_0001249 . obo:GENEPIO_0001650 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft NCBI BioSample identifier model"@en ; rdfs:subClassOf obo:GENEPIO_0001611 . obo:GENEPIO_0001651 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier"^^xsd:anyURI ; a owl:Class ; rdfs:label "INSDC institution code"@en ; rdfs:subClassOf obo:GENEPIO_0001803 . obo:GENEPIO_0001652 a owl:Class ; rdfs:label "draft IRIDA epidemiological case model"@en ; rdfs:subClassOf obo:GENEPIO_0001829 . obo:GENEPIO_0001653 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An identifier that had been used previously but is no longer promoted."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "previous (archaic) identifier"@en ; rdfs:subClassOf obo:GENEPIO_0001645 . obo:GENEPIO_0001654 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "geographic location datum"@en ; rdfs:subClassOf obo:IAO_0000109 . obo:GENEPIO_0001655 obo:IAO_0000115 "A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/OBI_0001930"^^xsd:anyURI ; a owl:Class ; rdfs:comment "A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable."@en ; rdfs:label "obsolete: categorical tree specification"@en ; owl:deprecated true . obo:GENEPIO_0001656 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "A geographic coordinate entity composed of both latitude and longitude components."@en ; rdfs:label "latitude and longitude coordinate (ISO 6709)"@en ; rdfs:subClassOf obo:GENEPIO_0001611 . obo:GENEPIO_0001657 obo:GENEPIO_0001763 """order: NCIT:C25464 # country ENVO:00000005 # state / province etc."""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg \"Canada: Vancouver\" or \"Germany: halfway down Zugspitze, Alps\""@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft NCBI BioSample geo_loc_name model"@en ; rdfs:subClassOf obo:GENEPIO_0001611, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100051 ] . obo:GENEPIO_0001658 a owl:Class ; rdfs:label "draft GenEpiO isolate sequencing model"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001659 obo:IAO_0000115 "A case ID is a unique identifier associated with a particular episode of care for an individual or animal." ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "case identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001660 obo:IAO_0000115 "An animal that has had a substantial part of its reproductive organs removed surgically."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI BioSample: neuter" ; a owl:Class ; rdfs:comment "Not a PATO phenotypic sex catigorical value."@en ; rdfs:label "neuter"@en ; rdfs:subClassOf obo:PATO_0001894 ; owl:disjointWith obo:PATO_0000383, obo:PATO_0000384 . obo:GENEPIO_0001661 obo:GENEPIO_0000005 "NCBI BioSample" ; obo:IAO_0000115 "'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other."@en ; obo:IAO_0000116 "Not a PATO phenotypic sex catigorical value."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI BioSample: 'pooled male and female'" ; a owl:Class ; rdfs:label "pooled male and female"@en ; rdfs:subClassOf obo:PATO_0001894 ; owl:equivalentClass [ a owl:Class ; owl:unionOf (obo:PATO_0000383 obo:PATO_0000384 ) ] . obo:GENEPIO_0001662 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasExactSynonym "undetermined"@en ; a owl:Class ; rdfs:label "in process"@en ; rdfs:subClassOf obo:GENEPIO_0001618 . obo:GENEPIO_0001663 a owl:Class ; rdfs:label "swimming / wading"@en ; rdfs:subClassOf obo:GENEPIO_0001277 . obo:GENEPIO_0001664 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment."@en ; rdfs:label "infection detail datum"@en ; rdfs:subClassOf obo:GENEPIO_0001222 . obo:GENEPIO_0001665 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000116 "This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "antibiotics required"@en ; rdfs:subClassOf obo:GENEPIO_0001664 . obo:GENEPIO_0001666 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "International Nucleotide Database Collaboration standard"@en ; oboInOwl:hasDbXref "INSDC" ; a owl:Class ; rdfs:label "INSDC standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001667 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "outcome of pregnancy associated with illness"@en ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:GENEPIO_0001668 obo:GENEPIO_0000005 "INSDC term (lower level)" ; obo:IAO_0000115 "a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage."@en ; obo:IAO_0000119 ; oboInOwl:hasDbXref obo:GENEPIO_0001666 ; a owl:Class ; rdfs:label "not provided"@en ; rdfs:subClassOf obo:GENEPIO_0001618 . obo:GENEPIO_0001669 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "stable health status"@en ; rdfs:seeAlso "http://purl.obolibrary.org/obo/GENEPIO_0002026"@en ; rdfs:subClassOf obo:GENEPIO_0002024, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001842 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001841 ] . obo:GENEPIO_0001670 a owl:Class ; rdfs:label "induced abortion"@en ; rdfs:subClassOf obo:GENEPIO_0001667 . obo:GENEPIO_0001671 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "live birth"@en ; rdfs:subClassOf obo:GENEPIO_0001667 . obo:GENEPIO_0001672 obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/VT_0002292"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: gestation duration (weeks)"@en ; owl:deprecated true . obo:GENEPIO_0001673 a owl:Class ; rdfs:label "date of pregnancy outcome"@en ; rdfs:subClassOf obo:GENEPIO_0001224, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001225 ] . obo:GENEPIO_0001674 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "contact specification - physician"@en ; rdfs:subClassOf obo:GENEPIO_0001606, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C25741 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002180 ; owl:someValuesFrom obo:GENEPIO_0001679 ] . obo:GENEPIO_0001675 a owl:Class ; rdfs:label "obsolete: matrix - solid"@en ; owl:deprecated true . obo:GENEPIO_0001676 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "contact specification - parent/guardian"@en ; rdfs:subClassOf obo:GENEPIO_0001606, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001541 ] . obo:GENEPIO_0001677 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "contact specification - patient"@en ; rdfs:subClassOf obo:GENEPIO_0001606, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0000093 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002180 ; owl:someValuesFrom obo:GENEPIO_0001679 ] . obo:GENEPIO_0001678 a owl:Class ; rdfs:label "draft GenEpiO case epidemiology record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001679 obo:GENEPIO_0001763 """order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The address component of a contact specification."@en ; a owl:Class ; rdfs:label "contact specification - address"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0001680 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0100001 "GENEPIO_0001829"@en ; a owl:Class ; rdfs:label "obsolete: draft IRIDA model"@en ; owl:deprecated true . obo:GENEPIO_0001681 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A datum related to the sequencing assay process applied to an isolate."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "laboratory sequencing datum"@en ; rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0001901"^^xsd:anyURI, "http://purl.obolibrary.org/obo/OBI_0400103"^^xsd:anyURI ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001682 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "host illness associated with"@en ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:GENEPIO_0001683 a owl:Class ; rdfs:label "draft subject demographic specification"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001684 a owl:Class ; rdfs:label "E. coli K antigen specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:CHEBI_73772 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106)" ] ) ] ] . obo:GENEPIO_0001685 a owl:Class ; rdfs:label "other antigen specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:CHEBI_59132 ], [ a owl:Restriction ; owl:onDataRange [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:maxLength "6"^^xsd:unsignedByte ] ) ] ; owl:onProperty obo:OBI_0002135 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0001686 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "E. coli serotype specification"@en ; rdfs:subClassOf obo:GENEPIO_0001718 . obo:GENEPIO_0001687 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:comment "Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap."@en ; rdfs:label "Salmonella serovar specification"@en ; rdfs:subClassOf obo:GENEPIO_0001718 . obo:GENEPIO_0001688 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A lab test specification indicates the inputs and outputs (results / conclusions) of a test."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "test specification"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001689 a owl:Class ; rdfs:label "listeria antigen"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:CHEBI_59132 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "(1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)" ] ) ] ] . obo:GENEPIO_0001690 a owl:Class ; rdfs:label "obsolete: matrix - fluid"@en ; owl:deprecated true . obo:GENEPIO_0001691 a owl:Class ; rdfs:label "listeria serotype 1/2a"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001692 a owl:Class ; rdfs:label "listeria serotype 1/2b"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001693 a owl:Class ; rdfs:label "listeria serotype 1/2c"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001694 a owl:Class ; rdfs:label "listeria serotype 1/2"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001695 a owl:Class ; rdfs:label "listeria serotype 3a"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001696 a owl:Class ; rdfs:label "listeria serotype 3b"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001697 a owl:Class ; rdfs:label "listeria serotype 4a"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001698 a owl:Class ; rdfs:label "listeria serotype 4b"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001699 a owl:Class ; rdfs:label "listeria serotype 4c"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001700 a owl:Class ; rdfs:label "listeria serotype 4d"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001701 a owl:Class ; rdfs:label "listeria serotype 4e"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001702 a owl:Class ; rdfs:label "non-monocytogenes listeria antigen"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001703 a owl:Class ; rdfs:label "listeria serotype 3c"@en ; rdfs:subClassOf obo:GENEPIO_0001689 . obo:GENEPIO_0001704 a owl:Class ; rdfs:label "textual test result"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:GENEPIO_0001705 obo:IAO_0000115 "This is an organizational category for grouping parameters relevant to biomedical research projects."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete: draft GenEpiO BioProject standard"@en ; owl:deprecated true . obo:GENEPIO_0001706 obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI BioSample: collection_code" ; a owl:Class ; rdfs:label "NCBI BioSample collection code"@en ; rdfs:subClassOf obo:GENEPIO_0001804 . obo:GENEPIO_0001707 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft NCBI BioSample host model"@en ; rdfs:subClassOf obo:GENEPIO_0001611, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000531 ] . obo:GENEPIO_0001708 a owl:Class ; rdfs:label "food - solid"@en ; rdfs:subClassOf obo:GENEPIO_0001249 . obo:GENEPIO_0001709 a owl:Class ; rdfs:label "lab test datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001710 a owl:Class ; rdfs:label "Xbal"@en ; rdfs:subClassOf obo:GENEPIO_0000044 . obo:GENEPIO_0001711 a owl:Class ; rdfs:label "Ascl"@en ; rdfs:subClassOf obo:GENEPIO_0000044 . obo:GENEPIO_0001712 a owl:Class ; rdfs:label "Smal"@en ; rdfs:subClassOf obo:GENEPIO_0000044 . obo:GENEPIO_0001713 a owl:Class ; rdfs:label "Blnl"@en ; rdfs:subClassOf obo:GENEPIO_0000047 . obo:GENEPIO_0001714 a owl:Class ; rdfs:label "Apal"@en ; rdfs:subClassOf obo:GENEPIO_0000047 . obo:GENEPIO_0001715 a owl:Class ; rdfs:label "Kpnl"@en ; rdfs:subClassOf obo:GENEPIO_0000047 . obo:GENEPIO_0001716 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "NCBI Biosample"@en ; a owl:Class ; rdfs:label "subgroup"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001717 obo:GENEPIO_0001763 "help:This is an optional additional subtype classification as per organism convention"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A viral subtype is a classification name for a virus according to some protocol."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "NCBI BioSample"@en ; a owl:Class ; rdfs:label "viral subtype"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001718 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "serotype specification"@en ; rdfs:subClassOf obo:GENEPIO_0001688, [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0001686 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0001687 ; owl:onProperty obo:RO_0002180 ] . obo:GENEPIO_0001719 obo:GENEPIO_0000005 "IRIDA"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref "SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002" ; a owl:Class ; rdfs:label "phage type specification"@en ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:GENEPIO_0001720 obo:IAO_0000231 obo:IAO_0000229 ; a owl:Class ; rdfs:label "obsolete: swab - food contact surface"@en ; owl:deprecated true . obo:GENEPIO_0001721 obo:IAO_0000112 "ATCC:26370" ; obo:IAO_0000115 "An NCBI culture collection is a composite identifier containing “institution code:collection code”."@en ; obo:IAO_0000600 "Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier."@en ; a owl:Class ; rdfs:label "NCBI culture collection"@en ; rdfs:subClassOf obo:GENEPIO_0001723 . obo:GENEPIO_0001722 obo:IAO_0000112 "UAM:Mamm:52179" ; obo:IAO_0000115 "The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides."@en ; oboInOwl:hasDbXref "INSDC:specimen_voucher"@en ; a owl:Class ; rdfs:label "NCBI specimen voucher"@en ; rdfs:seeAlso "http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier."^^xsd:anyURI ; rdfs:subClassOf obo:OBI_0001616 . obo:GENEPIO_0001723 a owl:Class ; rdfs:label "culture identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001724 obo:IAO_0000112 "human; dog; horse"@en ; obo:IAO_0000115 "The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen."@en ; obo:IAO_0000116 "Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into \"host\" field, yet field is listed as \"host common name\" which does not fit with requirement that scientific name be provided."@en ; obo:IAO_0000117 "Person: Damion Dooley" ; a owl:Class ; rdfs:label "subject organism common name"@en ; rdfs:subClassOf obo:NCIT_C42614, [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:GENEPIO_0001725 a owl:Class ; rdfs:label "temperature of air - average daily"@en ; rdfs:subClassOf obo:GENEPIO_0001626, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:ENVO_00002005 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:PATO_0000146 ] . obo:GENEPIO_0001726 obo:IAO_0000231 obo:IAO_0000229 ; a owl:Class ; rdfs:label "obsolete: swab - inanimate object surface"@en ; owl:deprecated true . obo:GENEPIO_0001727 obo:IAO_0000231 obo:IAO_0000229 ; a owl:Class ; rdfs:label "obsolete: swab - meat"@en ; owl:deprecated true . obo:GENEPIO_0001728 obo:IAO_0000231 obo:IAO_0000229 ; a owl:Class ; rdfs:label "obsolete: swab - rectal swab"@en ; owl:deprecated true . obo:GENEPIO_0001729 obo:IAO_0000231 obo:IAO_0000229 ; a owl:Class ; rdfs:label "obsolete: swab - tissue"@en ; owl:deprecated true . obo:GENEPIO_0001730 a owl:Class ; rdfs:label "unknown source"@en ; rdfs:subClassOf obo:CHMO_0002743 . obo:GENEPIO_0001731 oboInOwl:hasSynonym "patient sample"@en ; a owl:Class ; rdfs:label "human clinical specimen"@en ; rdfs:subClassOf obo:CHMO_0002743, obo:GENEPIO_0001237 . obo:GENEPIO_0001732 obo:IAO_0000116 "\"environment (swab or sampling)\" is a specific response for NCBI BioSample that could be mapped or unified with \"environment sample\" used elsewhere in GenEpiO"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/GENEPIO_0001246"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: environmental (swab or sampling)"@en ; owl:deprecated true . obo:GENEPIO_0001733 a owl:Class ; rdfs:label "avian - wild"@en ; rdfs:subClassOf obo:GENEPIO_0001247 . obo:GENEPIO_0001734 a owl:Class ; rdfs:label "avian - domesticated"@en ; rdfs:subClassOf obo:GENEPIO_0001247 . obo:GENEPIO_0001735 a owl:Class ; rdfs:label "human clinical specimen - invasive"@en ; rdfs:subClassOf obo:GENEPIO_0001731 . obo:GENEPIO_0001736 obo:IAO_0000115 "In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "Wikipedia"@en ; a owl:Class ; rdfs:comment "Normally falls within the bounds of 0 - 14"@en ; rdfs:label "pH measurement"@en ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0001737 a owl:Class ; rdfs:label "precipitation"@en ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:GENEPIO_0001738 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "assembly and annotation project objective"@en ; rdfs:subClassOf obo:GENEPIO_0001425 . obo:GENEPIO_0001739 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:ObjectProperty, owl:TransitiveProperty ; rdfs:comment """Damion Dooley's note: Intention is to have it be the inverse of \"before\". This allows axioms like \"B after A\" to be placed in class B, rather than having to phrase them as \"A before B\" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the \"causally downstream of\" and \"immediately causally downstream of\" RO relations, in a closed system where B cannot exist any other way."""@en ; rdfs:label "after"@en ; owl:inverseOf obo:RO_0002083 . obo:GENEPIO_0001740 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "line list row record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001741 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft GenEpiO component record"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001742 obo:GENEPIO_0000006 "region"@en ; obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subnational region is a type of subnational entity similar to a nation's state, province, or territory."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "subnational region"@en ; rdfs:subClassOf obo:ENVO_00000005 ; owl:disjointWith obo:NCIT_C25632, obo:NCIT_C87194, obo:NCIT_C89811 . obo:GENEPIO_0001743 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A data standard related to public health research and service delivery."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "public health data standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001744 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001745 obo:IAO_0000115 "A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:AnnotationProperty ; rdfs:label "user interface help"@en ; owl:deprecated true . obo:GENEPIO_0001746 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:AnnotationProperty ; rdfs:label "user interface hidden"@en ; owl:deprecated true . obo:GENEPIO_0001747 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Reagent: material studied was obtained by chemical reaction, precipitation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "reagent derived material from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0001748 obo:GENEPIO_0000006 "transcriptome"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Transcriptome: transcript and/or expression data."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "transcriptome data from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0001749 obo:GENEPIO_0000006 "proteome" ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Proteome material is protein or peptide sequences."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "proteome data derived from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0001750 obo:GENEPIO_0000006 "purified chromosome" ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Purified chromosome: one or more chromosomes or replicons were experimentally purified."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "purified chromosome from specimen"@en ; rdfs:subClassOf obo:OBI_0001882 . obo:GENEPIO_0001751 obo:GENEPIO_0000006 "targeted locus/loci"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard)."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "Targeted Locus Loci data capture"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0001752 obo:GENEPIO_0000006 "clone ends"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "CloneEnds: capturing clone end data."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "clone end data capture"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0001753 obo:GENEPIO_0000006 "exome"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Exome: capturing exon-specific data."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NCBI BioSample"@en, "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "exome specific data capture"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0001754 obo:GENEPIO_0000006 "random survey"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material"@en ; obo:IAO_0000116 "Is this with respect to an isolate or a specimen derived culture?"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54364/"^^xsd:anyURI ; a owl:Class ; rdfs:label "random survey data capture"@en ; rdfs:subClassOf obo:OBI_0001899 . obo:GENEPIO_0001755 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a collection of various human (and animal contact location) contact information specifications used in data standards."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contact specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0001756 obo:GENEPIO_0001763 """order: NCIT:C40978 # phone GENEPIO:0001896 # phone type""" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "contact specification - phone"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0001757 obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "millimetres per day"@en ; rdfs:subClassOf obo:UO_0000060 . obo:GENEPIO_0001758 obo:IAO_0100001 obo:UO_0010002 ; a owl:Class ; rdfs:label "obsolete: millisiemens"@en ; owl:deprecated true . obo:GENEPIO_0001759 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "millisiemens per centimetre"@en ; rdfs:subClassOf obo:UO_0000000 . obo:GENEPIO_0001760 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "cubic metre per second"@en ; rdfs:subClassOf obo:UO_0000000 . obo:GENEPIO_0001761 obo:GENEPIO_0000006 "umol/kg" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "micromole per kilogram"@en ; rdfs:subClassOf obo:UO_0000051 . obo:GENEPIO_0001762 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "micromole per litre"@en ; rdfs:subClassOf obo:UO_0000051 . obo:GENEPIO_0001763 obo:IAO_0000115 "A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:AnnotationProperty ; rdfs:label "user interface feature"@en . obo:GENEPIO_0001764 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "quality control record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001765 obo:IAO_0000115 "Standard draft: describing the minimum information needed for submission to a public database."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "1 - standard draft"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001766 obo:IAO_0000115 "High quality draft: describing sequences with little to no manual review."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "2 - high quality draft"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001767 obo:IAO_0000115 "Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "3 - improved high quality draft"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001768 obo:IAO_0000115 "Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "4 - annotation-directed improvement"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001769 obo:IAO_0000115 "Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "5 - non-contiguous finished"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001770 obo:IAO_0000115 "Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "6 - finished"@en ; rdfs:subClassOf obo:GENEPIO_0000091 . obo:GENEPIO_0001771 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428"@en ; obo:IAO_0000115 "The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:label "contig NG99"@en ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:GENEPIO_0001772 obo:IAO_0000115 "This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:AnnotationProperty ; rdfs:label "obsolete: user interface value specification"@en ; owl:deprecated true . obo:GENEPIO_0001773 obo:GENEPIO_0000001 "Assembly QC" ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 "Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contig LG50"@en ; rdfs:subClassOf obo:GENEPIO_0000093 . obo:GENEPIO_0001774 obo:GENEPIO_0000001 "Assembly QC" ; obo:IAO_0000114 "http://purl.obolibrary.org/obo/IAO_0000428" ; obo:IAO_0000115 "Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contig L99"@en ; rdfs:subClassOf obo:GENEPIO_0000093 . obo:GENEPIO_0001775 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject age at time of specimen collection"@en ; rdfs:subClassOf obo:GENEPIO_0001610 . obo:GENEPIO_0001776 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "A public health related data standard involving a particular species of pathogen."@en, "Damion Dooley"@en ; a owl:Class ; rdfs:label "pathogen specific data standard"@en ; rdfs:subClassOf obo:GENEPIO_0000143 . obo:GENEPIO_0001777 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft tuberculosis contextual data standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001778 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "draft PulseNet Canada Salmonella submission standard"@en ; rdfs:seeAlso "http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf" ; rdfs:subClassOf obo:GENEPIO_0000106, [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002468 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001559 ] [ a owl:Restriction ; owl:hasValue obo:GENEPIO_0002201 ; owl:onProperty ] [ a owl:Restriction ; owl:onProperty linkml:type_uri ; owl:someValuesFrom xsd:string ] [ a owl:Restriction ; owl:hasValue "PulseNet:Outbreak" ; owl:onProperty linkml:name ] ) ] ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0001779 obo:IAO_0000115 "A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme."@en ; obo:IAO_0000117 ; a owl:Class ; rdfs:label "PFGE Xbal pattern"@en ; rdfs:subClassOf obo:GENEPIO_0001289, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001710 ] . obo:GENEPIO_0001780 obo:IAO_0000115 "A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme."@en ; obo:IAO_0000117 ; a owl:Class ; rdfs:label "PFGE Blnl pattern"@en ; rdfs:subClassOf obo:GENEPIO_0001289, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001713 ] . obo:GENEPIO_0001781 obo:GENEPIO_0000006 "NLEP ID"@en ; obo:IAO_0000115 "An NLEP ID is a unique identifier code for a sample registered with the Canadian \"National Laboratory for Enteric Pathogens\" (NLEP)"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "Pulsenet Canada spreadsheet."@en ; a owl:Class ; rdfs:label "National Laboratory for Enteric Pathogens Identifier"@en ; rdfs:subClassOf obo:OBI_0001616 . obo:GENEPIO_0001782 obo:GENEPIO_0000005 "PulseNet spreadsheet" ; obo:IAO_0000115 "Date an uploaded sample was re-uploaded or had its metadata modified."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "PulseNet: UploadModifiedDate" ; a owl:Class ; rdfs:label "upload modified date"@en ; rdfs:subClassOf obo:GENEPIO_0001491, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0000024 ] . obo:GENEPIO_0001783 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "travel destination"@en ; rdfs:subClassOf obo:GENEPIO_0001058 . obo:GENEPIO_0001784 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain."@en ; rdfs:label "symptom duration"@en ; rdfs:subClassOf obo:GENEPIO_0001258, . obo:GENEPIO_0001785 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The city where a specimen was collected (taken) from a subject or environment"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "specimen collection location - city"@en ; rdfs:subClassOf obo:GENEPIO_0002162, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C80234 ] . obo:GENEPIO_0001786 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000231 obo:IAO_0000227 ; obo:IAO_0100001 obo:GENEPIO_0001785 ; a owl:Class ; rdfs:label "obsolete: sample city"@en ; owl:deprecated true . obo:GENEPIO_0001787 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the genus-level taxonomic name of an organism playing a pathogen role"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "genus of pathogen"@en ; rdfs:subClassOf obo:GENEPIO_0001183, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCBITaxon_genus ] . obo:GENEPIO_0001788 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the species-level taxonomic name of an organism playing a pathogen role"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "species of pathogen"@en ; rdfs:subClassOf obo:GENEPIO_0001183, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCBITaxon_species ] . obo:GENEPIO_0001789 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "symptom cessation date"@en ; rdfs:subClassOf obo:GENEPIO_0001258 . obo:GENEPIO_0001790 obo:IAO_0000115 "This is a catch-all category for listing specimen related terms"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen datum"@en ; rdfs:seeAlso obo:GENEPIO_0000027, obo:GENEPIO_0001196, obo:GENEPIO_0001429, obo:GENEPIO_0001532, obo:GENEPIO_0001724, obo:GENEPIO_0001808, obo:GENEPIO_0002094, obo:OBI_0000659, obo:OBI_0001884, obo:OBI_0001889, obo:OBI_0001903, obo:OBI_0100051, "http://purl.obolibrary.org/obo/GENEPIO_0002105"@en, "http://purl.obolibrary.org/obo/OBI_0001616"^^xsd:anyURI ; rdfs:subClassOf obo:IAO_0000027, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100051 ] . obo:GENEPIO_0001791 obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "isolate identifier specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001644 ] . obo:GENEPIO_0001792 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "data obfuscated"@en ; rdfs:seeAlso "https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/"^^xsd:anyURI ; rdfs:subClassOf obo:GENEPIO_0001646 . obo:GENEPIO_0001793 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "data aggregated"@en ; rdfs:subClassOf obo:GENEPIO_0001646 . obo:GENEPIO_0001794 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted)."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "limited data set"@en ; rdfs:subClassOf obo:GENEPIO_0001646 . obo:GENEPIO_0001795 obo:GENEPIO_0001763 "help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users."@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them."@en ; obo:IAO_0000116 "Damion Dooley's note: There is a case in the \"draft tuberculosis contextual data standard\" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000600 "Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/"@en ; a owl:Class ; rdfs:label "de-identified data"@en ; rdfs:subClassOf obo:GENEPIO_0001646 . obo:GENEPIO_0001796 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "data protected"@en ; rdfs:subClassOf obo:GENEPIO_0001646 . obo:GENEPIO_0001797 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A datum containing the name of persons or institute who collected a given specimen."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"^^xsd:anyURI ; a owl:Class ; rdfs:label "specimen collector"@en ; rdfs:subClassOf obo:GENEPIO_0001790, [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002468 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C25191 ] ) ] ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0002468 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C93874 ] ) ] ; owl:onProperty obo:RO_0002180 ] . obo:GENEPIO_0001798 obo:IAO_0000117 obo:IAO_0000123, "Damion Dooley" ; a owl:Class ; rdfs:label "NCBI BioSample culture identifier"@en ; rdfs:subClassOf obo:GENEPIO_0001723 . obo:GENEPIO_0001799 obo:IAO_0000115 "A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "user identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001800 a owl:Class ; rdfs:label "sequence identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001801 a owl:Class ; rdfs:label "metagenomic species identification"@en ; rdfs:subClassOf obo:GENEPIO_0001738 . obo:GENEPIO_0001802 obo:IAO_0000115 "Note: REPLACE WITH Citation: SIO_000174 ????"@en ; a owl:Class ; rdfs:label "document citation identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001803 a owl:Class ; rdfs:label "organization identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001804 a owl:Class ; rdfs:label "collection identifier"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001805 a owl:Class ; rdfs:label "variant calling / pathogen identification and clustering"@en ; rdfs:subClassOf obo:GENEPIO_0001738 . obo:GENEPIO_0001806 a owl:Class ; rdfs:label "isolate (pathogen) identification"@en ; rdfs:subClassOf obo:GENEPIO_0001738 . obo:GENEPIO_0001807 obo:IAO_0100001 "http://purl.obolibrary.org/obo/OBI_0001616"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: NCBI BioSample ID -"@en ; owl:deprecated true . obo:GENEPIO_0001808 obo:IAO_0000112 """1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female"""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission."@en ; obo:IAO_0000116 "NCBI BioSample record documentation refers to a \"BioSample title\", stating that it is \"auto-generated if one is not supplied by the submitter.\" This is distinct from any assigned BioSession accession, or other \"external sample identifier\" that may have been issued by the source database or repository."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "specimen title"@en ; rdfs:subClassOf obo:GENEPIO_0001790 . obo:GENEPIO_0001809 a owl:Class ; rdfs:label "draft GenEpiO isolate source context"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001810 obo:GENEPIO_0000005 "INSDC term (lower level)" ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns."@en ; obo:IAO_0000119 ; oboInOwl:hasDbXref obo:GENEPIO_0001666 ; a owl:Class ; rdfs:label "restricted access"@en ; rdfs:subClassOf obo:GENEPIO_0001618 . obo:GENEPIO_0001811 a owl:Class ; rdfs:label "State (United States of America)"@en ; rdfs:subClassOf obo:NCIT_C87194 . obo:GENEPIO_0001812 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "health status trend datum"@en ; rdfs:subClassOf obo:GENEPIO_0001170, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:OBI_0100026 [ a owl:Restriction ; owl:onProperty obo:RO_0000087 ; owl:someValuesFrom obo:OBI_0000093 ] ) ] ] . obo:GENEPIO_0001813 obo:GENEPIO_0000005 "http://www.itis.gov" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "Integrated Taxonomic Information System"@en ; oboInOwl:hasDbXref "ITIS" ; a owl:Class ; rdfs:label "ITIS"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001815 a owl:NamedIndividual ; rdfs:label "MSH"@en . obo:GENEPIO_0001816 a owl:NamedIndividual ; rdfs:label "NCI_Thesaurus"@en . obo:GENEPIO_0001817 a owl:NamedIndividual ; rdfs:label "NIFSTD"@en . obo:GENEPIO_0001818 obo:GENEPIO_0000005 "https://www.nlm.nih.gov/mesh/meshhome.html"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "Medical Subject Headings"@en ; oboInOwl:hasDbXref "MSH" ; a owl:Class ; rdfs:label "MESH"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001819 obo:GENEPIO_0000005 "https://ncit.nci.nih.gov/ncitbrowser/" ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "National Cancer Institude Thesaurus"@en ; oboInOwl:hasDbXref "NCI_Thesaurus", "NCIt" ; a owl:Class ; rdfs:label "NCIT"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001820 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology"^^xsd:anyURI ; a owl:Class ; rdfs:label "NIFSTD"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001821 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.snomed.org/snomed-ct"^^xsd:anyURI ; oboInOwl:hasDbXref "SNOMEDCT" ; a owl:Class ; rdfs:label "SNOMEDCT"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001822 obo:GENEPIO_0000005 "http://www.fao.org/fishery/collection/asfis/en" ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "UN FAO Fisheries and Aquaculture Statistics and Information Branch database"@en ; oboInOwl:hasDbXref "FAO ASFIS" ; a owl:Class ; rdfs:label "ASFIS"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001823 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "FTT"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001824 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "TGN"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001825 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Wikipedia"^^xsd:anyURI ; a owl:Class ; rdfs:label "Wikipedia"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001826 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "SWEETRealm"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001827 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.geonames.org/"^^xsd:anyURI ; a owl:Class ; rdfs:label "Geonames"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001828 obo:GENEPIO_0000005 "http://ecolexicon.ugr.es/en/index.htm" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "EcoLexicon"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001829 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.irida.ca/"^^xsd:anyURI ; a owl:Class ; rdfs:label "draft IRIDA standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0001830 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/ISO_3166-2"^^xsd:anyURI ; a owl:Class ; rdfs:label "ISO3166-1"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001831 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/ISO_3166-1"^^xsd:anyURI ; a owl:Class ; rdfs:label "ISO3166-2"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001832 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "American National Standards Institute"@en ; a owl:Class ; rdfs:label "ANSI INCITS 38"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001833 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley", "The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical."@en ; obo:IAO_0000119 "https://nhd.usgs.gov/gnis.html"^^xsd:anyURI ; a owl:Class ; rdfs:label "GNISID"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001834 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "LTER"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001835 obo:GENEPIO_0001763 """order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome""" ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A National Center for Biotechnology Information BioSample specification defines fields and terms that provide \"descriptions of biological source materials used in experimental assays\"."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://www.ncbi.nlm.nih.gov/biosample/"^^xsd:anyURI ; a owl:Class ; rdfs:label "NCBI BioSample Pathogen.cl standard"@en ; rdfs:seeAlso "https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/"^^xsd:anyURI ; rdfs:subClassOf obo:GENEPIO_0000115, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100051 ] . obo:GENEPIO_0001836 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.ncbi.nlm.nih.gov/bioproject/"@en ; a owl:Class ; rdfs:comment "NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/"@en ; rdfs:label "NCBI BioProject standard"@en ; rdfs:subClassOf obo:GENEPIO_0000115, [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001892 ] ) ] ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0002128 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0002147 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0000156 ] ) ] ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001896 ] ) ] ; owl:onProperty obo:RO_0002180 ] . obo:GENEPIO_0001837 obo:GENEPIO_0000005 "http://www.aha.org/content/00-10/overview0302.pdf"^^xsd:anyURI, "http://www.webcitation.org/5VBWPbFgY"^^xsd:anyURI ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "American Hospital Association HIPAA Standard"@en ; oboInOwl:hasDbXref "AHA HIPPA" ; a owl:Class ; rdfs:label "AHA HIPPA standard"@en ; rdfs:subClassOf obo:GENEPIO_0001743 . obo:GENEPIO_0001838 obo:GENEPIO_0000005 "http://www.ncbi.nlm.nih.gov/pubmed/"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites."@en ; obo:IAO_0000118 "NCBI PubMed"@en ; oboInOwl:hasDbXref "PMID" ; a owl:Class ; rdfs:label "PubMed"@en ; rdfs:subClassOf obo:MI_0489 . obo:GENEPIO_0001839 obo:GENEPIO_0000005 "http://www.pulsenetinternational.org/"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks."@en ; obo:IAO_0000118 "Pulse Net International BioSample Metadata"@en ; oboInOwl:hasDbXref "PulseNet" ; a owl:Class ; rdfs:label "PulseNet submission standard"@en ; rdfs:seeAlso "https://www.cdc.gov/pulsenet/pathogens/index.html"^^xsd:anyURI, "https://www.nml-lnm.gc.ca/Pulsenet/index-eng.htm"@en ; rdfs:subClassOf obo:GENEPIO_0001743 . obo:GENEPIO_0001840 obo:GENEPIO_0000005 "AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf" ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref obo:GENEPIO_0001837, obo:GENEPIO_0001845, "AHA Hippa: Good"@en ; a owl:Class ; rdfs:label "good health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002025, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001848 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:NCIT_C115935 ] . obo:GENEPIO_0001841 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref obo:GENEPIO_0001845 ; a owl:Class ; rdfs:label "fair health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002025, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001669 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0002023 ] . obo:GENEPIO_0001842 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref obo:GENEPIO_0001837 ; a owl:Class ; rdfs:label "serious health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002025, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001846 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001669 ] . obo:GENEPIO_0001843 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A health status history datum is a record of the longer-term pattern or presence of a given patient's health status."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "health status history datum"@en ; rdfs:subClassOf obo:GENEPIO_0001170, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:OBI_0100026 [ a owl:Restriction ; owl:onProperty obo:RO_0000087 ; owl:someValuesFrom obo:OBI_0000093 ] ) ] ] . obo:GENEPIO_0001844 obo:IAO_0000112 "(0,0) is the origin of the cartesian coordinate system."@en ; obo:IAO_0000115 """\"In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry.\""""@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Origin_(mathematics)"^^xsd:anyURI ; rdfs:label "origin"@en ; rdfs:subClassOf . obo:GENEPIO_0001845 obo:GENEPIO_0000005 "https://en.wikipedia.org/wiki/Medical_state"@en ; obo:IAO_0000115 "United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000118 "National Health Service terminology"@en ; a owl:Class ; rdfs:label "NHS standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0001846 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase \"critical but stable\" is misleading by the very nature of \"critical\". The NHS however has it as one of its central terms. The use of \"stable\" also points to a health trend, rather than a state. A separate \"health status trend datum\" has been set up to capture this."@en ; rdfs:label "critical but stable health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002024, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0002228 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001842 ] . obo:GENEPIO_0001847 obo:GENEPIO_0000005 "NHS Terms: https://en.wikipedia.org/wiki/Medical_state" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "comfortable health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002024, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0002023 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001848 ] . obo:GENEPIO_0001848 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "progressing well health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002024, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001847 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001840 ] . obo:GENEPIO_0001849 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state."@en ; rdfs:label "discharged from hospital"@en ; rdfs:subClassOf obo:GENEPIO_0002019, obo:GENEPIO_0002024 . obo:GENEPIO_0001850 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A data item which is about the collection state of a datum at some point in time."@en ; obo:IAO_0000116 """Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request"""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made."@en ; rdfs:label "datum status"@en ; rdfs:seeAlso """INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting"""@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0001851 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A categorical choice indicating that a datum is available for retrieval."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "In theory any datum that has a recorded value has 'recorded' for its datum status."@en ; rdfs:label "recorded"@en ; rdfs:subClassOf obo:GENEPIO_0001850 . obo:GENEPIO_0001852 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Patient is awaiting physician and/or assessment."@en ; obo:IAO_0000116 "Very similar to 'datum status' 'in process' status."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref obo:GENEPIO_0001837 ; a owl:Class ; rdfs:label "undetermined health status - awaiting assessment"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002025 . obo:GENEPIO_0001853 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasExactSynonym "deteriorating"@en ; a owl:Class ; rdfs:label "worsening health trend"@en ; rdfs:subClassOf obo:GENEPIO_0001812, [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0002026 ] . obo:GENEPIO_0001854 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001855 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001856 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001857 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001858 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001859 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates."@en ; obo:IAO_0000117 "Damion Dooley"@en ; rdfs:subClassOf obo:BFO_0000141 . obo:GENEPIO_0001860 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001861 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001862 obo:GENEPIO_0001920 """/^[N+](:\\d(\\.\\d+)?)$/, $lat /^S(:\\d(\\.\\d+)?)$/, '-' + $lat"""^^xsd:string ; obo:GENEPIO_1919 """/^(:[-S+N])?(:[1-8]?[0-9](:\\.\\d{1,6})?)$/, $lat$degree.$decimal /^(:[-S+N])?(:90(:\\.0{1,6})?))$/, $lat$degree.$decimal"""^^xsd:string ; obo:GENEPIO_1921 "/^(\\d(\\.\\d+)?)$/, '+\\1'"^^xsd:string ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A decimal latitude measurement in degrees in conformance with the ISO 6709 standard."@en ; obo:IAO_0000116 """This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]'"""@en ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:OBI_0001931, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001620 ] . obo:GENEPIO_0001863 obo:GENEPIO_1919 """/^(:[-W+E])?(:(1[0-7]|[1-9])?[0-9])(:\\.\\d{1,6})?)$/, $long$degree.$decimal /^(:[-W+E])?(:180(:\\.0{1,6})?)$,$long$degree.$decimal"""^^xsd:string ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A decimal longitude measurement in degrees in conformance with the ISO 6709 standard."@en ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:OBI_0001931, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001621 ] . obo:GENEPIO_0001864 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001865 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension"@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001866 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001867 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001868 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000116 "Damion Dooley's note: IAO lat/long can't be made a subclass of \"angular coordinate\" or disjoint contradiction arises with \"immaterial entity\""@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001869 obo:IAO_0000117 obo:IAO_0000428, "Damion Dooley" . obo:GENEPIO_0001870 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001871 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001872 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001873 obo:IAO_0000115 "A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end."@en ; obo:IAO_0000117 "Damion Dooley" ; rdfs:label "datetime range intermediate"@en ; rdfs:subClassOf obo:GENEPIO_0001876, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001878 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001877 ] . obo:GENEPIO_0001874 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001875 obo:IAO_0000116 "This seems to be covered by 'datetime range intermediate'"@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001876 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:label "datetime range item"@en . obo:GENEPIO_0001877 rdfs:comment "The ending date of a process"@en ; rdfs:label "datetime range end"@en ; rdfs:subClassOf obo:GENEPIO_0001876, [ a owl:Restriction ; owl:onProperty obo:BFO_0000062 ; owl:someValuesFrom obo:GENEPIO_0001878 ] . obo:GENEPIO_0001878 obo:IAO_0000117 "Damion Dooley" ; rdfs:comment "The starting date of a process"@en ; rdfs:label "datetime range start"@en ; rdfs:subClassOf obo:GENEPIO_0001876, [ a owl:Restriction ; owl:onProperty obo:BFO_0000063 ; owl:someValuesFrom obo:GENEPIO_0001877 ] . obo:GENEPIO_0001879 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001880 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001881 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A datetime set item is a datetime that has been grouped semantically under a given type of process"@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001882 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001883 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001884 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001885 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:GENEPIO_0001996 ] . obo:GENEPIO_0001886 obo:IAO_0000114 obo:IAO_0000428, "A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time."@en ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:BFO_0000029 . obo:GENEPIO_0001887 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001888 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A Canadian postal code is a postal code that pertains to a geographic region of Canada."@en ; obo:IAO_0000116 "Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account."@en ; owl:disjointWith obo:NCIT_C25720 . obo:GENEPIO_0001889 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001890 obo:IAO_0000115 "A \"USA zip code\" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C25720" ; a owl:Class ; rdfs:label "obsolete: US postal code"@en ; owl:deprecated true . obo:GENEPIO_0001892 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "entity history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001893 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "generic range history record"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . obo:GENEPIO_0001894 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001895 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001896 rdfs:subClassOf obo:OBI_0000938 . obo:GENEPIO_0001897 obo:GENEPIO_0000006 "home"@en ; a owl:NamedIndividual . obo:GENEPIO_0001898 obo:GENEPIO_0000006 "mobile"@en . obo:GENEPIO_0001899 obo:GENEPIO_0000006 "work"@en . obo:GENEPIO_0001900 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; rdfs:comment "A set does not have a direct distance metric between its members."@en ; rdfs:subClassOf obo:BFO_0000141 . obo:GENEPIO_0001901 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001902 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements."@en ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001903 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001904 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:NCIT_C40978 . obo:GENEPIO_0001905 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001906 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001907 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001908 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Plane_(geometry)"^^xsd:anyURI . obo:GENEPIO_0001910 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001911 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:GENEPIO_0001919 . obo:GENEPIO_0001912 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001916 ] . obo:GENEPIO_0001913 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001912 ] . obo:GENEPIO_0001914 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001913 ] . obo:GENEPIO_0001915 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001914 ] . obo:GENEPIO_0001916 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001917 ] . obo:GENEPIO_0001918 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002087 ; owl:someValuesFrom obo:GENEPIO_0001915 ] . obo:GENEPIO_0001919 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:GENEPIO_0001920 obo:GENEPIO_0000006 "UI regex normalize"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:label "user interface regular epression normalize"@en . obo:GENEPIO_0001921 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A product name and model number of a manufacturer's genomic (dna) sequencer."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "sequencing instrument model"@en ; rdfs:subClassOf obo:OBI_0000832 . obo:GENEPIO_0001922 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Circle"^^xsd:anyURI ; a owl:Class ; rdfs:label "circle"@en ; rdfs:subClassOf obo:GENEPIO_0001934, obo:GENEPIO_0001996, , [ a owl:Restriction ; owl:onClass obo:GENEPIO_0002035 ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:onClass obo:PATO_0002390 ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0001923 oboInOwl:hasDbXref "NCBI SRA: ILLUMINA" ; a owl:Class ; rdfs:label "Illumina platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0001924 oboInOwl:hasDbXref "NCBI SRA: COMPLETE_GENOMICS" ; a owl:Class ; rdfs:comment "Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: \"Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).\"" ; rdfs:label "Complete Genomics platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0001925 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "earth area boundary census"@en ; rdfs:subClassOf obo:APOLLO_SV_00000173, [ a owl:Restriction ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0002017 ; owl:onProperty obo:RO_0002180 ], [ a owl:Restriction ; owl:onClass obo:GENEPIO_0001996 ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0001926 oboInOwl:hasDbXref "NCBI SRA: LS454" ; a owl:Class ; rdfs:label "Roche LS454 platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0001927 oboInOwl:hasDbXref "NCBI SRA: PACBIO_SMRT" ; a owl:Class ; rdfs:label "PacBio platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0001928 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD 4hq" ; a owl:Class ; rdfs:label "SOLiD 4hq System"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001929 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD 5500" ; a owl:Class ; rdfs:label "SOLiD 5500"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001930 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD 5500xl" ; a owl:Class ; rdfs:label "SOLiD 5500xl"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001931 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD PI System" ; a owl:Class ; rdfs:label "SOLiD PI System"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001932 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD System 2.0" ; a owl:Class ; rdfs:label "SOLiD System 2.0"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001933 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD System 3.0" ; a owl:Class ; rdfs:label "SOLiD System 3.0"@en ; rdfs:subClassOf obo:OBI_0000696 . obo:GENEPIO_0001934 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A two dimensional entity is an entity composed of one or more points on a two dimensional surface."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "2D entity"@en ; rdfs:subClassOf obo:GENEPIO_0001884 . obo:GENEPIO_0001935 oboInOwl:hasDbXref "NCBI SRA: Ion Torrent PGM" ; a owl:Class . obo:GENEPIO_0001936 oboInOwl:hasDbXref "NCBI SRA: 454 GS FLX Titanium" ; a owl:Class ; rdfs:label "454 Genome Sequencer FLX Titanium"@en ; rdfs:subClassOf obo:GENEPIO_0001937 . obo:GENEPIO_0001937 oboInOwl:hasDbXref "NCBI SRA: 454 GS" ; a owl:Class ; rdfs:label "454 Genome Sequencer"@en ; rdfs:subClassOf obo:GENEPIO_0001921, obo:OBI_0400103 . obo:GENEPIO_0001938 oboInOwl:hasDbXref "NCBI SRA: 454 GS Junior" ; a owl:Class ; rdfs:label "454 Genome Sequencer Junior"@en ; rdfs:subClassOf obo:GENEPIO_0001937 . obo:GENEPIO_0001939 a owl:Class . obo:GENEPIO_0001940 obo:GENEPIO_0000005 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" ; obo:IAO_0000115 "Whether any method was used to select for or against, enrich, or screen the material being sequenced."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: LIBRARY_SELECTION" ; a owl:Class ; rdfs:label "library selection"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001941 obo:IAO_0000115 "Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C)."@en ; oboInOwl:hasDbXref "NCBI SRA: 5-methylcytidine antibody" ; a owl:Class ; rdfs:label "5-methylcytidine antibody method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001942 obo:IAO_0000115 "Cap-analysis gene expression."@en ; oboInOwl:hasDbXref "NCBI SRA: CAGE" ; a owl:Class ; rdfs:label "CAGE method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001943 obo:IAO_0000115 "Cot-filtered highly repetitive genomic DNA"@en ; oboInOwl:hasDbXref "NCBI SRA: CF-H" ; a owl:Class ; rdfs:label "CF-H method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001944 obo:IAO_0000115 "Cot-filtered moderately repetitive genomic DNA"@en ; oboInOwl:hasDbXref "NCBI SRA: CF-M" ; a owl:Class ; rdfs:label "CF-M method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001945 obo:IAO_0000115 "Cot-filtered single/low-copy genomic DNA"@en ; oboInOwl:hasDbXref "NCBI SRA: CF-S" ; a owl:Class ; rdfs:label "CF-S method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001946 obo:IAO_0000115 "Cot-filtered theoretical single-copy genomic DNA"@en ; oboInOwl:hasDbXref "NCBI SRA: CF-T" ; a owl:Class ; rdfs:label "CF-T method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001947 obo:IAO_0000115 "Chromatin immunoprecipitation"@en ; oboInOwl:hasDbXref "NCBI SRA: ChIP" ; a owl:Class ; rdfs:label "ChIP method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001948 obo:IAO_0000115 "Deoxyribonuclease (MNase) digestion"@en ; oboInOwl:hasDbXref "NCBI SRA: DNAse" ; a owl:Class ; rdfs:label "DNAse method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001949 obo:IAO_0000115 "Hypo-methylated partial restriction digest"@en ; oboInOwl:hasDbXref "NCBI SRA: HMPR" ; a owl:Class ; rdfs:label "HMPR method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001950 obo:IAO_0000115 "Selection by hybridization in array or solution."@en ; oboInOwl:hasDbXref "NCBI SRA: Hybrid Selection" ; a owl:Class ; rdfs:label "Hybrid Selection method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001951 obo:IAO_0000115 "Enrichment by methyl-CpG binding domain."@en ; oboInOwl:hasDbXref "NCBI SRA: MBD2 protein methyl-CpG binding domain" ; a owl:Class ; rdfs:label "MBD2 protein methyl-CpG binding domain method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001952 obo:IAO_0000115 "Methyl Filtrated"@en ; oboInOwl:hasDbXref "NCBI SRA: MF" ; a owl:Class ; rdfs:label "MF method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001953 obo:IAO_0000115 "Micrococcal Nuclease (MNase) digestion"@en ; oboInOwl:hasDbXref "NCBI SRA: MNase" ; a owl:Class ; rdfs:label "MNase method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001954 obo:IAO_0000115 "Methylation Spanning Linking Library"@en ; oboInOwl:hasDbXref "NCBI SRA: MSLL" ; a owl:Class ; rdfs:label "MSLL method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001955 obo:IAO_0000115 "Source material was selected by designed primers."@en ; oboInOwl:hasDbXref "NCBI SRA: PCR" ; a owl:Class ; rdfs:label "PCR method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001956 obo:IAO_0000115 "Rapid Amplification of cDNA Ends."@en ; oboInOwl:hasDbXref "NCBI SRA: RACE" ; a owl:Class ; rdfs:label "RACE method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001957 obo:IAO_0000115 "Source material was selected by randomly generated primers."@en ; oboInOwl:hasDbXref "NCBI SRA: RANDOM PCR" ; a owl:Class ; rdfs:label "RANDOM PCR method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001958 obo:IAO_0000115 "Random selection by shearing or other method."@en ; oboInOwl:hasDbXref "NCBI SRA: RANDOM" ; a owl:Class ; rdfs:label "RANDOM method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001959 obo:IAO_0000115 "Source material was selected by reverse transcription PCR"@en ; oboInOwl:hasDbXref "NCBI SRA: RT-PCR" ; a owl:Class ; rdfs:label "RT-PCR method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001960 obo:IAO_0000115 "Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling."@en ; oboInOwl:hasDbXref "NCBI SRA: Reduced Representation" ; a owl:Class ; rdfs:label "Reduced Representation method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001961 obo:IAO_0000115 "DNA fractionation using restriction enzymes."@en ; oboInOwl:hasDbXref "NCBI SRA: Restriction Digest" ; a owl:Class ; rdfs:label "Restriction Digest method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001962 obo:IAO_0000115 "PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA."@en ; oboInOwl:hasDbXref "NCBI SRA: cDNA" ; a owl:Class ; rdfs:label "cDNA method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001963 obo:IAO_0000115 "Physical selection of size appropriate targets."@en ; oboInOwl:hasDbXref "NCBI SRA: size fractionation" ; a owl:Class ; rdfs:label "size fractionation method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001964 obo:IAO_0000115 "Other library enrichment, screening, or selection process."@en ; oboInOwl:hasDbXref "NCBI SRA: other" ; a owl:Class ; rdfs:label "other library method"@en ; rdfs:subClassOf obo:GENEPIO_0001940 . obo:GENEPIO_0001965 obo:GENEPIO_0000005 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" ; obo:IAO_0000115 "The library source specifies the type of source material that is being sequenced."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "library source"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001966 obo:IAO_0000115 "Genomic DNA (includes PCR products from genomic DNA)."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: GENOMIC" ; a owl:Class ; rdfs:label "genomic source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001967 obo:IAO_0000115 "Mixed material from metagenome."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasDbXref "NCBI SRA: METAGENOMIC" ; a owl:Class ; rdfs:label "metagenomic source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001968 obo:IAO_0000115 "Transcription products from community targets"@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: METATRANSCRIPTOMIC" ; a owl:Class ; rdfs:label "metatranscriptomic source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001969 obo:IAO_0000115 "Other, unspecified, or unknown library source material."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: OTHER" ; a owl:Class ; rdfs:label "other library source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001970 obo:IAO_0000115 "Synthetic DNA."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: SYNTHETIC" ; a owl:Class ; rdfs:label "synthetic source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001971 obo:IAO_0000115 "Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries)."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: TRANSCRIPTOMIC" ; a owl:Class ; rdfs:label "transcriptomic source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001972 obo:IAO_0000115 "Viral RNA."@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref "NCBI SRA: VIRAL RNA" ; a owl:Class ; rdfs:label "viral RNA source"@en ; rdfs:subClassOf obo:GENEPIO_0001965 . obo:GENEPIO_0001973 obo:IAO_0000115 "Sequencing technique intended for this library."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" ; a owl:Class ; rdfs:label "library strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001974 obo:IAO_0000115 "Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA"@en ; oboInOwl:hasDbXref "NCBI SRA: AMPLICON" ; a owl:Class ; rdfs:label "amplicon strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001975 obo:IAO_0000115 "MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status."@en ; oboInOwl:hasDbXref "NCBI SRA: Bisulfite-Seq" ; a owl:Class ; rdfs:label "Bisulfite-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001976 obo:IAO_0000115 "Clone end (5', 3', or both) sequencing."@en ; oboInOwl:hasDbXref "NCBI SRA: CLONEEND" ; a owl:Class ; rdfs:label "clone end strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001977 obo:IAO_0000115 "Genomic clone based (hierarchical) sequencing."@en ; oboInOwl:hasDbXref "NCBI SRA: CLONE" ; a owl:Class ; rdfs:label "clone strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001978 obo:IAO_0000115 "Concatenated Tag Sequencing"@en ; oboInOwl:hasDbXref "NCBI SRA: CTS" ; a owl:Class ; rdfs:label "CTS strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001979 obo:IAO_0000115 "Direct sequencing of chromatin immunoprecipitates."@en ; oboInOwl:hasDbXref "NCBI SRA: ChIP-Seq" ; a owl:Class ; rdfs:label "ChIP-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001980 obo:IAO_0000115 "Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI."@en ; oboInOwl:hasDbXref "NCBI SRA: DNase-Hypersensitivity" ; a owl:Class ; rdfs:label "DNase-Hypersensitivity strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001981 obo:IAO_0000115 "Single pass sequencing of cDNA templates"@en ; oboInOwl:hasDbXref "NCBI SRA: EST" ; a owl:Class ; rdfs:label "EST strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001982 obo:IAO_0000115 "Sequencing intended to finish (close) gaps in existing coverage."@en ; oboInOwl:hasDbXref "NCBI SRA: FINISHING" ; a owl:Class ; rdfs:label "finishing strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001983 obo:IAO_0000115 "Full-length sequencing of cDNA templates"@en ; oboInOwl:hasDbXref "NCBI SRA: FL-cDNA" ; a owl:Class ; rdfs:label "FL-cDNA strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001984 obo:IAO_0000115 "Direct sequencing of methylated fractions sequencing strategy."@en ; oboInOwl:hasDbXref "NCBI SRA: MBD-Seq" ; a owl:Class ; rdfs:label "MBD-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001985 obo:IAO_0000115 "Direct sequencing following MNase digestion."@en ; oboInOwl:hasDbXref "NCBI SRA: MNase-Seq" ; a owl:Class ; rdfs:label "MNase-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001986 obo:IAO_0000115 "Methylation-Sensitive Restriction Enzyme Sequencing strategy."@en ; oboInOwl:hasDbXref "NCBI SRA: MRE-Seq" ; a owl:Class ; rdfs:label "MRE-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001987 obo:IAO_0000115 "Methylated DNA Immunoprecipitation Sequencing strategy."@en ; oboInOwl:hasDbXref "NCBI SRA: MeDIP-Seq" ; a owl:Class ; rdfs:label "MeDIP-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001988 obo:IAO_0000115 "Library strategy not listed."@en ; oboInOwl:hasDbXref "NCBI SRA: OTHER" ; a owl:Class ; rdfs:label "other library strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001989 obo:IAO_0000115 "Shotgun of pooled clones (usually BACs and Fosmids)."@en ; oboInOwl:hasDbXref "NCBI SRA: POOLCLONE" ; a owl:Class ; rdfs:label "pool clone strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001990 obo:IAO_0000115 "Random sequencing of whole transcriptome."@en ; oboInOwl:hasDbXref "NCBI SRA: RNA-Seq" ; a owl:Class ; rdfs:label "RNA-Seq strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001991 obo:IAO_0000115 "Random sequencing of a whole chromosome or other replicon isolated from a genome."@en ; oboInOwl:hasDbXref "NCBI SRA: WCS" ; a owl:Class ; rdfs:label "WCS strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001992 obo:IAO_0000115 "Random sequencing of the whole genome."@en ; oboInOwl:hasDbXref "NCBI SRA: WGS" ; a owl:Class ; rdfs:label "WGS strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001993 obo:IAO_0000115 "Random sequencing of exonic regions selected from the genome."@en ; oboInOwl:hasDbXref "NCBI SRA: WXS" ; a owl:Class ; rdfs:label "WXS strategy"@en ; rdfs:subClassOf obo:GENEPIO_0001973 . obo:GENEPIO_0001994 obo:IAO_0000115 "Free form text describing the protocol by which the sequencing library was constructed."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly"@en ; a owl:Class ; rdfs:label "library construction protocol"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0001995 obo:IAO_0000115 "The submitter's name for this library."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly"@en ; oboInOwl:hasDbXref "NCBI SRA: LIBRARY_NAME"@en ; a owl:Class ; rdfs:label "library name"@en ; rdfs:subClassOf obo:GENEPIO_0001681, obo:IAO_0000300 . obo:GENEPIO_0001996 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "2D boundary"@en ; rdfs:subClassOf obo:GENEPIO_0001884 . obo:GENEPIO_0001997 obo:GENEPIO_0000006 "cfu/100mL"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid."@en ; obo:IAO_0000116 "Should this be deprecated? Need to find working examples that actually use / 100mL."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "colony forming unit per 100 milliliter"@en ; rdfs:subClassOf obo:UO_0000212 . obo:GENEPIO_0001998 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "decimal quantity unit"@en ; rdfs:subClassOf obo:GENEPIO_0001909 . obo:GENEPIO_0001999 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - dataset features and provenance"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002000 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case specimen characteristics"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002001 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case subject characteristics"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002002 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case risk factors"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002003 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case clinical presentation"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002004 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case laboratory testing"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002005 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case medication"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002006 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft isolate whole genome sequencing model"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0002007 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "draft tuberculosis - case model"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002008 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "Mycobacterium tuberculosis lineage"@en ; rdfs:seeAlso """A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html"""^^rdfs:Literal, """Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html"""^^rdfs:Literal ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002009 a owl:Class ; rdfs:label "TB lineage 2 - East-Asian, includes Bejing"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002010 a owl:Class ; rdfs:label "TB lineage 3 - East-African Indian, includes CAS/Delhi"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002011 a owl:Class ; rdfs:label "TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002012 a owl:Class ; rdfs:label "TB lineage 1 - Indo-Oceanic"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002013 a owl:Class ; rdfs:label "TB lineage 5 - West African 1"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002014 a owl:Class ; rdfs:label "TB lineage 6 - West African 2"@en ; rdfs:subClassOf obo:GENEPIO_0002008 . obo:GENEPIO_0002015 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:comment "An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens."@en ; rdfs:label "isolate preparation facility"@en ; rdfs:subClassOf obo:OBI_0000245 . obo:GENEPIO_0002016 a owl:Class ; rdfs:label "plant product"@en ; rdfs:subClassOf obo:GENEPIO_0000028 . obo:GENEPIO_0002017 a owl:Class ; rdfs:label "geospatial name"@en ; rdfs:subClassOf obo:NCIT_C42614, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001886 ] . obo:GENEPIO_0002018 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A personal health datum is a datum that pertains to the health situation or history of an individual."@en ; obo:IAO_0000116 """Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom""" ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "personal health datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0002019 obo:IAO_0000115 "A host hospital service status indicates the state of a host's interaction with hospital medical services."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "host hospital service status"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002020 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "admitted to hospital"@en ; rdfs:subClassOf obo:GENEPIO_0002019 . obo:GENEPIO_0002021 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Received treatment but not admitted."@en ; oboInOwl:hasDbXref obo:GENEPIO_0001837 ; a owl:Class ; rdfs:label "treated and released (not admitted to hospital)"@en ; rdfs:subClassOf obo:GENEPIO_0002019 . obo:GENEPIO_0002022 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Received treatment. Transferred to a different facility."@en ; oboInOwl:hasDbXref obo:GENEPIO_0001837 ; a owl:Class ; rdfs:label "treated and transferred"@en ; rdfs:subClassOf obo:GENEPIO_0002019 . obo:GENEPIO_0002023 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "satisfactory health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002024, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001841 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001847 ] . obo:GENEPIO_0002024 obo:GENEPIO_0001763 "depth:1" ; a owl:Class ; rdfs:label "subject health status (UK NHS)"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002025 obo:GENEPIO_0001763 "depth:1" ; a owl:Class ; rdfs:label "subject health status (AHA)"@en ; rdfs:seeAlso "http://purl.obolibrary.org/obo/GENEPIO_0002019"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002026 a owl:Class ; rdfs:label "stable health trend"@en ; rdfs:seeAlso "http://purl.obolibrary.org/obo/GENEPIO_0001669"@en ; rdfs:subClassOf obo:GENEPIO_0001812, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001853 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001550 ] . obo:GENEPIO_0002027 obo:IAO_0000115 "An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/STATO_0000228"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: ordinal variable"@en ; owl:deprecated true . obo:GENEPIO_0002028 a owl:Class ; rdfs:label "mapping (reference based)"@en ; rdfs:subClassOf obo:GENEPIO_0000090 . obo:GENEPIO_0002029 a owl:Class ; rdfs:label "data protection item"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0002030 a owl:Class ; rdfs:label "subject provided consent"@en ; rdfs:subClassOf obo:GENEPIO_0002032 . obo:GENEPIO_0002031 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:comment "An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings."@en ; rdfs:label "ordinal value specification"@en ; rdfs:subClassOf obo:OBI_0001930 . obo:GENEPIO_0002032 a owl:Class ; rdfs:label "consent datum"@en ; rdfs:subClassOf obo:GENEPIO_0002029 . obo:GENEPIO_0002033 a owl:Class ; rdfs:label "agency provided consent"@en ; rdfs:subClassOf obo:GENEPIO_0002032 . obo:GENEPIO_0002034 obo:IAO_0000117 ; dc:date "2019-11-17T00:43:00Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "draft ISO sequence repository field"@en ; rdfs:subClassOf linkml:SlotDefinition . obo:GENEPIO_0002035 obo:IAO_0000112 "Centre of circle, ellipse or parabola; centre of mass."@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point."@en ; obo:IAO_0000116 "Probably a better formal math defn?"@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "centre point"@en ; rdfs:subClassOf . obo:GENEPIO_0002036 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000116 """This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug'""" ; obo:IAO_0000117 "Damion Dooley"@en, "This is a collection of antibiotic resistance process parameters and outputs"@en ; a owl:Class ; rdfs:label "phenotypic antimicrobial drug susceptibility test datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0002037 obo:IAO_0000115 "The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT)"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85539" ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance phenotype"@en ; owl:deprecated true . obo:GENEPIO_0002038 obo:IAO_0000115 "Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85560" ; a owl:Class ; rdfs:label "obsolete: antibiotic intermediate resistance (I)"@en ; owl:deprecated true . obo:GENEPIO_0002039 obo:IAO_0000115 "Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85561" ; a owl:Class ; rdfs:label "obsolete: antibiotic nonsensitive (high resistance)"@en ; owl:deprecated true . obo:GENEPIO_0002040 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive."@en ; obo:IAO_0000116 "Damion Dooley note: Is this the same as \"indeterminate\"?"@en ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "N", "ND" ; a owl:Class ; rdfs:label "antibiotic resistance not defined"@en ; rdfs:subClassOf obo:ARO_3004299 . obo:GENEPIO_0002041 obo:IAO_0000115 "Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85562" ; a owl:Class ; rdfs:label "obsolete: antibiotic resistant (R)"@en ; owl:deprecated true . obo:GENEPIO_0002042 obo:IAO_0000115 "Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85563" ; a owl:Class ; rdfs:label "obsolete: antibiotic sensitive (S)"@en ; owl:deprecated true . obo:GENEPIO_0002043 obo:IAO_0000115 "Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85559" ; a owl:Class ; rdfs:label "obsolete: sensitive - dose dependent"@en ; owl:deprecated true . obo:GENEPIO_0002044 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A MIC test measurement resulting from a laboratory dilution method."@en ; obo:IAO_0000116 "Damion Dooley's note: is this still useful? Currently \"MIC dilution measurement specification' refers directly via 'is about' to \"broth dilution method\" but that may be too specific."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "MIC dilution measurement datum"@en ; rdfs:subClassOf obo:IAO_0000032, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C128985 ] . obo:GENEPIO_0002045 obo:IAO_0000115 "The type of assay used to determine the minimum inhibitory concentration."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85540" ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance testing method"@en ; owl:deprecated true . obo:GENEPIO_0002046 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/NCIT_C85555"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: agar dilution evidence"@en ; owl:deprecated true . obo:GENEPIO_0002047 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "antimicrobial resistance testing method device or reagent"@en ; rdfs:subClassOf obo:OBI_0000968 . obo:GENEPIO_0002048 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 ""@en ; a owl:Class ; rdfs:label "antimicrobial resistant plasmid type"@en ; rdfs:subClassOf obo:GENEPIO_0002036 . obo:GENEPIO_0002049 obo:IAO_0000115 "The instrumentation used to determine minimum inhibitory concentration values."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004390"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance testing platform"@en ; owl:deprecated true . obo:GENEPIO_0002050 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004400"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Microscan"@en ; owl:deprecated true . obo:GENEPIO_0002051 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004401"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Phoenix"@en ; owl:deprecated true . obo:GENEPIO_0002052 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004402"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Sensititre"@en ; owl:deprecated true . obo:GENEPIO_0002053 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004403"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Vitek"@en ; owl:deprecated true . obo:GENEPIO_0002054 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004409"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Trek"@en ; owl:deprecated true . obo:GENEPIO_0002055 obo:IAO_0100001 obo:ARO_3004399 ; a owl:Class ; rdfs:label "obsolete: manual - noncommercial"@en ; owl:deprecated true . obo:GENEPIO_0002056 obo:IAO_0000115 "The manufacturer of an antibiotic resistance lab typing platform"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004404"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance testing platform vendor"@en ; owl:deprecated true . obo:GENEPIO_0002057 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004407"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Siemens"@en ; owl:deprecated true . obo:GENEPIO_0002058 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004406"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Biomérieux"@en ; owl:deprecated true . obo:GENEPIO_0002059 obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004405"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: Becton Dickinson"@en ; owl:deprecated true . obo:GENEPIO_0002060 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 ; oboInOwl:hasSynonym "E-Test"@en, "Epsilometer test"@en ; a owl:Class ; rdfs:label "Etest (device)"@en ; rdfs:subClassOf obo:GENEPIO_0002047 . obo:GENEPIO_0002061 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "GM-NEG"@en ; rdfs:subClassOf obo:GENEPIO_0002047 . obo:GENEPIO_0002062 obo:IAO_0000115 "The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004360"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance testing reference standard"@en ; owl:deprecated true . obo:GENEPIO_0002063 obo:IAO_0000115 "BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:ARO_3004365 ; oboInOwl:hasAlternativeId "BSAC"^^rdfs:Literal ; a owl:Class ; rdfs:label "obsolete: British Society for Antimicrobial Chemotherapy (BSAC)"@en ; owl:deprecated true . obo:GENEPIO_0002064 obo:IAO_0000115 "The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards"@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000118 "NCCLS"@en ; obo:IAO_0000119 "http://clsi.org"^^xsd:anyURI ; obo:IAO_0100001 obo:ARO_3004366 ; oboInOwl:hasAlternativeId "CLSI" ; a owl:Class ; rdfs:comment "On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI"@en ; rdfs:label "obsolete: Clinical and Laboratory Standards Institute (CLSI)"@en ; owl:deprecated true . obo:GENEPIO_0002065 obo:IAO_0000115 "DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations."@de ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.din.de/en/din-and-our-partners/din-e-v"^^xsd:anyURI ; obo:IAO_0100001 obo:ARO_3004367 ; oboInOwl:hasAlternativeId "DIN"^^rdfs:Literal ; a owl:Class ; rdfs:label "Deutsches Institut für Normung"@de, "obsolete: German Institute for Standardization (DIN)"@en ; owl:deprecated true . obo:GENEPIO_0002066 obo:IAO_0000115 "EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.eucast.org/"^^xsd:anyURI ; obo:IAO_0100001 obo:ARO_3004368 ; oboInOwl:hasAlternativeId "EUCAST"^^rdfs:Literal ; a owl:Class ; rdfs:label "obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST)"@en ; owl:deprecated true . obo:GENEPIO_0002067 obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 obo:ARO_3004366 ; oboInOwl:hasAlternativeId "NCCLS"^^rdfs:Literal ; a owl:Class ; rdfs:label "obsolete: National Committee on Clinical Laboratory Standards (NCCLS)"@en ; owl:deprecated true . obo:GENEPIO_0002068 obo:IAO_0000115 "La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites."@fr, "The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents."@en ; obo:IAO_0000116 "This isn't at moment considered a valid EBI antibiogram choice?" ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "http://www.sfm-microbiologie.org/"^^xsd:anyURI ; obo:IAO_0100001 obo:ARO_3004369 ; oboInOwl:hasAlternativeId "SFM"^^rdfs:Literal ; a owl:Class ; rdfs:label "obsolete: Société Française de Microbiologie (SFM)" ; owl:deprecated true . obo:GENEPIO_0002069 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "SIR"^^rdfs:Literal ; a owl:Class ; rdfs:label "SIR"@en ; rdfs:subClassOf obo:ARO_3004360 . obo:GENEPIO_0002070 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasAlternativeId "WRG"^^rdfs:Literal ; a owl:Class ; rdfs:label "WRG"@en ; rdfs:subClassOf obo:ARO_3004360 . obo:GENEPIO_0002071 a owl:Class ; rdfs:label "first line tuberculosis drug"@en ; rdfs:subClassOf obo:GENEPIO_0001039 . obo:GENEPIO_0002072 a owl:Class ; rdfs:label "last resort antibiotic"@en ; rdfs:subClassOf obo:GENEPIO_0001187 . obo:GENEPIO_0002073 obo:GENEPIO_0000006 "NIAID standard"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards"^^xsd:anyURI ; a owl:Class ; rdfs:label "National Institute of Allergy and Infectious Disease standard"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0002074 obo:IAO_0000115 "A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "RefSeq accession identifier"@en ; rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/refseq/about/" ; rdfs:subClassOf . obo:GENEPIO_0002075 obo:IAO_0000115 "A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "Genomic Standards Consortium (GSC) standard"@en ; rdfs:seeAlso "http://gensc.org/"^^xsd:anyURI ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0002076 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A landform, biome or built environment at site that a given specimen was collected from."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen collection site - geographic feature"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002077 obo:IAO_0000112 "A particular human patient, or a given animal or plant."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An investigative subject which is an organism."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject organism"@en ; rdfs:subClassOf obo:NCIT_C79916, [ a owl:Restriction ; owl:onProperty obo:RO_0000086 ; owl:someValuesFrom obo:OBI_0001169 ] . obo:GENEPIO_0002078 obo:GENEPIO_0001763 "help=The number of passages should be expressed as a numerical value."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The number of serial iterations that an isolate is grown in one environment."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "number of passages"@en ; rdfs:subClassOf obo:GENEPIO_0001054, obo:STATO_0000047 . obo:GENEPIO_0002079 obo:GENEPIO_0001763 "help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation."@en ; obo:IAO_0000115 "A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "passage protocol"@en ; rdfs:subClassOf obo:GENEPIO_0001054, . obo:GENEPIO_0002080 obo:IAO_0000115 "The unit provided for an antibiotic drug test dosage."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004372"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: drug minimum inhibitory concentration unit"@en ; owl:deprecated true . obo:GENEPIO_0002081 obo:GENEPIO_0001763 """order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing""" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft sequence repository data - specimen collection"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002082 obo:GENEPIO_0001763 """order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Contact information for an organization related to specimen collection, processing or storage."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "contact specification - specimen related organization"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0002083 obo:GENEPIO_0001763 "dateFormat:ISO 8601", """order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository contextual data standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0002084 obo:GENEPIO_0001763 """order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium""" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft sequence repository data - isolate"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002085 obo:GENEPIO_0001763 """order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm""" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft sequence repository data - sequencing"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002086 obo:GENEPIO_0001763 """order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The geographical origin of the sample by city, region, country or latitude and logitude."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - geographic location"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002087 obo:GENEPIO_0001763 """order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol""" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:label "draft sequence repository data - isolate passage history"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002088 obo:GENEPIO_0001763 """order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform"""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - antibiogram"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002089 obo:GENEPIO_0001763 """order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - virulence"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002090 obo:GENEPIO_0001763 """order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - sequencing quality control"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002091 obo:GENEPIO_0001763 """order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - submission to NCBI/DDBJ"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002092 obo:GENEPIO_0001763 """order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status"""@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 ""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft sequence repository data - submission to EBI"@en ; rdfs:seeAlso "https://www.ebi.ac.uk/ena/submit/pathogen-data"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002093 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "sequencing dna extraction method datum"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0002094 obo:IAO_0000115 "The tool or device used to extract a specimen."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen collection device"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:GENEPIO_0002095 obo:IAO_0000115 "The name and version of the software used to merge paired-end reads before assembly."@en ; a owl:Class ; rdfs:label "read paired-end merging software"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0002096 obo:GENEPIO_0000001 "Sequencing" ; obo:IAO_0000115 "The name and version of the software product used for removal of adapter sequences from demultiplexed data reads"@en ; obo:IAO_0000119 "GROUP: IRIDA Ontology (Emma)" ; oboInOwl:inSubset "GENEPIO" ; a owl:Class ; rdfs:label "read adapter trimming software"@en ; rdfs:subClassOf obo:GENEPIO_0001681 . obo:GENEPIO_0002097 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "Adapted from NIAID GSCID-BRC metadata working group"@en ; obo:IAO_0000600 "Note that this is expressed in a particular format in some standards."@en ; a owl:Class ; rdfs:label "specimen collection location - state/province/territory/region"@en ; rdfs:subClassOf obo:GENEPIO_0002162, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:GENEPIO_0001742 obo:NCIT_C25632 obo:NCIT_C87194 obo:NCIT_C89811 ) ] ] . obo:GENEPIO_0002098 obo:IAO_0000115 """A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a \"Naïve\", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question."""@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004432"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: wild type (WT)"@en ; owl:deprecated true . obo:GENEPIO_0002099 obo:IAO_0000115 "A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004433"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: non-wild type (NWT)"@en ; owl:deprecated true . obo:GENEPIO_0002100 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the maximum concentration of a drug applied during an an assay."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "test drug maximum concentration"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0002101 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is the minimum concentration of a drug applied during an an assay."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "test drug minimum concentration"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0002102 obo:IAO_0000115 "The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004430"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance tissue specificity"@en ; owl:deprecated true . obo:GENEPIO_0002103 obo:GENEPIO_0001763 "depth:1", """order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased"""@en ; a owl:Class ; rdfs:label "subject health status (NCIT)"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002104 obo:GENEPIO_0001763 """order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone""" ; a owl:Class ; rdfs:label "contact specification - professional role"@en ; rdfs:subClassOf obo:GENEPIO_0001755 . obo:GENEPIO_0002105 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An organization related to the collection, isolate production, sequencing or storage of specimen material or data."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen processing organization type"@en ; rdfs:subClassOf obo:OBI_0000245 . obo:GENEPIO_0002106 obo:GENEPIO_0001763 """order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food""" ; obo:IAO_0000115 "This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen."@en ; a owl:Class ; rdfs:label "draft sequence repository data - food specimen"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002107 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment."@en ; obo:IAO_0000116 "Chris has proposed this term for OBI as \"enrichment culture medium\""@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "isolation medium"@en ; rdfs:subClassOf obo:OBI_0000079 . obo:GENEPIO_0002108 obo:GENEPIO_0001763 """order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This record details a person's travel movement and duration for epidemiological analysis."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft travel log specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002109 obo:GENEPIO_0001763 """order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A standard for European Bioinformatics Institute (EBI) antibiogram data submission"@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft EBI antimicrobial susceptibility test V. 2017-08-30"@en ; rdfs:seeAlso "https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0002110 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A MIC test measurement resulting from a laboratory diffusion method."@en ; obo:IAO_0000116 "Damion Dooley's note: is this still useful? Currently \"MIC diffusion measurement specification' refers directly via 'is about' to \"Disk Diffusion Method\"."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "MIC diffusion measurement datum"@en ; rdfs:subClassOf obo:IAO_0000032, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C128985 ] . obo:GENEPIO_0002111 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "antimicrobial resistance testing reference standard version"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:GENEPIO_0002112 obo:IAO_0000115 "This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units."@en ; a owl:Class ; rdfs:label "draft sequence repository data - antibiogram MIC measurement"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002113 a owl:Class ; rdfs:label "time value specification"@en ; rdfs:subClassOf obo:OBI_0001931, [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:UO_0000003 ; owl:onProperty obo:IAO_0000039 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:dateTime ] . obo:GENEPIO_0002114 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The process of collecting a portion of feces from an organism."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; oboInOwl:hasExactSynonym "stool collection"@en ; a owl:Class ; rdfs:label "feces collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002115 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The process of collecting a portion of urine from an organism."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "sputum collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002116 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "rinsing for specimen collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002117 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The process of collecting specimen material using a swab collection device."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "swabbing for specimen collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002118 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "exudate collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002119 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The removal or collection of specimen material through the use of suction."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "vacuuming for specimen collection"@en ; rdfs:subClassOf obo:OBI_0600005 . obo:GENEPIO_0002120 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; obo:IAO_0000600 "NOTE: there are different types of tubes with coloured caps indicating different preservatives etc."@en ; a owl:Class ; rdfs:label "tube containing media or preservative"@en ; rdfs:subClassOf obo:NCIT_C41277 . obo:GENEPIO_0002121 obo:IAO_0000117 "Emma Griffiths"@en ; obo:IAO_0000600 "NOTE: there are different types of tubes with coloured caps indicating different preservatives etc."@en ; a owl:Class ; rdfs:label "tube containing antimicrobial"@en ; rdfs:subClassOf obo:NCIT_C41277 . obo:GENEPIO_0002122 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "Whirlpak sampling bag"@en ; rdfs:subClassOf obo:NCIT_C43167 . obo:GENEPIO_0002123 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "spoon"@en ; rdfs:subClassOf obo:NCIT_C43167 . obo:GENEPIO_0002124 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "fork"@en ; rdfs:subClassOf obo:NCIT_C43167 . obo:GENEPIO_0002125 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "hand scoop"@en ; rdfs:subClassOf obo:NCIT_C43167 . obo:GENEPIO_0002126 obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "trier"@en ; rdfs:subClassOf obo:NCIT_C43167 . obo:GENEPIO_0002127 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "vaccum device"@en ; rdfs:subClassOf obo:GENEPIO_0002094 . obo:GENEPIO_0002128 a owl:Class ; rdfs:label "investigation identifier specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001628 ] . obo:GENEPIO_0002129 obo:GENEPIO_0001763 """order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "draft Enterobase contextual data standard"@en ; rdfs:subClassOf obo:GENEPIO_0000106 . obo:GENEPIO_0002130 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "virulence factor name"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000547 ] . obo:GENEPIO_0002131 obo:GENEPIO_0001763 "help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models."@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The laboratory protocol used to determine virulence phenotypes and markers."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "virulence testing protocol name"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000547 ] . obo:GENEPIO_0002132 obo:GENEPIO_0001763 "help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs."@en ; obo:IAO_0000115 "The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "detection limit"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IDO_0000547 ] . obo:GENEPIO_0002133 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Disease_cluster"@en ; a owl:Class ; rdfs:label "disease cluster"@en ; rdfs:subClassOf obo:IAO_0000100 . obo:GENEPIO_0002134 obo:IAO_0000114 obo:IAO_0000122, obo:IAO_0000428 ; obo:IAO_0000115 "A disease cluster in which two or more cases have been linked by an infectious disease transmission process."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "infectious disease cluster"@en ; rdfs:subClassOf obo:GENEPIO_0002133 . obo:GENEPIO_0002135 obo:GENEPIO_0001763 "help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier"@en ; obo:IAO_0000115 "Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture)."@en ; oboInOwl:hasAlternativeId "ENA Webin:environmental_feature"@en ; a owl:Class ; rdfs:label "EBI ENA Webin environmental feature"@en ; rdfs:subClassOf obo:GENEPIO_0001790 . obo:GENEPIO_0002136 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ena"@en ; a owl:Class ; rdfs:label "EBI European Nucleotide Archive Webin"@en ; rdfs:seeAlso "https://www.ebi.ac.uk/ena/WebFeat/"@en ; rdfs:subClassOf obo:NCIT_C103180 . obo:GENEPIO_0002137 obo:GENEPIO_0001763 "help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X)."@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The breadth of coverage is the percentage of the genome that was sequenced to a prescribed depth of coverage."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "breadth of coverage"@en ; rdfs:subClassOf obo:GENEPIO_0001568 . obo:GENEPIO_0002138 obo:IAO_0000115 "The mean contig length is the count of base pairs in the average size contig of the sequence assembly."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "mean contig length"@en ; rdfs:subClassOf obo:GENEPIO_0001568, obo:IAO_0000032 . obo:GENEPIO_0002139 obo:GENEPIO_0001763 """order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software""" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads."@en ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:label "raw sequence data processing datum"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002140 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Name of strain from which sample was obtained OR name of isolate from which sample was obtained."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen strain or isolate identifier"@en ; rdfs:subClassOf obo:GENEPIO_0001342 . obo:GENEPIO_0002141 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format \"d[d.dddd] N|S d[dd.dddd] W|E\", eg, 38.98 N 77.11 W"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/"@en ; a owl:Class ; rdfs:label "latitude and longitude coordinate (NCBI BioSample format)"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "\\s*(\\d(.\\d{1,4})?|[1-8]\\d(.\\d{1,4})?|90(.0{1,4})?)\\s*[WEwe]\\s*(\\d(.\\d{1,4})?|[1-9]\\d(.\\d{1,4})?|1[0-7]\\d(.\\d{1,4})?|180(.0{1,4})?)\\s*[NSns]\\s*" ] ) ] ] . obo:GENEPIO_0002142 a owl:Class ; rdfs:label "decimal value specification"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:decimal ] . obo:GENEPIO_0002143 a owl:Class ; rdfs:label "floating point value specification"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:float ] . obo:GENEPIO_0002144 obo:GENEPIO_0000006 "unsigned integer"@en ; obo:IAO_0000115 "A 32 bit number having a range 0 - 4294967295."@en ; a owl:Class ; rdfs:label "unsigned integer value specification"@en ; rdfs:subClassOf obo:GENEPIO_0002166, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:unsignedInt ] . obo:GENEPIO_0002145 a owl:Class ; rdfs:label "date value specification"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:unionOf (obo:UO_0000033 obo:UO_0000034 obo:UO_0000035 obo:UO_0000036 ) ] ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:UO_0000003 ; owl:onProperty obo:IAO_0000039 ], [ a owl:Restriction ; owl:allValuesFrom xsd:dateTime ; owl:onProperty obo:OBI_0002135 ] . obo:GENEPIO_0002146 obo:IAO_0000115 "A specification for the size of an assembled genome as measured in base pairs."@en ; obo:IAO_0000116 "This is a decimal because the megabasepair unit may involve a fractional component."@en ; a owl:Class ; rdfs:label "assembly genome size specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001561 ], [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:unionOf (obo:UO_0000244 obo:UO_0000328 obo:UO_0000329 ) ] ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0002147 a owl:Class ; rdfs:label "sequencing facility name specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001891 ] . obo:GENEPIO_0002148 obo:GENEPIO_0000006 "date (ISO 8601)"@en ; obo:IAO_0000115 "A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime"@en ; a owl:Class ; rdfs:label "date value specification (ISO 8601)"@en ; rdfs:subClassOf obo:GENEPIO_0002145 . obo:GENEPIO_0002149 a owl:Class ; rdfs:label "strain identifier specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001429 ] . obo:GENEPIO_0002150 obo:IAO_0000115 "A MIC test measurement resulting from a laboratory diffusion method."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "MIC diffusion measurement specification"@en ; rdfs:subClassOf obo:OBI_0001931, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:ARO_3004391 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:ARO_3004371 ], [ a owl:Restriction ; owl:onClass obo:UO_0000016 ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:positiveInteger ; owl:withRestrictions ([ xsd:minExclusive "5"^^xsd:positiveInteger ] [ xsd:maxExclusive "100"^^xsd:positiveInteger ] ) ] ] . obo:GENEPIO_0002151 obo:GENEPIO_0000006 "unsigned short"@en ; obo:IAO_0000115 "A 16 bit integer ranging from 0 - 65535"@en ; a owl:Class ; rdfs:label "unsigned short integer value specification"@en ; rdfs:subClassOf obo:GENEPIO_0002144, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:unsignedShort ] . obo:GENEPIO_0002152 a owl:Class ; rdfs:label "genomic sequence length specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:unionOf (obo:UO_0000244 obo:UO_0000329 ) ] ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0002153 obo:IAO_0000115 "A MIC test measurement resulting from a laboratory dilution method."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "MIC dilution measurement specification"@en ; rdfs:subClassOf obo:OBI_0001931, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:ARO_3004397 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:ARO_3004371 ], [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:unionOf (obo:UO_0000273 obo:UO_0000274 ) ] ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ([ xsd:minInclusive "0.01"^^xsd:float ] [ xsd:maxInclusive "2048.0"^^xsd:float ] ) ] ; owl:onProperty obo:OBI_0002135 ] . obo:GENEPIO_0002154 a owl:Class ; rdfs:comment "The date on which a specimen was collected, in ISO 8601 format."@en ; rdfs:label "specimen collection date (ISO 8601)"@en ; rdfs:subClassOf obo:GENEPIO_0002148, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001619 ] . obo:GENEPIO_0002155 a owl:Class ; rdfs:label "date of diagnosis (ISO 8601)"@en ; rdfs:subClassOf obo:GENEPIO_0002148, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom ] . obo:GENEPIO_0002156 obo:IAO_0000115 "A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject age specification"@en ; rdfs:subClassOf obo:GENEPIO_0002176, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0002077 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001169 ], [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:unionOf (obo:UO_0000033 obo:UO_0000034 obo:UO_0000035 obo:UO_0000036 ) ] ; owl:onProperty obo:IAO_0000039 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:decimal ; owl:withRestrictions ([ xsd:minInclusive 0 ] ) ] ] . obo:GENEPIO_0002157 a owl:Class ; rdfs:label "subject age at time of specimen collection specification"@en ; rdfs:subClassOf obo:GENEPIO_0002156, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001775 ] . obo:GENEPIO_0002158 obo:GENEPIO_0000006 "boolean"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A boolean value specification indicates a presence (true value) or absence (false value) of a given feature." ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "boolean value specification"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:STATO_0000090 ], [ a owl:Restriction ; owl:onDataRange xsd:boolean ; owl:onProperty obo:OBI_0002135 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0002159 a owl:Class ; rdfs:label "specimen identifier specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001616 ] . obo:GENEPIO_0002160 a owl:Class ; rdfs:label "email address specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C42775 ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "[A-Za-z0-9]+([_.\\-][A-Za-z0-9]+)*\\@[A-Za-z0-9]+([.\\-][A-Za-z0-9]+){1,3}" ] ) ] ; owl:onProperty obo:OBI_0002135 ] . obo:GENEPIO_0002161 a owl:Class ; rdfs:label "region, province, state or territory specification"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:GENEPIO_0001742 obo:NCIT_C25632 obo:NCIT_C87194 obo:NCIT_C89811 ) ] ] . obo:GENEPIO_0002162 obo:IAO_0000115 "A specification for a geographic location that a specimen was collected at."@en ; a owl:Class ; rdfs:label "specimen collection site specification"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom ] . obo:GENEPIO_0002163 a owl:Class ; rdfs:label "subject organism common name specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001724 ] . obo:GENEPIO_0002164 obo:IAO_0000115 "A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "subject identifier specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001616 ] . obo:GENEPIO_0002165 obo:IAO_0000115 "Name of disease in a subject that is related to a given investigation, study and/or specimen."@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NIAID GSCID-BRC metadata working group"@en ; a owl:Class ; rdfs:comment """Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067"""@en ; rdfs:label "subject disease specification"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001617 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:DOID_4 ] . obo:GENEPIO_0002166 obo:GENEPIO_0000006 "unsigned long integer"@en ; obo:IAO_0000115 "A 64 bit integer ranging from 0 - 18446744073709551615"@en ; a owl:Class ; rdfs:label "unsigned long integer value specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom xsd:unsignedLong ] . obo:GENEPIO_0002167 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen collection site"@en ; rdfs:seeAlso obo:NCIT_C87913 ; rdfs:subClassOf obo:GENEPIO_0001886, [ a owl:Class ; owl:unionOf (obo:ENVO_00000005 obo:NCIT_C25464 obo:NCIT_C80234 ) ] . obo:GENEPIO_0002168 obo:IAO_0000115 "The unit provided for an antibiotic drug test dosage."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "drug MIC unit specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:ARO_3004372 ] . obo:GENEPIO_0002169 obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000598 "A datum specification for the maximum concentration of a drug applied during an an assay."@en ; a owl:Class ; rdfs:label "test drug maximum concentration specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onProperty obo:IAO_0000039 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:UO_0000016 obo:UO_0000274 ) ] ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0002100 ] . obo:GENEPIO_0002170 obo:IAO_0000115 "This is the minimum concentration of a drug applied during an an assay."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "test drug minimum concentration specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onProperty obo:IAO_0000039 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:UO_0000016 obo:UO_0000274 ) ] ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0002101 ] . obo:GENEPIO_0002171 a owl:Class ; rdfs:label "listeria antigen specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001689 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "(1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)" ] ) ] ] . obo:GENEPIO_0002172 a owl:Class ; rdfs:label "URL specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom ], [ a owl:Restriction ; owl:onDataRange [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "url" ] ) ] ; owl:onProperty obo:OBI_0002135 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0002173 obo:IAO_0000115 "A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip."@en ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "travel destination specification"@en ; rdfs:subClassOf obo:OBI_0001930, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0001783 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:NCIT_C25464 obo:NCIT_C80234 ) ] ] . obo:GENEPIO_0002174 obo:IAO_0000115 "A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:label "specimen source substance specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GENEPIO_0000134 ] . obo:GENEPIO_0002175 obo:IAO_0000116 "Damion Dooley note: OBI has a variety of subclasses like \"blood specimen\" and \"colon specimen\" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic \"derives from some [uberon term]\". GenEpiO takes a different approach in describing this class with lists for \"subject anatomical site\", \"subject body product\", and \"plant anatomy\"."@en ; a owl:Class ; rdfs:label "specimen from organism specification"@en ; rdfs:subClassOf obo:GENEPIO_0001342, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0001479 ] . obo:GENEPIO_0002176 a owl:Class ; rdfs:label "duration specification"@en ; rdfs:subClassOf obo:GENEPIO_0002142, [ a owl:Restriction ; owl:onClass obo:UO_0000003 ; owl:onProperty obo:IAO_0000039 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:decimal ; owl:withRestrictions ([ xsd:minInclusive 0 ] ) ] ] . obo:GENEPIO_0002177 a owl:NamedIndividual ; rdfs:label "_test_individual"@en . obo:GENEPIO_0002178 obo:IAO_0000115 "A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference)."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; obo:IAO_0100001 linkml:SlotDefinition ; dc:date "2019-04-17T23:04:53Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "obsolete: field specification"@en ; rdfs:subClassOf obo:OBI_0000658 ; owl:deprecated true . obo:GENEPIO_0002179 obo:IAO_0000115 "LabID assigned by NLEP"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:31:44Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:LabID"@en . obo:GENEPIO_0002180 obo:IAO_0000115 "Country where isolate was collected"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:32:45Z"^^xsd:dateTime ; a owl:NamedIndividual ; rdfs:label "SourceCountry"@en . obo:GENEPIO_0002181 obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0100001 "http://purl.obolibrary.org/obo/ARO_3004431"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: antimicrobial resistance phenotype - epidemiological cut-off values"@en ; owl:deprecated true . obo:GENEPIO_0002182 obo:IAO_0000115 "Country where isolate was collected"@en ; obo:IAO_0000116 "Currently not used for PulseNet Canada"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:37:19Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SourceCountry"@en . obo:GENEPIO_0002183 obo:IAO_0000115 "(Province for PNC) where isolate was collected."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:38:09Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SourceState"@en . obo:GENEPIO_0002184 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:40:57Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SourceCity"@en . obo:GENEPIO_0002185 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:41:35Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "PulseNet Canada field"@en ; rdfs:subClassOf linkml:SlotDefinition . obo:GENEPIO_0002186 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:41:56Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "PulseNet Canada Salmonella field"@en ; rdfs:subClassOf obo:GENEPIO_0002185 . obo:GENEPIO_0002187 obo:IAO_0000115 "Site of the source type where isolate was collected, e.g. blood, CSF, etc."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:47:10Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SourceSite"@en . obo:GENEPIO_0002188 obo:IAO_0000115 "The source type of the isolate, e.g. human, environmental, etc."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:48:49Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SourceType"@en . obo:GENEPIO_0002189 obo:IAO_0000115 "Other countries where the patient traveled"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:49:47Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:Traveled_To"@en . obo:GENEPIO_0002190 obo:IAO_0000115 "Further description of the source type, e.g. bovine, chicken"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:51:02Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:TypeDetails"@en . obo:GENEPIO_0002191 obo:IAO_0000115 "Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:52:01Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:SubmittedNumber"@en . obo:GENEPIO_0002192 obo:IAO_0000115 "(Province for PNC) additional number used to identify the isolate"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:53:47Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:OtherStateIsolate"@en . obo:GENEPIO_0002193 obo:IAO_0000115 "Age of patient when isolate was collected"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:54:24Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:PatientAge"@en . obo:GENEPIO_0002194 obo:IAO_0000115 "Sex of patient when isolate was collected"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:55:04Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:PatientSex"@en . obo:GENEPIO_0002195 obo:IAO_0000115 "Date of collection"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T23:56:33Z"^^xsd:dateTime ; a obo:GENEPIO_0002148, obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:IsolatDate"@en . obo:GENEPIO_0002196 obo:IAO_0000115 "Date the isolate is uploaded to the national database after initial upload"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:21:46Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:UploadModifiedDate"@en . obo:GENEPIO_0002197 obo:IAO_0000115 "Antigenic Formula"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:23:18Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:AntigenForm"@en . obo:GENEPIO_0002198 obo:IAO_0000115 "Subspecies, I - VI (roman numerals)"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:24:11Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:Subspecies"@en . obo:GENEPIO_0002199 obo:IAO_0000115 "O polysaccharide (LPS) Group"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:24:53Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:OGroup"@en . obo:GENEPIO_0002200 obo:IAO_0000115 "Serotype of isolate"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:25:22Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:Serotype"@en . obo:GENEPIO_0002201 obo:IAO_0000115 "Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#)"@en ; obo:IAO_0000116 "Currently not used for PulseNet Canada"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:27:08Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:Outbreak"@en . obo:GENEPIO_0002202 obo:IAO_0000115 "Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP)"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:28:01Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:cdc_id"@en . obo:GENEPIO_0002203 obo:IAO_0000115 "Enzyme name present if part of that national list."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:28:35Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:ListMember"@en . obo:GENEPIO_0002204 obo:IAO_0000115 "Phage type"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:29:20Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:Phagetype"@en . obo:GENEPIO_0002205 obo:IAO_0000115 "Provides LabID, gel and lane information"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:29:58Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:TEMP"@en . obo:GENEPIO_0002206 obo:IAO_0000115 "Status of the isolate; this is only confirmed once CDC runs it."@en ; obo:IAO_0000116 "Currently not used for PulseNet Canada"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:30:44Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:Status"@en . obo:GENEPIO_0002207 obo:IAO_0000116 "Currently not used for PulseNet Canada"@en, "checked if the isolate is part of NARMS."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:35:55Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:NARMS-EB"@en . obo:GENEPIO_0002208 obo:IAO_0000115 "Checked if the isolate is part of FoodNet."@en ; obo:IAO_0000116 "Currently not used for PulseNet Canada"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:36:39Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:FoodNet"@en . obo:GENEPIO_0002209 obo:IAO_0000115 "XbaI gel where the isolate is located, lane of gel"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:38:57Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-XbaI-file"@en . obo:GENEPIO_0002210 obo:IAO_0000115 "XbaI pattern assigned by CDC (format XXXXXX.####)"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:39:23Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-XbaI-pattern"@en . obo:GENEPIO_0002211 obo:IAO_0000115 "The date the XbaI gel is run"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:40:05Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-XbaI-rundate"@en . obo:GENEPIO_0002212 obo:IAO_0000115 "Once the XbaI pattern is named, the status is confirmed by CDC"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:41:39Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-XbaI-status"@en . obo:GENEPIO_0002213 obo:IAO_0000115 "BlnI gel where the isolate is located, lane of gel"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:42:11Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-BlnI-file"@en . obo:GENEPIO_0002214 obo:IAO_0000115 "BlnI pattern assigned by CDC (format XXXXXX.####)."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:42:42Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-BlnI-pattern"@en . obo:GENEPIO_0002215 obo:IAO_0000115 "The date the BlnI gel is run"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:43:50Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-BlnI-rundate"@en . obo:GENEPIO_0002216 obo:IAO_0000115 "Once the BlnI pattern is named, the status is confirmed by CDC"@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:44:44Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-BlnI-status"@en . obo:GENEPIO_0002217 obo:IAO_0000115 "SpeI gel where the isolate is located, lane of gel."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:45:15Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-SpeI-file"@en . obo:GENEPIO_0002218 obo:IAO_0000115 "SpeI pattern assigned by CDC (format XXXXXX.####)."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:45:41Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-SpeI-pattern"@en . obo:GENEPIO_0002219 obo:IAO_0000115 "The date the SpeI gel is run."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:46:21Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-SpeI-rundate"@en . obo:GENEPIO_0002220 obo:IAO_0000115 "Once the SpeI pattern is named, the status is confirmed by CDC."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:47:00Z"^^xsd:dateTime ; a obo:GENEPIO_0002186, owl:NamedIndividual ; rdfs:label "PulseNet:PFGE-SpeI-status"@en . obo:GENEPIO_0002221 obo:IAO_0000115 "Date WHICH (PH?) lab received isolate."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-18T00:57:28Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:ReceivedDate"@en . obo:GENEPIO_0002222 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-05-03T02:44:38Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "specimen collection service"@en ; rdfs:subClassOf obo:GENEPIO_0002225 . obo:GENEPIO_0002223 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-05-03T02:49:24Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "bioinformatics analysis service"@en ; rdfs:subClassOf obo:GENEPIO_0002225 . obo:GENEPIO_0002224 obo:IAO_0000115 "An isolate preparation service prepares isolates for molecular sequencing."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-05-03T02:51:51Z"^^xsd:dateTime ; a owl:Class ; rdfs:label obo:IAO_0000428, "isolate preparation service"@en ; rdfs:subClassOf obo:GENEPIO_0002225 . obo:GENEPIO_0002225 obo:GENEPIO_0001763 """order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service"""@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-05-03T02:52:19Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "specimen related service"@en ; rdfs:subClassOf obo:OBI_0001173 . obo:GENEPIO_0002226 obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-05-03T03:24:33Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "specimen repository/biobank service"@en ; rdfs:subClassOf obo:GENEPIO_0002225 . obo:GENEPIO_0002227 obo:IAO_0000117 ; dc:date "2019-11-17T00:54:44Z"^^xsd:dateTime ; a obo:GENEPIO_0002034, owl:NamedIndividual ; rdfs:label "ISO_23418.organization_contact.service"@en . obo:GENEPIO_0002228 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable."@en ; obo:IAO_0000117 ; dc:date "2019-11-19T22:17:43Z"^^xsd:dateTime ; oboInOwl:hasSynonym "grave"@en ; a owl:Class ; rdfs:label "critical health status"@en ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0002024, obo:GENEPIO_0002025, [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0001846 ] . obo:GENEPIO_0002229 obo:IAO_0000115 "Date the isolate uploaded to the national database."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-04-17T22:47:51Z"^^xsd:dateTime ; a obo:GENEPIO_0002185, owl:NamedIndividual ; rdfs:label "PulseNet:UploadDate"@en . obo:GENEPIO_0002230 obo:IAO_0000115 "A datum indicating one of six defined subspecies of Salmonella."@en ; obo:IAO_0000117 ; obo:IAO_0000119 ; dc:date "2019-11-25T08:45:41Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "Salmonella subspecies"@en ; rdfs:seeAlso ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:GENEPIO_0002231 obo:IAO_0000115 "A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme."@en ; obo:IAO_0000117 ; dc:date "2019-11-25T09:07:26Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "PFGE Spel pattern"@en ; rdfs:subClassOf obo:GENEPIO_0001289 . obo:GENEPIO_0002232 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A collection of organisms that is indicative of faecal contamination."""@en ; obo:IAO_0000117 ; obo:IAO_0000119 ; dc:date "2020-02-08T20:15:43Z"^^xsd:dateTime ; a owl:Class ; rdfs:comment "Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present"@en ; rdfs:label "fecal indicator"@en ; rdfs:subClassOf obo:PCO_0000000 . obo:GENEPIO_0002233 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An isolate derived from a food sample."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-06-28T23:41:26Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "food isolate"@en ; rdfs:subClassOf obo:NCIT_C53471 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:FOODON_00002403 obo:NCIT_C53471 ) ] . obo:GENEPIO_0002234 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes."@en ; obo:IAO_0000117 ; dc:date "2020-04-24T19:06:05Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "microbial 16S RNA typing"@en ; rdfs:subClassOf obo:GENEPIO_0001420 . obo:GENEPIO_0002236 obo:IAO_0000117 ; dc:date "2021-04-24T18:32:24Z"^^xsd:dateTime ; a owl:NamedIndividual, linkml:Example ; rdfs:label "CanCOGeN:specimen collector sample ID example" ; linkml:value "prov_rona_99" . obo:GENEPIO_0002464 a owl:Class ; rdfs:label "E. coli H antigen specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001077 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56)" ] ) ] ] . obo:GENEPIO_0002465 a owl:Class ; rdfs:label "E. coli O antigen specification"@en ; rdfs:subClassOf obo:GENEPIO_0002468, [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:GENEPIO_0001076 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0002135 ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "O([1-9][0-9][0-9])" ] ) ] ] . obo:GENEPIO_0002468 obo:GENEPIO_0000006 "string"@en ; a owl:Class ; rdfs:label "string value specification"@en ; rdfs:subClassOf obo:OBI_0001933, [ a owl:Restriction ; owl:onDataRange xsd:string ; owl:onProperty obo:OBI_0002135 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GENEPIO_0002469 a owl:ObjectProperty ; rdfs:label "obsolete: has string value specification"@en ; rdfs:range obo:GENEPIO_0002468 ; rdfs:subPropertyOf obo:OBI_0001938 ; owl:deprecated true . obo:GENEPIO_0002470 a owl:ObjectProperty ; rdfs:label "obsolete: has categorical specification of"@en ; owl:deprecated true . obo:GENEPIO_0002471 a owl:ObjectProperty ; rdfs:label "obsolete: has categorical value specification"@en ; rdfs:range obo:OBI_0001930 ; rdfs:subPropertyOf obo:OBI_0001938 ; owl:deprecated true . obo:GENEPIO_0002682 obo:IAO_0000115 "A sequencing platform brand provided by Helicos corporation (now defunct)."@en ; obo:IAO_0000117 ; dc:date "2020-04-24T22:50:49Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "Helicos platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0002683 obo:IAO_0000115 "A sequencing platform provided by the Ion Torrent company."@en ; obo:IAO_0000117 ; dc:date "2020-04-24T22:54:06Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "Ion Torrent platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0002684 obo:IAO_0000115 "A sequencing platform provided by Life Technologies Corporation"@en ; obo:IAO_0000117 ; obo:IAO_0000118 "Sequencing by Oligonucleotide Ligation and Detection"@en ; dc:date "2020-04-24T22:55:31Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "SOLiD sequening platform"@en ; rdfs:subClassOf obo:GENEPIO_0000071 . obo:GENEPIO_0002713 obo:IAO_0100001 obo:OBI_0002822 ; a owl:Class ; rdfs:label "obsolete: drag swab"@en ; owl:deprecated true . obo:GENEPIO_0002749 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-06-28T20:07:25Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "rinse"@en ; rdfs:subClassOf obo:OBI_0100051 ; owl:equivalentClass [ a owl:Restriction ; owl:onProperty obo:RO_0002353 ; owl:someValuesFrom obo:GENEPIO_0002116 ] . obo:GENEPIO_0002750 obo:IAO_0000115 "Animal rinse is a rinse derived from animal material of one or more animals."@en ; obo:IAO_0000117 "Damion Dooley"^^xsd:string ; dc:date "2019-06-28T20:11:45Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "animal rinse"@en ; rdfs:subClassOf obo:GENEPIO_0002749 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0001636 obo:GENEPIO_0002749 ) ] . obo:GENEPIO_0003358 obo:IAO_0100001 obo:OBI_0002824 ; a owl:Class ; rdfs:label "obsolete: surface wipe"@en ; owl:deprecated true . obo:GENEPIO_0100300 rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0100301 rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0100302 rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_0100303 rdfs:subClassOf obo:IAO_0000027 . obo:GENEPIO_1919 obo:GENEPIO_0000006 "UI regex validate"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:label "user interface regular expression validate"@en . obo:GENEPIO_1921 obo:GENEPIO_0000006 "UI regex format"@en ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:label "user interface regular expression display format"@en . obo:GEO_000000788 rdfs:subClassOf obo:GENEPIO_0001866, obo:GENEPIO_0001867, [ a owl:Restriction ; owl:onProperty obo:RO_0002001 ; owl:someValuesFrom obo:GENEPIO_0001338 ], [ a owl:Restriction ; owl:onClass obo:GENEPIO_0001907 ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:GO_0000003 a owl:Class . obo:GO_0008150 a owl:Class ; rdfs:subClassOf obo:BFO_0000015 . obo:HP_0000118 obo:GENEPIO_0000006 "symptom"@en ; oboInOwl:hasDbXref "http://purl.obolibrary.org/obo/SYMP_0000462" ; rdfs:subClassOf obo:BFO_0000019 . obo:HP_0012830 obo:GENEPIO_0000006 "position of phenotype abnormality"@en ; a owl:Class ; rdfs:subClassOf obo:BFO_0000019 . obo:HP_0031292 a owl:Class ; rdfs:subClassOf obo:ARO_3004430 . obo:IAO_0000030 rdfs:subClassOf obo:BFO_0000031 . obo:IAO_0000032 rdfs:subClassOf obo:IAO_0000109 . obo:IAO_0000039 obo:GENEPIO_0000006 "has unit"@en ; a owl:ObjectProperty ; owl:inverseOf . obo:IAO_0000109 oboInOwl:hasDbXref "http://www.ebi.ac.uk/efo/EFO_0001444"^^xsd:anyURI . obo:IAO_0000136 a owl:ObjectProperty ; rdfs:domain obo:IAO_0000030 ; rdfs:label "is about"@en . obo:IAO_0000416 rdfs:comment "Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards"@en . obo:IAO_0000577 rdfs:comment """Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of \"postal code\" one can place particular national postal code systems like the US Postal code."""@en . obo:ICO_0000288 obo:IAO_0000117 ; dc:date "2020-04-24T22:38:17Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "pregnant woman"@en ; rdfs:subClassOf obo:GENEPIO_0001206 . obo:IDO_0000495 a owl:Class ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:OGMS_0000063 [ a owl:Restriction ; owl:onProperty obo:BFO_0000054 ; owl:someValuesFrom obo:OBI_1110040 ] [ a owl:Restriction ; owl:onProperty obo:RO_0000057 ; owl:someValuesFrom obo:IDO_0000531 ] ) ] . obo:IDO_0000531 a owl:Class ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0100026 [ a owl:Restriction ; owl:onProperty obo:RO_0001015 ; owl:someValuesFrom obo:OBI_0000925 ] ) ] . obo:IDO_0000547 a owl:Class . obo:IDO_0000569 a owl:Class . obo:IDO_0000581 a owl:Class . obo:IDO_0000629 a owl:Class ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GENEPIO_0001171 [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:IDO_0000531 ] ) ] . obo:IDO_0000659 a owl:Class . obo:IDO_0100629 rdfs:subClassOf obo:PCO_0000000 . obo:MI_0489 obo:GENEPIO_0000005 "http://www.ontobee.org/ontology/MI" ; obo:GENEPIO_0000006 "data source"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Database that originally provided the interaction record for exchange purposes."@en ; oboInOwl:hasDbXref "PMID:14755292" ; a owl:Class ; rdfs:comment """Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields."""@en ; rdfs:label "source database"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:MMO_0000344 obo:GENEPIO_0000006 "tissue collection (necropsy)"@en ; obo:IAO_0000115 "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed]"@en ; a owl:Class ; rdfs:label "necropsy"@en ; rdfs:subClassOf obo:OBI_0600005 . rdfs:subClassOf obo:IAO_0000027 . obo:NCBITaxon_1 rdfs:subClassOf obo:OBI_0100026 . obo:NCBITaxon_2157 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The Archaea constitute a domain and kingdom of single-celled microorganisms"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Archaea"^^xsd:anyURI . obo:NCBITaxon_6447 obo:IAO_0000118 "clam, squid, octopus"@en . obo:NCBITaxon_7742 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0000086 ; owl:someValuesFrom obo:PATO_0001894 ] . obo:NCBITaxon_genus a owl:Class ; rdfs:subClassOf . obo:NCBITaxon_species a owl:Class ; rdfs:subClassOf . obo:NCBITaxon_subspecies a owl:Class ; rdfs:label "subspecies"@en ; rdfs:subClassOf . obo:NCIT_C100128 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C103180 obo:IAO_0000114 obo:IAO_0000122 ; a owl:Class ; rdfs:subClassOf obo:OBI_0000658 . obo:NCIT_C103245 a owl:Class ; rdfs:subClassOf obo:NCIT_C41275 . obo:NCIT_C105370 obo:IAO_0000116 "Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity"@en ; a owl:Class ; rdfs:subClassOf obo:CHEBI_33697 . obo:NCIT_C106561 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:NCIT_C113419 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C114551 a owl:Class ; rdfs:subClassOf obo:BFO_0000023 . obo:NCIT_C115935 obo:GENEPIO_0000006 "healthy"@en ; a owl:Class ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0000026, obo:GENEPIO_0000110, obo:GENEPIO_0001212, obo:GENEPIO_0002103, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001840 ] . obo:NCIT_C1225 a owl:Class ; rdfs:subClassOf obo:OMIT_0021725 . obo:NCIT_C124295 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001170, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:ICO_0000288 ] . obo:NCIT_C12471 a owl:Class ; rdfs:subClassOf obo:ARO_3004430 . obo:NCIT_C126054 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002103 . obo:NCIT_C127784 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C128985 obo:IAO_0000116 """NCIT offers this alternate definition which GenEpiO intends: \"A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited.\""""@en ; oboInOwl:hasAlternativeId "MIC" ; a owl:Class ; rdfs:seeAlso "Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user"@en ; rdfs:subClassOf obo:OBI_0000070 . obo:NCIT_C13235 a owl:Class ; rdfs:subClassOf obo:NCIT_C49641 . obo:NCIT_C13308 a owl:Class ; rdfs:subClassOf obo:UBERON_0006925 . obo:NCIT_C13347 a owl:Class ; rdfs:subClassOf obo:UBERON_0006314 . obo:NCIT_C14419 a owl:Class ; rdfs:subClassOf obo:BFO_0000027 . obo:NCIT_C15189 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:NCIT_C15327 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:NCIT_C15346 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001186 . obo:NCIT_C15631 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:NCIT_C16143 a owl:Class ; rdfs:subClassOf obo:OBI_0000245 . obo:NCIT_C16731 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001206 . obo:NCIT_C16960 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C17445 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C17471 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C17627 obo:GENEPIO_0000162 "A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Emma Griffiths"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002094 . obo:NCIT_C17734 a owl:Class ; rdfs:subClassOf obo:PCO_0000001 . obo:NCIT_C20108 a owl:Class ; rdfs:subClassOf obo:NCIT_C103180 . obo:NCIT_C20587 a owl:Class ; rdfs:subClassOf obo:PCO_0000001 . obo:NCIT_C25155 a owl:Class ; rdfs:subClassOf obo:GO_0000003 . obo:NCIT_C25189 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001206 . obo:NCIT_C25190 a owl:Class ; rdfs:subClassOf obo:OBI_0100026 . obo:NCIT_C25191 a owl:Class ; rdfs:subClassOf obo:NCIT_C42614 . obo:NCIT_C25251 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001543, obo:GENEPIO_0001645 . obo:NCIT_C25392 rdfs:subClassOf obo:OBI_0000245 . obo:NCIT_C25464 rdfs:seeAlso "http://purl.obolibrary.org/obo/GEO_000000396"^^xsd:anyURI ; rdfs:subClassOf . obo:NCIT_C25610 obo:GENEPIO_0000006 "diseased"@en ; oboInOwl:hasExactSynonym "sick"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0000026, obo:GENEPIO_0000110, obo:GENEPIO_0002103 . obo:NCIT_C25621 rdfs:subClassOf obo:IAO_0000577 . obo:NCIT_C25632 obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:subClassOf obo:ENVO_00000005 ; owl:disjointWith obo:NCIT_C87194, obo:NCIT_C89811 . obo:NCIT_C25667 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001543, obo:GENEPIO_0001645 . obo:NCIT_C25690 a owl:Class ; rdfs:subClassOf . obo:NCIT_C25717 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:NCIT_C25720 obo:GENEPIO_1919 "/^(:\\d{5}(-\\d{4})?)/, $zip" ; rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ([ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:BFO_0000029 [ a owl:Restriction ; owl:onProperty obo:RO_0001025 ; owl:someValuesFrom obo:GAZ_00002459 ] ) ] ] [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C25621 ] ) ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ([ xsd:pattern "[A-Za-z0-9]+([_.\\-][A-Za-z0-9]+)*\\@[A-Za-z0-9]+([.\\-][A-Za-z0-9]+){1,3}" ] ) ] ; owl:onProperty obo:OBI_0002135 ] . obo:NCIT_C25741 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001251, obo:NCIT_C53287 . obo:NCIT_C28147 a owl:Class ; rdfs:subClassOf obo:NCIT_C49641 . obo:NCIT_C28221 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:NCIT_C28554 obo:GENEPIO_0000006 "deceased"@en ; a owl:Class ; rdfs:subClassOf obo:ExO_0000038, obo:GENEPIO_0000026, obo:GENEPIO_0000110, obo:GENEPIO_0001212, obo:GENEPIO_0002024, obo:GENEPIO_0002025, obo:GENEPIO_0002103, , [ a owl:Restriction ; owl:onProperty obo:RO_0002083 ; owl:someValuesFrom obo:GENEPIO_0002228 ] ; owl:disjointWith obo:NCIT_C37987 . obo:NCIT_C37984 a owl:Class ; rdfs:subClassOf obo:ENVO_00000073 . obo:NCIT_C37987 a owl:Class ; rdfs:subClassOf . obo:NCIT_C3833 rdfs:subClassOf obo:BFO_0000019 . obo:NCIT_C40978 obo:GENEPIO_0000006 "phone"@en ; rdfs:subClassOf obo:IAO_0000577 . obo:NCIT_C41085 a owl:Class ; rdfs:subClassOf obo:NCIT_C60776 . obo:NCIT_C41256 rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C41275 a owl:Class ; rdfs:subClassOf obo:NCIT_C43186 . obo:NCIT_C41277 obo:GENEPIO_0000162 "A hollow cylinder, especially one for holding or conveying liquids."@en ; obo:IAO_0000117 "Damion Dooley"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002094 . obo:NCIT_C42614 a owl:Class ; rdfs:subClassOf obo:IAO_0000300 . obo:NCIT_C42709 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001251, obo:NCIT_C25190 . obo:NCIT_C42775 obo:IAO_0000116 "Damion Dooley's note: It can also be used as an authorization token in some identification processes."@en ; oboInOwl:hasExactSynonym obo:IAO_0000429 . obo:NCIT_C42856 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002094 . obo:NCIT_C43167 a owl:Class ; rdfs:subClassOf obo:NCIT_C43186 . obo:NCIT_C43169 a owl:Class ; rdfs:subClassOf obo:NCIT_C43186 . obo:NCIT_C43186 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002094 . obo:NCIT_C43209 a owl:Class ; rdfs:subClassOf obo:NCIT_C41275 . obo:NCIT_C43214 a owl:Class ; rdfs:subClassOf obo:NCIT_C41275 . obo:NCIT_C45908 a owl:Class ; rdfs:subClassOf obo:PATO_0001894 . obo:NCIT_C45910 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000116 "Damion Dooley's note: here \"sample\" means more than one specimen merged together."@en ; oboInOwl:hasExactSynonym "pooled"@en ; a owl:Class ; rdfs:subClassOf obo:PATO_0000047 . obo:NCIT_C48443 rdfs:subClassOf . obo:NCIT_C48519 a owl:Class ; rdfs:subClassOf obo:UO_0000006 . obo:NCIT_C48531 a owl:Class ; rdfs:subClassOf obo:UO_0000006 . obo:NCIT_C49641 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001432 . obo:NCIT_C52009 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:NCIT_C53287 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:NCIT_C53471 a owl:Class ; rdfs:subClassOf obo:OBI_0100051 . obo:NCIT_C54014 a owl:Class ; rdfs:subClassOf obo:PATO_0000383 . obo:NCIT_C60776 a owl:Class ; rdfs:subClassOf obo:IAO_0000027 . obo:NCIT_C62649 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001251, obo:NCIT_C100128 . obo:NCIT_C63362 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002127 . obo:NCIT_C68615 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001126, obo:GENEPIO_0001224, [ a owl:Restriction ; owl:onProperty obo:GENEPIO_0001739 ; owl:someValuesFrom obo:GENEPIO_0001225 ] . obo:NCIT_C70810 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001126 . obo:NCIT_C71164 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001247 . obo:NCIT_C71898 obo:GENEPIO_0000006 "brand name"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:NCIT_C74723 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001626 . obo:NCIT_C77683 a owl:Class ; rdfs:subClassOf obo:BFO_0000029 . obo:NCIT_C79916 obo:IAO_0000115 "An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI]"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NCIT Thesaurus"@en ; a owl:Class ; rdfs:label "investigative subject"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:NCIT_C80234 obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; rdfs:seeAlso "http://semanticscience.org/resource/SIO_000665"@en ; rdfs:subClassOf obo:ENVO_00000062, . obo:NCIT_C82508 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002103 . obo:NCIT_C85540 obo:GENEPIO_0000006 "antimicrobial resistance testing method"@en ; rdfs:subClassOf obo:OBI_0000011 . obo:NCIT_C85555 a owl:Class ; rdfs:subClassOf obo:NCIT_C85540 . obo:NCIT_C85596 obo:GENEPIO_0000006 "E-test (Epsilometry)"@en ; a owl:Class ; rdfs:subClassOf obo:NCIT_C85540 . obo:NCIT_C85697 a owl:Class ; rdfs:subClassOf obo:ARO_3004397 . obo:NCIT_C87194 obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; obo:IAO_0000114 obo:IAO_0000428 ; rdfs:subClassOf obo:ENVO_00000005 ; owl:disjointWith obo:NCIT_C89811 . obo:NCIT_C87500 a owl:Class ; rdfs:subClassOf obo:NCBITaxon_43738 . obo:NCIT_C87913 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0002167 . obo:NCIT_C89084 a owl:Class ; rdfs:subClassOf obo:IAO_0000027 . obo:NCIT_C89811 obo:GENEPIO_0001763 "lookup:http://purl.obolibrary.org/obo/GAZ_00000448" ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:subClassOf obo:ENVO_00000005 . obo:NCIT_C93044 a owl:Class ; rdfs:subClassOf obo:OBI_0100026 . obo:NCIT_C93582 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000119 "http://purl.obolibrary.org/obo/ncit.owl"^^xsd:anyURI ; a owl:Class ; rdfs:subClassOf obo:NCIT_C42614 . obo:NCIT_C93874 obo:GENEPIO_0000006 "organization name"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "NCI Thesaurus"@en ; a owl:Class ; rdfs:subClassOf obo:NCIT_C42614 . obo:NCIT_C98904 a owl:Class ; rdfs:subClassOf obo:DOID_7 . obo:NCRO_0000230 a owl:Class ; rdfs:label "antibiotic treatment"@en ; rdfs:subClassOf obo:GENEPIO_0001186 . obo:OAE_0002678 obo:GENEPIO_0000006 "fetal death (miscarriage/still birth)"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001667 . obo:OBI_0000093 a owl:Class . obo:OBI_0000181 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002001 ; owl:someValuesFrom obo:GENEPIO_0001886 ] . obo:OBI_0000245 a owl:Class . obo:OBI_0000626 rdfs:subClassOf obo:ERO_0001286 . obo:OBI_0000689 oboInOwl:hasDbXref "NCBI SRA: 454 GS 20" ; rdfs:subClassOf obo:GENEPIO_0001937 . obo:OBI_0000696 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD System" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0000697 oboInOwl:hasDbXref "NCBI SRA: HELICOS" . obo:OBI_0000702 oboInOwl:hasDbXref "NCBI SRA: 454 GS FLX" ; rdfs:subClassOf obo:GENEPIO_0001937 . obo:OBI_0000703 oboInOwl:hasDbXref "NCBI SRA: Illumina Genome Analyzer II" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0000706 oboInOwl:hasDbXref "NCBI SRA: ABI_SOLID" . obo:OBI_0000717 oboInOwl:hasDbXref "NCBI SRA: Helicos HeliScope" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0000718 a owl:Class ; rdfs:label "pathogen role" ; rdfs:subClassOf obo:GENEPIO_0001172 . obo:OBI_0000925 rdfs:comment "Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in'"@en ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0100026 [ a owl:Restriction ; owl:onProperty obo:RO_0002451 ; owl:someValuesFrom obo:TRANS_0000000 ] ) ] . obo:OBI_0000973 obo:IAO_0000115 "A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement."@en . obo:OBI_0001141 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:OBI_0001167 rdfs:subClassOf . obo:OBI_0001169 rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:OBI_0001479 obo:IAO_0000116 "Damion Dooley note: OBI has a variety of subclasses like \"blood specimen\" and \"colon specimen\" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic \"derives from some [uberon term]\". GenEpiO takes a different approach in describing this class with lists for \"subject anatomical site\", \"subject body product\", and \"plant anatomy\"."@en ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0100051 [ a owl:Restriction ; owl:onProperty obo:RO_0001000 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:GENEPIO_0000025 obo:GENEPIO_0000028 ) ] ] ) ] . obo:OBI_0001614 obo:GENEPIO_1919 "^SAM[NED](\\w)?\\d+$"^^xsd:string ; rdfs:seeAlso "http://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000350"^^xsd:anyURI, "http://www.ncbi.nlm.nih.gov/Sequin/acc.html"^^xsd:anyURI, "https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/"^^xsd:anyURI ; rdfs:subClassOf . obo:OBI_0001615 oboInOwl:inSubset "NCBI BioProject" ; rdfs:subClassOf , [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:OBI_0000066 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000112 ], [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001836 ] . obo:OBI_0001616 oboInOwl:hasSynonym "sample identifier"@en . obo:OBI_0001619 obo:GENEPIO_0000006 "specimen collection date"@en ; rdfs:subClassOf obo:GENEPIO_0001356 . obo:OBI_0001620 obo:GENEPIO_0001763 "help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location."@en ; obo:IAO_0000116 "Damion Dooley's note: IAO lat/long can't be made a subclass of \"angular coordinate\" or disjoint contradiction arises."@en ; rdfs:comment """See http://www.csgnetwork.com/gpscoordconv.html See http://www.geomidpoint.com/latlon.html See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 See http://www.w3.org/2003/01/geo/wgs84_pos"""@en ; rdfs:subClassOf obo:GENEPIO_0001654 . obo:OBI_0001621 rdfs:subClassOf obo:GENEPIO_0001654 . obo:OBI_0001622 oboInOwl:inSubset "NCBI BioProject", "NIAID GSCID-BRC" ; rdfs:subClassOf obo:NCIT_C42614, [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:OBI_0000066 ] . obo:OBI_0001627 rdfs:comment """Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. \" 'country name' inheres in some 'sovereign state/country'\". Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs \"Republic of China\"). Both point to needing a single entity with multiple names."""@en ; rdfs:subClassOf obo:GENEPIO_0002017, [ a owl:Restriction ; owl:onProperty obo:RO_0000052 ; owl:someValuesFrom obo:NCIT_C25464 ] . obo:OBI_0001628 oboInOwl:hasExactSynonym "http://purl.obolibrary.org/obo/OMIABIS_0000006"^^xsd:anyURI . obo:OBI_0001880 obo:GENEPIO_0000006 "specimen provider PI organization"@en . obo:OBI_0001882 obo:GENEPIO_0000006 "target material"@en ; oboInOwl:hasExactSynonym "NCBI BioProject: Material" ; rdfs:comment "Used in NCBI BioProject specifcation"@en . obo:OBI_0001884 obo:GENEPIO_0000006 "specimen sample scope"@en . obo:OBI_0001888 rdfs:subClassOf obo:NCIT_C25190 . obo:OBI_0001889 a owl:Class ; rdfs:subClassOf obo:NCIT_C25190 . obo:OBI_0001891 obo:GENEPIO_0000006 "sequencing facility"@en ; a owl:Class . obo:OBI_0001892 obo:GENEPIO_0000006 "project objective"@en ; oboInOwl:hasExactSynonym "NCBI BioProject: Objective" ; a owl:Class . obo:OBI_0001893 a owl:Class . obo:OBI_0001894 rdfs:subClassOf obo:GENEPIO_0001681 . obo:OBI_0001896 obo:GENEPIO_0000006 "project method"@en . obo:OBI_0001903 obo:GENEPIO_0000006 "specimen provider PI email"@en ; rdfs:subClassOf obo:GENEPIO_0001790 . obo:OBI_0001904 rdfs:subClassOf obo:GENEPIO_0002225 . obo:OBI_0001927 obo:GENEPIO_0000006 "specifies"@en . obo:OBI_0001930 obo:GENEPIO_0000006 "categorical"@en ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:STATO_0000252 ], [ a owl:Restriction ; owl:onDataRange xsd:anyURI ; owl:onProperty obo:OBI_0002135 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:OBI_0001931 obo:GENEPIO_0000006 "scalar"@en . obo:OBI_0001933 rdfs:comment """Damion Dooley's note: Often a value specification may need to allow for a \"data item state\" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state."""@en . obo:OBI_0001941 obo:GENEPIO_0000001 "Assembly QC"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000119 "http://www.nature.com/nature/journal.../409860a0.html"^^xsd:anyURI ; oboInOwl:inSubset "GENEPIO"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001632 . obo:OBI_0002000 oboInOwl:hasDbXref "NCBI SRA: Illumina Genome Analyzer IIx" . obo:OBI_0002001 rdfs:subClassOf obo:GENEPIO_0001939 . obo:OBI_0002002 rdfs:subClassOf obo:GENEPIO_0001939 . obo:OBI_0002003 oboInOwl:hasDbXref "NCBI SRA: Illumina MiSeq" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0002007 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD 3 Plus System" . obo:OBI_0002012 oboInOwl:hasDbXref "NCBI SRA: PacBio RS" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0002021 oboInOwl:hasDbXref "NCBI SRA: Illumina NextSeq" ; rdfs:subClassOf obo:GENEPIO_0001921 . obo:OBI_0002022 rdfs:subClassOf obo:GENEPIO_0001939 . obo:OBI_0002024 oboInOwl:hasDbXref "NCBI SRA: AB SOLiD 4 System" . obo:OBI_0002027 oboInOwl:hasDbXref "NCBI SRA: Illumina Genome Analyzer IIe" . obo:OBI_0002048 rdfs:subClassOf obo:GENEPIO_0001939 . obo:OBI_0002049 rdfs:subClassOf obo:GENEPIO_0001939 . obo:OBI_0002135 a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . obo:OBI_0002822 rdfs:subClassOf obo:NCIT_C17627 . obo:OBI_0002824 rdfs:subClassOf obo:NCIT_C17627 . obo:OBI_0100051 oboInOwl:hasExactSynonym "sample"@en ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0001000 ; owl:someValuesFrom obo:GENEPIO_0000134 ] . obo:OGMS_0000031 obo:GENEPIO_0000006 "disease (OGMS)"@en . obo:OGMS_0000063 a owl:Class . obo:OGMS_0000073 obo:IAO_0000117 ; dc:date "2019-09-08T23:41:09Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "diagnosis"@en ; rdfs:subClassOf obo:GENEPIO_0001192 . obo:OGMS_0000087 obo:IAO_0000115 "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en ; a owl:Class ; rdfs:label "extended organism"@en ; rdfs:subClassOf obo:UBERON_0000465 . obo:OMIABIS_0001008 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; oboInOwl:hasDbXref obo:GENEPIO_0002073, "NIAID: Comorbidity" ; oboInOwl:hasNarrowSynonym "complications"@en ; a owl:Class ; rdfs:subClassOf obo:OGMS_0000073 . obo:OMIT_0001642 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001843, obo:OMIT_0020789 . obo:OMIT_0004227 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001212, obo:GENEPIO_0001843, obo:OMIT_0020789 . obo:OMIT_0006951 a owl:Class ; rdfs:subClassOf obo:OBI_0600044 . obo:OMIT_0012122 obo:IAO_0000412 "http://purl.obolibrary.org/obo/omit"^^xsd:anyURI ; rdfs:subClassOf obo:IAO_0000027 . obo:OMIT_0012935 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001843, obo:OMIT_0020789 . obo:OMIT_0013001 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001843, obo:OMIT_0020789 . obo:OMIT_0017096 obo:IAO_0000115 "Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable."@en ; obo:IAO_0000117 "Damion Dooley"@en ; oboInOwl:hasSynonym "grave"@en ; a owl:Class ; rdfs:subClassOf obo:OMIT_0020789 . obo:OMIT_0019022 rdfs:subClassOf obo:OBI_0600044 . obo:OMIT_0020789 a owl:Class ; rdfs:subClassOf obo:BFO_0000019 . obo:OMIT_0020917 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A type of Shiga toxin found in E. coli"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000118 "Stx1"^^xsd:string ; obo:IAO_0000119 ; obo:IAO_0000412 ; oboInOwl:hasDbXref obo:OMIT_0020917 ; a owl:Class ; rdfs:label "Shiga toxin 1"@en ; rdfs:subClassOf obo:NCIT_C1225 . obo:OMIT_0020918 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1"@en ; obo:IAO_0000117 "Damion Dooley"@en ; obo:IAO_0000118 "Stx2"^^xsd:string ; obo:IAO_0000119 ; obo:IAO_0000412 ; oboInOwl:hasDbXref obo:OMIT_0020918 ; a owl:Class ; rdfs:label "Shiga toxin 2"@en ; rdfs:subClassOf obo:NCIT_C1225 . obo:OMIT_0021725 a owl:Class ; rdfs:subClassOf obo:PR_000000001 . obo:OMIT_0027406 obo:GENEPIO_0000006 "MLST typing"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001688 . obo:OMIT_0027578 a owl:Class ; rdfs:subClassOf obo:OBI_0600005 . obo:OMP_0000207 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001688, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:NCIT_C53471 ] . obo:OMRSE_00000013 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000115 "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments."@en ; a owl:Class ; rdfs:label "physician role"@en ; rdfs:subClassOf obo:GENEPIO_0001537 . obo:PATO_0000047 a owl:Class . obo:PATO_0000146 a owl:Class ; rdfs:comment "Damion's Note: Future use might prefer: CMO_0000015 body temperature."@en . obo:PATO_0000383 oboInOwl:hasDbXref "NCBI BioSample: female"@en ; a owl:Class . obo:PATO_0000384 oboInOwl:hasDbXref "NCBI BioSample: male" ; a owl:Class . obo:PATO_0000460 obo:IAO_0000114 obo:IAO_0000122 . obo:PATO_0001340 oboInOwl:hasDbXref "NCBI BioSample: hermaphrodite" . obo:PATO_0001585 a owl:Class . obo:PATO_0001827 obo:IAO_0000116 "This value is not present in NCBI BioSample host sex."@en . obo:PATO_0001894 obo:IAO_0000115 "Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior."@en ; obo:IAO_0000116 """Note that NCBI Biosample has these values allowed: male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected"""@en ; obo:IAO_0000119 "NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/" ; a owl:Class . obo:PATO_0002390 obo:IAO_0000114 obo:IAO_0000428 ; rdfs:comment "Damion Dooley's note: We can't say radius is a subclass of \"linear coordinate\" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. \"length\" as quality unfortunately can't pertain to abstract entities, only \"real\" ones."@en . obo:PCO_0000000 rdfs:subClassOf obo:BFO_0000040 . obo:PCO_0000031 rdfs:subClassOf obo:BFO_0000040 . obo:PCO_0000033 obo:GENEPIO_0000006 "social gathering"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001444 . obo:PECO_0007027 rdfs:subClassOf obo:BFO_0000003 . obo:PO_0009011 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0000025 . obo:RBO_00000017 rdfs:subClassOf obo:ENVO_01000254 . obo:RO_0000052 a owl:ObjectProperty ; rdfs:label "inheres in"@en . obo:RO_0000057 a owl:ObjectProperty ; rdfs:label "has participant" . obo:RO_0000086 a owl:ObjectProperty . obo:RO_0001001 rdfs:label "derives into"@en . obo:RO_0001015 a owl:ObjectProperty ; rdfs:label "location of" . obo:RO_0001025 a owl:ObjectProperty ; rdfs:label "located in" . obo:RO_0002001 a owl:ObjectProperty ; rdfs:label "aligned with"@en . obo:RO_0002083 obo:IAO_0000115 "T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)"@en ; a owl:ObjectProperty . obo:RO_0002091 rdfs:label "starts during"@en . obo:RO_0002092 rdfs:label "happens during"@en . obo:RO_0002180 a owl:AsymmetricProperty, owl:IrreflexiveProperty, owl:ObjectProperty ; rdfs:label "has component"@en . obo:RO_0002220 a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "adjacent to" . obo:RO_0002224 rdfs:label "starts with"@en . obo:RO_0002230 rdfs:label "ends with"@en . obo:RO_0002233 a owl:ObjectProperty ; rdfs:label "has input", "has input"@en ; rdfs:subPropertyOf obo:RO_0000057 . obo:RO_0002234 a owl:ObjectProperty ; rdfs:label "has output", "has output"@en ; rdfs:subPropertyOf obo:RO_0000057 . obo:RO_0002350 a owl:AsymmetricProperty, owl:IrreflexiveProperty, owl:ObjectProperty ; rdfs:label "member of" . obo:RO_0002351 a owl:ObjectProperty ; rdfs:label "has member" . obo:RO_0002352 rdfs:label "input of"@en . obo:RO_0002353 rdfs:label "output of"@en . obo:SO_0000149 obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:GENEPIO_0001425, [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:SO_0001462 ] . obo:SO_0000353 obo:GENEPIO_0000006 "sequence assembly"@en ; oboInOwl:hasExactSynonym "http://edamontology.org/data_0925"^^xsd:anyURI, "http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data'"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001425, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0100026 ], [ a owl:Restriction ; owl:onClass obo:SO_0001462 ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . obo:SO_0001026 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:subClassOf obo:BFO_0000027 . obo:SO_0001027 a owl:Class . obo:SO_0001260 a owl:Class ; rdfs:subClassOf obo:BFO_0000027 . obo:SO_0001462 a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002351 ; owl:someValuesFrom obo:SO_0000149 ] . obo:SO_0001505 oboInOwl:hasExactSynonym "http://purl.obolibrary.org/obo/ERO_0002173"^^xsd:anyURI ; a owl:Class . obo:STATO_0000010 obo:GENEPIO_0000006 "n-dimensional coordinate system"@en ; rdfs:comment """Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? Linear offset can be decimal or integer or complex, or a count. - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit Angular offset can be radians or degrees."""@en . obo:STATO_0000013 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001865 . obo:STATO_0000015 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001866 . obo:STATO_0000016 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001867 . obo:STATO_0000022 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001864 . obo:STATO_0000024 a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001866 . obo:STATO_0000047 obo:IAO_0000116 "Damion Dooley's note: Unfortunately an IAO \"count\" cannot be a subclass of immaterial entity \"linear coordinate\" as this leads to disjoint conflict."@en ; rdfs:comment "Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for."@en, "Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!"@en ; rdfs:subClassOf obo:IAO_0000109 . obo:STATO_0000064 rdfs:subClassOf obo:STATO_0000047 . obo:STATO_0000069 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:STATO_0000087 a owl:Class ; rdfs:subClassOf obo:STATO_0000252 . obo:STATO_0000090 a owl:Class ; rdfs:subClassOf obo:STATO_0000087 . obo:STATO_0000184 a owl:Class . obo:STATO_0000190 a owl:Class ; rdfs:subClassOf obo:STATO_0000232 . obo:STATO_0000221 a owl:Class ; rdfs:subClassOf obo:STATO_0000258 . obo:STATO_0000228 a owl:Class ; rdfs:subClassOf obo:STATO_0000252 . obo:STATO_0000232 a owl:Class ; rdfs:subClassOf obo:STATO_0000047 . obo:STATO_0000251 a owl:Class ; rdfs:subClassOf obo:STATO_0000258 . obo:STATO_0000252 a owl:Class ; rdfs:subClassOf obo:STATO_0000258 . obo:STATO_0000258 obo:GENEPIO_0000006 "variable type"@en ; a owl:Class ; rdfs:subClassOf obo:IAO_0000030 . obo:SYMP_0000092 rdfs:subClassOf obo:ARO_3004430 . obo:SYMP_0000462 rdfs:subClassOf obo:BFO_0000019 . obo:TRANS_0000000 obo:IAO_0000115 "A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:comment "TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host."@en ; rdfs:label "transmission of infection"@en ; rdfs:subClassOf obo:GO_0008150 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:GO_0008150 [ a owl:Restriction ; owl:onProperty obo:RO_0002233 ; owl:someValuesFrom obo:IDO_0000659 ] [ a owl:Restriction ; owl:onProperty obo:RO_0002234 ; owl:someValuesFrom obo:OBI_0000925 ] [ a owl:Restriction ; owl:onProperty obo:RO_0002404 ; owl:someValuesFrom obo:IDO_0000495 ] ) ] . obo:TRANS_0000001 obo:IAO_0000115 "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "direct transmission"@en ; rdfs:subClassOf obo:TRANS_0000000 . obo:TRANS_0000002 obo:IAO_0000115 "Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "indirect transmission"@en ; rdfs:subClassOf obo:TRANS_0000000 . obo:TRANS_0000006 obo:IAO_0000115 "Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "congenital"@en ; rdfs:subClassOf obo:TRANS_0000001 . obo:TRANS_0000007 obo:GENEPIO_0000006 "contact transmission"@en ; obo:IAO_0000115 "Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "contact"@en ; rdfs:subClassOf obo:TRANS_0000001 . obo:TRANS_0000008 obo:IAO_0000115 "Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "droplet spread"@en ; rdfs:subClassOf obo:TRANS_0000001 . obo:TRANS_0000012 obo:IAO_0000115 "Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products."@en ; obo:IAO_0000119 "https://www.ebi.ac.uk/ols/ontologies/trans"^^xsd:anyURI ; a owl:Class ; rdfs:label "vehicle-born ingestion"@en ; rdfs:subClassOf obo:TRANS_0000002 . obo:UBERON_0000000 rdfs:subClassOf obo:BFO_0000003 . obo:UBERON_0000061 rdfs:subClassOf obo:GENEPIO_0000025, obo:UBERON_0001062 . obo:UBERON_0000062 rdfs:subClassOf obo:UBERON_0000061 . obo:UBERON_0000174 rdfs:subClassOf obo:GENEPIO_0001636 . obo:UBERON_0000179 rdfs:subClassOf obo:UBERON_0006314 . obo:UBERON_0000463 obo:GENEPIO_0000006 "organism body product"@en ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0003001 ; owl:someValuesFrom obo:OBI_0100026 ] . obo:UBERON_0001003 rdfs:subClassOf obo:ARO_3004430 . obo:UBERON_0001052 oboInOwl:hasSynonym "rectal"@en . obo:UBERON_0001090 rdfs:subClassOf obo:UBERON_0007794 . obo:UBERON_0001130 rdfs:seeAlso "http://purl.obolibrary.org/obo/BTO_0000818"^^xsd:anyURI . obo:UBERON_0001268 rdfs:subClassOf obo:UBERON_0007794 . obo:UBERON_0001359 obo:GENEPIO_0000006 "cerebrospinal fluid (CSF)"@en . obo:UBERON_0001836 rdfs:subClassOf obo:UBERON_0000456, obo:UBERON_0006314 . obo:UBERON_0001969 rdfs:subClassOf obo:UBERON_0000179 . obo:UBERON_0001977 rdfs:subClassOf obo:UBERON_0006314 . obo:UBERON_0002391 rdfs:subClassOf obo:UBERON_0000179 . obo:UBERON_0003134 rdfs:subClassOf obo:ARO_3004430 . obo:UBERON_0003135 rdfs:subClassOf obo:ARO_3004430 . obo:UBERON_0005172 rdfs:subClassOf obo:UBERON_0000062 . obo:UBERON_0005181 rdfs:subClassOf obo:UBERON_0000468 . obo:UBERON_0006314 rdfs:subClassOf obo:GENEPIO_0001636 . obo:UBERON_0007109 rdfs:subClassOf obo:UBERON_0001988 . obo:UBERON_0007311 rdfs:subClassOf obo:UBERON_0006314, obo:UBERON_0006538 . obo:UBERON_0007378 rdfs:subClassOf obo:GENEPIO_0001636 . obo:UBERON_0007779 rdfs:subClassOf obo:UBERON_0006314 . obo:UBERON_0007794 rdfs:subClassOf obo:UBERON_0000456, obo:UBERON_0006314 . obo:UBERON_0008291 obo:GENEPIO_0000006 "poultry fluff"@en ; obo:IAO_0000116 "Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed."@en ; rdfs:subClassOf obo:GENEPIO_0001636 . obo:UBERON_0034945 rdfs:subClassOf obo:UBERON_0000174 . obo:UBERON_0034946 rdfs:subClassOf obo:UBERON_0034945 . obo:UO_0000000 rdfs:comment """Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: [1] R. Hodgson and P. J. Keller, \"QUDT-quantities, units, dimensions and data types in OWL and XML.\" Online (September 2011) http://www. qudt.org [2] M. van Assem, H. Rijgersberg, and J. Top, \"Ontology of units of measure and related concepts.\" Semantic Web 4, no. 1 (2013): 3-13. [3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, \"The Units Ontology: a tool for integrating units of measurement in science.\" Database2012 (2012): bas033."""@en ; rdfs:subClassOf obo:BFO_0000141 . obo:UO_0000006 a owl:Class . obo:UO_0000016 oboInOwl:hasAlternativeId "mm"^^rdfs:Literal . obo:UO_0000051 a owl:Class . obo:UO_0000060 a owl:Class . obo:UO_0000210 a owl:Class . obo:UO_0000212 a owl:Class . obo:UO_0000213 obo:GENEPIO_0000006 "cfu/mL" ; obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" . obo:UO_0000274 oboInOwl:hasAlternativeId "µg/ml"^^rdfs:Literal . obo:UO_0000328 a owl:Class . obo:VT_0002292 rdfs:subClassOf obo:IAO_0000416, . obo:XCO_0000412 obo:GENEPIO_0000006 "ongoing pregnancy"@en ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001667, obo:GENEPIO_0001682 . terms:date "2022-01-29"^^xsd:date ; terms:description "The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata."@en ; terms:license ; terms:title "Genomic Epidemiology Ontology"@en ; oboInOwl:default-namespace "GENEPIO"^^xsd:string ; a owl:Ontology ; owl:imports , , , , , , , , , , , , , , , ; owl:versionIRI . odes_field:date a owl:AnnotationProperty . temp_import:date a owl:AnnotationProperty . obo:hancestro_0004 a owl:Class ; rdfs:label "ancestral group"@en ; rdfs:subClassOf obo:GENEPIO_0001170 . obo:sep_00196 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000117 "Damion Dooley" ; rdfs:subClassOf obo:GENEPIO_0001790 . a owl:ObjectProperty ; rdfs:label "is unit of" . dc:creator a owl:AnnotationProperty . dc:date a owl:AnnotationProperty . terms:description a owl:AnnotationProperty . terms:license a owl:AnnotationProperty . terms:title a owl:AnnotationProperty . obo:GENEPIO_0000006 "MLVA typing"@en ; obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001688 . rdfs:subClassOf obo:IAO_0000300 . rdfs:comment "Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height."@en ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:RO_0002001 ; owl:someValuesFrom ] . obo:IAO_0000115 "In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit."@en ; obo:IAO_0000117 "Damion Dooley" ; obo:IAO_0000119 "https://en.wikipedia.org/wiki/Polygon" ; rdfs:subClassOf obo:GENEPIO_0001934, obo:GENEPIO_0001996 . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001744 . obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000117 "Damion Dooley"@en . a owl:Class ; rdfs:subClassOf obo:ENVO_01000658, obo:NCIT_C80234 . oboInOwl:hasDbXref "PulseNet: Key"@en ; rdfs:subClassOf obo:IAO_0000577 . a owl:Class ; rdfs:subClassOf obo:IAO_0000577 . a owl:Class ; rdfs:subClassOf . obo:IAO_0000114 obo:IAO_0000428 ; obo:IAO_0000117 "Damion Dooley" ; a owl:Class ; rdfs:label "medical health record (history / timeline)"@en ; rdfs:subClassOf obo:GENEPIO_0001741 . a owl:Class ; rdfs:subClassOf obo:IAO_0000577 . obo:GENEPIO_0001763 "depth:1", "lookup" ; rdfs:subClassOf obo:GENEPIO_0001170 ; owl:equivalentClass [ a owl:Class ; owl:unionOf (obo:NCIT_C28554 obo:NCIT_C37987 ) ] . obo:IAO_0000412 ; a owl:Class ; rdfs:label "Bacterial bacteriophage typing"@en ; rdfs:seeAlso "http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004" ; rdfs:subClassOf obo:OBI_0000070 . obo:IAO_0000114 obo:IAO_0000122 ; rdfs:subClassOf obo:GENEPIO_0002047 . obo:IAO_0100001 "http://purl.obolibrary.org/obo/hancestro_0004"^^xsd:anyURI ; a owl:Class ; rdfs:label "obsolete: ancestral group"@en ; owl:deprecated true . oboInOwl:hasDbXref "http://purl.obolibrary.org/obo/PATO_0000011"^^xsd:anyURI . a owl:Class . rdfs:subClassOf obo:BFO_0000023 . a owl:Class ; rdfs:subClassOf obo:IAO_0000032 . a owl:Class ; rdfs:subClassOf obo:IAO_0000027 . obo:IAO_0000600 "A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)"@en ; rdfs:subClassOf obo:OBI_0000181, [ a owl:Restriction ; owl:onProperty obo:RO_0002351 ; owl:someValuesFrom obo:NCBITaxon_9606 ] . a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001170 . a owl:Class ; rdfs:subClassOf obo:IAO_0000416 . oboInOwl:default-namespace a owl:AnnotationProperty . oboInOwl:hasDbXref a owl:AnnotationProperty . rdfs:comment a owl:AnnotationProperty . rdfs:label a owl:AnnotationProperty ; rdfs:label "label" . rdfs:seeAlso a owl:AnnotationProperty ; rdfs:label "see also" . xsd:QName a rdfs:Datatype . xsd:date a rdfs:Datatype . xsd:dateTime a rdfs:Datatype . xsd:float a rdfs:Datatype . xsd:integer a rdfs:Datatype . xsd:nonNegativeInteger a rdfs:Datatype . xsd:string a rdfs:Datatype . owl:Thing rdfs:comment """Welcome to the GenEpiO ontology! The \"information content entity\" class has many GenEpiO terms. \"data item > measurement data item\" has many datum terms; see \"data representational model\" for collections of terms set up for compatibility with 3rd party sources. Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use."""@en . owl:qualifiedCardinality a owl:AnnotationProperty . obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch."@en ; obo:IAO_0000119 ; a owl:ObjectProperty ; rdfs:label "exactMatch"@en . obo:IAO_0000114 obo:IAO_0000428 ; a owl:Class ; rdfs:subClassOf obo:GENEPIO_0001251 . a owl:Class ; rdfs:subClassOf obo:IAO_0000300 . linkml:Definition obo:IAO_0000115 "Base class for definitions."@en ; a owl:Class ; rdfs:subClassOf linkml:Element . linkml:Element obo:IAO_0000115 "A named element in the model."@en ; a owl:Class ; rdfs:subClassOf obo:OBI_0000658 . linkml:Example obo:IAO_0000115 "Usage example and description."@en ; a owl:Class ; rdfs:subClassOf linkml:Element . linkml:LocalName obo:IAO_0000115 "An attributed label."@en ; a owl:Class ; rdfs:subClassOf linkml:Element . linkml:PermissibleValue obo:IAO_0000115 "A permissible value, accompanied by intended text and an optional mapping to a concept URI."@en ; a owl:Class ; rdfs:subClassOf linkml:Element . linkml:SchemaDefinition obo:IAO_0000115 "A collection of subset, type, slot and class definitions."@en ; a owl:Class ; rdfs:subClassOf linkml:Definition . linkml:SlotDefinition obo:IAO_0000115 "The definition of a property or a slot."@en ; a owl:Class ; rdfs:subClassOf linkml:Definition . linkml:abstract obo:IAO_0000115 "An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated."@en ; a owl:DatatypeProperty ; rdfs:range xsd:boolean ; rdfs:subPropertyOf owl:topDataProperty . linkml:comments obo:IAO_0000115 "Notes and comments about an element intended for external consumption."@en ; a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:created_on obo:IAO_0000115 "Date/time at which the element was created."@en ; a owl:DatatypeProperty ; rdfs:range [ a rdfs:Datatype ; owl:unionOf (xsd:date xsd:dateTime xsd:dateTimeStamp ) ] ; rdfs:subPropertyOf owl:topDataProperty . linkml:data_collection_state obo:IAO_0000112 "Not Applicable; Missing; Not Collected; Not Provided; Restricted Access"@en ; obo:IAO_0000115 "A value (string or URI) indicating the data collection state an instance of a slot has."@en ; a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:description obo:IAO_0000115 "A description of the element's purpose and use"@en ; a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:exact_mappings obo:IAO_0000115 "A list of terms from different schemas or terminology systems that have identical meaning."@en ; a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:examples a owl:ObjectProperty ; rdfs:range linkml:Example . linkml:from_schema obo:IAO_0000115 "Id of the schema that defined the element."@en ; a owl:DatatypeProperty ; rdfs:range xsd:anyURI . linkml:identifier a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:imported_from obo:IAO_0000115 "The imports entry that this element was derived from. Empty means primary source"@en ; a owl:DatatypeProperty ; rdfs:range xsd:string ; rdfs:subPropertyOf owl:topDataProperty . linkml:local_name_source obo:IAO_0000115 "The ncname of the source of the name."@en ; obo:IAO_0000117 ; odes_field:date "2021-04-26T22:15:07Z"^^xsd:dateTime ; temp_import:date "2021-04-26T22:15:07Z"^^xsd:dateTime ; a owl:DatatypeProperty ; rdfs:domain linkml:LocalName ; rdfs:label "local_name_source"@en ; rdfs:range xsd:NCName ; rdfs:subPropertyOf owl:topDataProperty . linkml:local_name_value obo:IAO_0000115 "A name assigned to an element in a given ontology."@en ; a owl:DatatypeProperty ; rdfs:domain linkml:LocalName ; rdfs:range xsd:string ; rdfs:subPropertyOf owl:topDataProperty . linkml:local_names obo:IAO_0000115 "An object relation between a LinkML SlotDefinition to a LocalName."@en ; a owl:ObjectProperty . linkml:maximum_value obo:IAO_0000115 "For slots with ranges of type number, the value must be equal to or lowe than this"@en ; a owl:DatatypeProperty ; rdfs:range xsd:int ; rdfs:subPropertyOf owl:topDataProperty . linkml:meaning a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:minimum_value obo:IAO_0000115 "For slots with ranges of type number, the value must be equal to or higher than this"@en ; a owl:DatatypeProperty ; rdfs:range xsd:int ; rdfs:subPropertyOf owl:topDataProperty . linkml:multivalued obo:IAO_0000115 "true means that slot can have more than one value"@en ; a owl:DatatypeProperty ; rdfs:range xsd:boolean ; rdfs:subPropertyOf owl:topDataProperty . linkml:name obo:IAO_0000115 "The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class."@en ; a owl:DatatypeProperty ; rdfs:range xsd:string ; rdfs:subPropertyOf owl:topDataProperty . linkml:pattern obo:IAO_0000115 "The string value of the slot must conform to this regular expression"@en ; a owl:DatatypeProperty ; rdfs:range xsd:string ; rdfs:subPropertyOf owl:topDataProperty . linkml:permissible_values obo:IAO_0000115 "A list of possible values for a slot range."@en ; a owl:DatatypeProperty ; rdfs:subPropertyOf owl:topDataProperty . linkml:recommended obo:IAO_0000115 "true if this slot is not required, but is recommended."@en ; a owl:DatatypeProperty ; rdfs:range xsd:boolean ; rdfs:subPropertyOf owl:topDataProperty . linkml:required obo:IAO_0000115 "true means that the slot must be present in the loaded definition."@en ; a owl:DatatypeProperty ; rdfs:range xsd:boolean ; rdfs:subPropertyOf owl:topDataProperty . linkml:see_also obo:IAO_0000115 "A reference."@en ; a owl:DatatypeProperty ; rdfs:range xsd:anyURI ; rdfs:subPropertyOf owl:topDataProperty . linkml:status obo:IAO_0000112 "IAO:0000122 ('ready for release')"@en ; obo:IAO_0000115 "status of the element."@en ; a owl:DatatypeProperty ; rdfs:range xsd:anyURI ; rdfs:subPropertyOf owl:topDataProperty . linkml:type_uri obo:IAO_0000115 "The uri that defines the possible values for the type definition"@en ; a owl:DatatypeProperty ; rdfs:comment "URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)"@en ; rdfs:subPropertyOf owl:topDataProperty . linkml:value a owl:DatatypeProperty ; rdfs:domain linkml:Example ; rdfs:subPropertyOf owl:topDataProperty . linkml:value_description obo:IAO_0000115 "Description of what the value is doing."@en ; a owl:DatatypeProperty ; rdfs:domain linkml:Example ; rdfs:range xsd:string ; rdfs:subPropertyOf owl:topDataProperty . linkml:values_from obo:IAO_0000115 ; a owl:DatatypeProperty ; rdfs:range xsd:anyURI ; rdfs:subPropertyOf owl:topDataProperty . [] obo:GENEPIO_0001763 "lookup" ; a owl:Axiom ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001567 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:NCBITaxon_33090 obo:NCBITaxon_33213 obo:NCBITaxon_9606 ) ] ] . [] a owl:Axiom ; rdfs:label "Clinical/host-associated pathogen"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001569 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000002 ] . [] a owl:Axiom ; rdfs:label "Pathogen.cl"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001569 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . [] a owl:Axiom ; rdfs:label "environmental/food/other"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001590 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000002 ] . [] a owl:Axiom ; rdfs:label "Pathogen.env"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001590 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . [] a owl:Axiom ; rdfs:label "host description"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001614 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001835 ] . [] obo:GENEPIO_0000005 "https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf"^^xsd:anyURI ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000118 ; owl:annotatedSource obo:CHEBI_63611 ; owl:annotatedTarget "Mfx" . [] obo:GENEPIO_0001763 "lookup" ; a owl:Axiom ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001785 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:NCIT_C80234 ] . [] a owl:Axiom ; rdfs:label "Condition"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:ExO_0000038 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001837 ] . [] a owl:Axiom ; rdfs:label "Objective"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001836 ; owl:annotatedTarget [ a owl:Restriction ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001892 ] ) ] ; owl:onProperty obo:RO_0002180 ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ] . [] a owl:Axiom ; rdfs:label "Condition"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:ExO_0000038 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001845 ] . [] a owl:Axiom ; rdfs:comment "The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021"@en ; rdfs:label "Project Accession"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001836 ; owl:annotatedTarget [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass obo:GENEPIO_0002128 ; owl:onProperty obo:RO_0002180 ] . [] a owl:Axiom ; rdfs:label "Methodology"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001836 ; owl:annotatedTarget [ a owl:Restriction ; owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ; owl:onClass [ a owl:Class ; owl:intersectionOf (obo:OBI_0001930 [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom obo:OBI_0001896 ] ) ] ; owl:onProperty obo:RO_0002180 ] . [] a owl:Axiom ; rdfs:label "Good"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0001840 ; owl:annotatedTarget obo:GENEPIO_0001837 . [] a owl:Axiom ; rdfs:label "satisfactory"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0001840 ; owl:annotatedTarget obo:GENEPIO_0001845 . [] a owl:Axiom ; rdfs:label "fair"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001841 ; owl:annotatedTarget obo:GENEPIO_0002025 . [] a owl:Axiom ; rdfs:label "Stable"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0001841 ; owl:annotatedTarget obo:GENEPIO_0001845 . [] a owl:Axiom ; rdfs:label "Serious"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0001842 ; owl:annotatedTarget obo:GENEPIO_0001837 . [] a owl:Axiom ; rdfs:label "critical but stable"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001846 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "Comfortable"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001847 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "progressing well"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001848 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "discharged"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0001849 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "Treated and Released"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0002021 ; owl:annotatedTarget obo:GENEPIO_0001837 . [] a owl:Axiom ; rdfs:label "Treated and Transferred"@en ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:GENEPIO_0002022 ; owl:annotatedTarget obo:GENEPIO_0001837 . [] a owl:Axiom ; rdfs:label "satisfactory"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0002023 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] obo:GENEPIO_0001763 "lookup" ; a owl:Axiom ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0002097 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:GENEPIO_0001742 obo:NCIT_C25632 obo:NCIT_C87194 obo:NCIT_C89811 ) ] ] . [] a owl:Axiom ; rdfs:label "critical"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0002228 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "critical"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0002228 ; owl:annotatedTarget obo:GENEPIO_0002025 . [] a owl:Axiom ; rdfs:label "deceased"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:NCIT_C28554 ; owl:annotatedTarget obo:GENEPIO_0002024 . [] a owl:Axiom ; rdfs:label "Project Description"@en ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:OBI_0001615 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0000112 ] . [] a owl:Axiom ; rdfs:label "Description*" ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:OBI_0001615 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:RO_0002350 ; owl:someValuesFrom obo:GENEPIO_0001836 ] . [] a owl:Axiom ; rdfs:label "Comorbidity" ; owl:annotatedProperty oboInOwl:hasDbXref ; owl:annotatedSource obo:OMIABIS_0001008 ; owl:annotatedTarget obo:GENEPIO_0002073 . [] owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger . [] owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger . [] a owl:AllDisjointClasses ; owl:members (obo:GENEPIO_0000106 obo:GENEPIO_0001342 obo:GENEPIO_0002178 obo:NCIT_C103180 ) . [] a owl:AllDisjointClasses ; owl:members (obo:GENEPIO_0000147 obo:GENEPIO_0001007 obo:GENEPIO_0001835 obo:GENEPIO_0001836 ) . [] a owl:AllDifferent ; owl:distinctMembers (obo:GENEPIO_0002179 obo:GENEPIO_0002182 obo:GENEPIO_0002183 obo:GENEPIO_0002184 obo:GENEPIO_0002187 obo:GENEPIO_0002188 obo:GENEPIO_0002189 obo:GENEPIO_0002190 obo:GENEPIO_0002191 obo:GENEPIO_0002192 obo:GENEPIO_0002193 obo:GENEPIO_0002194 obo:GENEPIO_0002195 obo:GENEPIO_0002196 obo:GENEPIO_0002197 obo:GENEPIO_0002198 obo:GENEPIO_0002199 obo:GENEPIO_0002200 obo:GENEPIO_0002201 obo:GENEPIO_0002202 obo:GENEPIO_0002203 obo:GENEPIO_0002204 obo:GENEPIO_0002205 obo:GENEPIO_0002206 obo:GENEPIO_0002207 obo:GENEPIO_0002208 obo:GENEPIO_0002209 obo:GENEPIO_0002210 obo:GENEPIO_0002211 obo:GENEPIO_0002212 obo:GENEPIO_0002213 obo:GENEPIO_0002214 obo:GENEPIO_0002215 obo:GENEPIO_0002216 obo:GENEPIO_0002217 obo:GENEPIO_0002218 obo:GENEPIO_0002219 obo:GENEPIO_0002220 obo:GENEPIO_0002221 obo:GENEPIO_0002229 ) . [] obo:GENEPIO_0001763 "lookup" ; a owl:Axiom ; owl:annotatedProperty rdfs:subClassOf ; owl:annotatedSource obo:GENEPIO_0000117 ; owl:annotatedTarget [ a owl:Restriction ; owl:onProperty obo:OBI_0001927 ; owl:someValuesFrom [ a owl:Class ; owl:unionOf (obo:ENVO_00000005 obo:NCIT_C80234 ) ] ] .