diff --git a/ttl/generated/chebi-dead.ttl b/ttl/generated/chebi-dead.ttl index 16aae260..5ee1c57b 100644 --- a/ttl/generated/chebi-dead.ttl +++ b/ttl/generated/chebi-dead.ttl @@ -10,8 +10,8 @@ a owl:Ontology ; rdfs:label "NIF ChEBI deprecated" ; skos:altLabel "chebidead" ; - owl:versionInfo "2023-07-26" ; - prov:wasGeneratedBy . + owl:versionInfo "2024-01-26" ; + prov:wasGeneratedBy . ### Annotations @@ -427,4 +427,4 @@ CHEBI:50895 rdfs:label "cefalotin"^^xsd:string ; CHEBI:50911 rdfs:label "neurotoxin"^^xsd:string ; rdfs:subClassOf owl:DeprecatedClass . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2 diff --git a/ttl/generated/chebislim.ttl b/ttl/generated/chebislim.ttl index 080a0924..277ed1d8 100644 --- a/ttl/generated/chebislim.ttl +++ b/ttl/generated/chebislim.ttl @@ -21,19 +21,19 @@ a owl:Ontology ; rdfs:label "NIF ChEBI slim" ; skos:altLabel "chebislim" ; - owl:versionInfo "2023-07-26" ; - prov:wasDerivedFrom , - ; + owl:versionInfo "2024-01-26" ; + prov:wasDerivedFrom , + ; prov:qualifiedDerivation [ a prov:Derivation ; - prov:entity ; + prov:entity ; prov:hadActivity [ a prov:Activity ; - prov:startedAtTime "2023-07-27T04:35:47Z" ; - prov:used ; + prov:startedAtTime "2024-01-26T19:47:23Z" ; + prov:used ; prov:wasAssociatedWith [ a prov:SoftwareAgent ; ilxtr:implementationOf ; - ilxtr:versionString "3.10.12 (af44d0b8114cb82c40a07bb9ee9c1ca8a1b3688c, Jul 22 2023, 08:19:47) [PyPy 7.3.12 with GCC 12.3.1 20230526]" ] ] ] ; - oboInOwl:date "26:07:2023 23:21"^^xsd:string ; - prov:wasGeneratedBy . + ilxtr:versionString "3.10.13 (fc59e61cfbff, Jan 24 2024, 00:15:15) [PyPy 7.3.15 with GCC 12.3.1 20230825]" ] ] ] ; + oboInOwl:date "26:01:2024 00:30"^^xsd:string ; + prov:wasGeneratedBy . ### Object Properties @@ -1581,7 +1581,6 @@ CHEBI:2877 a owl:Class ; "HMDB:HMDB0001894"^^xsd:string, "KEGG:C11045"^^xsd:string, "KEGG:D02381"^^xsd:string, - "MetaCyc:CPD-5583"^^xsd:string, "Patent:US3492131"^^xsd:string, "PDBeChem:PME"^^xsd:string, "PMID:1771173"^^xsd:string, @@ -1622,6 +1621,10 @@ CHEBI:2877 a owl:Class ; "PMID:27728881"^^xsd:string, "PMID:27840415"^^xsd:string, "PMID:27845306"^^xsd:string, + "PMID:30000570"^^xsd:string, + "PMID:37291632"^^xsd:string, + "PMID:37297402"^^xsd:string, + "PMID:37454665"^^xsd:string, "Reaxys:2223850"^^xsd:string, "Wikipedia:Aspartame"^^xsd:string ; rdfs:label "aspartame"^^xsd:string ; @@ -1635,6 +1638,9 @@ CHEBI:2877 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:has_functional_parent ; owl:someValuesFrom CHEBI:49339 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:195544 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:27027 ], @@ -6560,7 +6566,10 @@ CHEBI:5115 a owl:Class ; "Wikipedia:Fluorobenzene"^^xsd:string ; rdfs:label "monofluorobenzene"^^xsd:string ; definition: "The simplest member of the class of monofluorobenzenes that is benzene carrying a single fluoro substituent."^^xsd:string ; - rdfs:subClassOf CHEBI:83575 ; + rdfs:subClassOf CHEBI:83575, + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C6H5F"^^xsd:string ; chebi:inchi "InChI=1S/C6H5F/c7-6-4-2-1-3-5-6/h1-5H"^^xsd:string ; @@ -17199,13 +17208,17 @@ CHEBI:10033 a owl:Class ; oboInOwl:hasDbXref "Beilstein:1293536"^^xsd:string, "CAS:81-81-2"^^xsd:string, "DrugBank:DB00682"^^xsd:string, + "FooDB:FDB022750"^^xsd:string, "HMDB:HMDB0001935"^^xsd:string, "KEGG:C01541"^^xsd:string, "KEGG:D08682"^^xsd:string, + "LINCS:LSM-1405"^^xsd:string, "Patent:US2427578"^^xsd:string, "Patent:US2765321"^^xsd:string, "Patent:US2777859"^^xsd:string, "Patent:US3239529"^^xsd:string, + "Pesticides:warfarin"^^xsd:string, + "PMCID:PMC10207235"^^xsd:string, "PMID:13358873"^^xsd:string, "PMID:15578879"^^xsd:string, "PMID:18294321"^^xsd:string, @@ -17232,6 +17245,10 @@ CHEBI:10033 a owl:Class ; "PMID:26142525"^^xsd:string, "PMID:26203765"^^xsd:string, "PMID:26238769"^^xsd:string, + "PMID:37359384"^^xsd:string, + "PMID:37648560"^^xsd:string, + "PMID:37755126"^^xsd:string, + "PPDB:681"^^xsd:string, "Reaxys:1293536"^^xsd:string, "Wikipedia:Warfarin"^^xsd:string ; rdfs:label "warfarin"^^xsd:string ; @@ -17258,25 +17275,33 @@ CHEBI:10033 a owl:Class ; [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:55347 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C19H16O4"^^xsd:string ; + chebi:mass "308.333"^^xsd:string ; + chebi:monoisotopicmass "308.10486"^^xsd:string ; oboInOwl:hasExactSynonym "rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "1-(4'-Hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, - "2H-1-Benzopyran-2-one, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-"^^xsd:string, - "3-(1'-Phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, - "3-(Acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, - "3-(Alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, - "3-(alpha-Phenyl-beta-acetylaethyl)-4-hydroxycumarin"^^xsd:string, - "3-(alpha-Phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, - "4-Hydroxy-3-(3-oxo-1-phenyl-butyl)-cumarin"^^xsd:string, - "4-Hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, - "(+/-)-Warfarin"^^xsd:string, - "(Phenyl-1 acetyl-2 ethyl) 3-hydroxy-4 coumarine"^^xsd:string, - "(RS)-Warfarin"^^xsd:string, + oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string, + "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, + "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]coumarin"^^xsd:string, + "(+-)-warfarin"^^xsd:string, + "(RS)-warfarin"^^xsd:string, + "Brumolin"^^xsd:string, "Coumafene"^^xsd:string, "DL-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, "DL-warfarin"^^xsd:string, + "Kumadu"^^xsd:string, + "Kumatox"^^xsd:string, + "rac-1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, + "rac-3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, "rac-warfarin"^^xsd:string, "racemic warfarin"^^xsd:string, + "Ratron"^^xsd:string, + "Rodafarin"^^xsd:string, "Warf 10"^^xsd:string, "warfarin"^^xsd:string, "warfarina"^^xsd:string, @@ -21323,7 +21348,10 @@ CHEBI:16134 a owl:Class ; owl:someValuesFrom CHEBI:77941 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:78433 ] ; + owl:someValuesFrom CHEBI:78433 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "H3N"^^xsd:string ; chebi:inchi "InChI=1S/H3N/h1H3"^^xsd:string ; @@ -27304,7 +27332,7 @@ CHEBI:17135 a owl:Class ; "PMID:22436224"^^xsd:string, "PMID:22444994"^^xsd:string ; rdfs:label "long-chain fatty alcohol"^^xsd:string ; - definition: "A fatty alcohol with a chain length ranging from C13-C23."^^xsd:string ; + definition: "A fatty alcohol with a chain length ranging from C13 to C22."^^xsd:string ; rdfs:subClassOf CHEBI:24026 ; chebi:charge "0"^^xsd:string ; chebi:formula "HOR"^^xsd:string ; @@ -31006,8 +31034,7 @@ CHEBI:17824 a owl:Class ; "YMDB:YMDB01718"^^xsd:string ; rdfs:label "propan-2-ol"^^xsd:string ; definition: "A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group."^^xsd:string ; - rdfs:subClassOf CHEBI:35681, - CHEBI:167095, + rdfs:subClassOf CHEBI:167095, [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:48356 ] ; @@ -32064,15 +32091,14 @@ CHEBI:18140 a owl:Class ; chebi:formula "HX"^^xsd:string ; chebi:mass "1.008"^^xsd:string ; chebi:monoisotopicmass "1.00783"^^xsd:string ; - chebi:smiles "[F,Cl,Br,I]"^^xsd:string ; + chebi:smiles "*[H]"^^xsd:string ; oboInOwl:hasAlternativeId "CHEBI:5599"^^xsd:string, "CHEBI:13368"^^xsd:string, "CHEBI:37140"^^xsd:string ; oboInOwl:hasExactSynonym "hydrogen halide"^^xsd:string, "hydrogen halides"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "HX"^^xsd:string, - "hydrogen halides"^^xsd:string ; + oboInOwl:hasRelatedSynonym "hydrogen halides"^^xsd:string ; oboInOwl:id "CHEBI:18140"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -35674,7 +35700,8 @@ CHEBI:24026 a owl:Class ; chebi:smiles "O[*]"^^xsd:string ; oboInOwl:hasExactSynonym "fatty alcohol"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "alcool gras"^^xsd:string, + oboInOwl:hasRelatedSynonym "a fatty alcohol"^^xsd:string, + "alcool gras"^^xsd:string, "fatty alcohols"^^xsd:string, "Fettalkohol"^^xsd:string, "Fettalkohole"^^xsd:string ; @@ -38547,7 +38574,10 @@ CHEBI:26078 a owl:Class ; owl:someValuesFrom CHEBI:77746 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:84735 ] ; + owl:someValuesFrom CHEBI:84735 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "H3O4P"^^xsd:string ; chebi:inchi "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)"^^xsd:string ; @@ -42136,6 +42166,9 @@ CHEBI:27870 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:has_functional_parent ; owl:someValuesFrom CHEBI:15956 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:195545 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:75771 ] ; @@ -46500,6 +46533,9 @@ CHEBI:29073 a owl:Class ; [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:77962 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:78006 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:85046 ], @@ -52477,6 +52513,9 @@ CHEBI:32550 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:18019 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_conjugate_base_of ; + owl:someValuesFrom CHEBI:133538 ], [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:194466 ], @@ -53412,7 +53451,7 @@ CHEBI:32644 a owl:Class ; CHEBI:32646 a owl:Class ; oboInOwl:hasDbXref "Gmelin:326567"^^xsd:string ; rdfs:label "methioninium"^^xsd:string ; - definition: "A sulfur-containing amino-acid anion that is the conjugate acid of methionine, arising from protonation of the amino group."^^xsd:string ; + definition: "A sulfur-containing amino-acid cation that is the conjugate acid of methionine, arising from protonation of the amino group."^^xsd:string ; rdfs:subClassOf CHEBI:33719, [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_acid_of ; @@ -57569,12 +57608,19 @@ CHEBI:33709 a owl:Class ; CHEBI:33710 a owl:Class ; rdfs:label "alpha-amino-acid residue"^^xsd:string ; + definition: "An amino-acid residue derived from an alpha-amino acid."^^xsd:string ; rdfs:subClassOf CHEBI:33708, [ a owl:Restriction ; owl:onProperty chebi2:is_substituent_group_from ; owl:someValuesFrom CHEBI:33704 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C2H2NOR"^^xsd:string ; + chebi:mass "56.043"^^xsd:string ; + chebi:monoisotopicmass "56.01364"^^xsd:string ; + chebi:smiles "*-NC([*])C(-*)=O"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "alpha-amino-acid residues"^^xsd:string ; + oboInOwl:hasRelatedSynonym "alpha-amino-acid residues"^^xsd:string, + "an alpha-amino acid residue"^^xsd:string ; oboInOwl:id "CHEBI:33710"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -58508,7 +58554,10 @@ CHEBI:34856 a owl:Class ; CHEBI:38785, [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; - owl:someValuesFrom CHEBI:167868 ] ; + owl:someValuesFrom CHEBI:167868 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C4H9NO"^^xsd:string ; chebi:inchi "InChI=1S/C4H9NO/c1-3-6-4-2-5-1/h5H,1-4H2"^^xsd:string ; @@ -63770,6 +63819,7 @@ CHEBI:36791 a owl:Class ; "PMID:24424469"^^xsd:string, "PMID:24469525"^^xsd:string, "PMID:24528284"^^xsd:string, + "PMID:34406668"^^xsd:string, "Wikipedia:Escitalopram"^^xsd:string ; rdfs:label "escitalopram"^^xsd:string ; definition: "A 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile that has S-configuration at the chiral centre. It is the active enantiomer of citalopram."^^xsd:string ; @@ -63886,7 +63936,10 @@ CHEBI:36810 a owl:Class ; owl:someValuesFrom CHEBI:46787 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:78298 ] ; + owl:someValuesFrom CHEBI:78298 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C7H5F3"^^xsd:string ; chebi:inchi "InChI=1S/C7H5F3/c8-7(9,10)6-4-2-1-3-5-6/h1-5H"^^xsd:string ; @@ -73324,7 +73377,8 @@ CHEBI:46766 a owl:Class ; CHEBI:46767 a owl:Class ; rdfs:label "pyrrolidinecarboxylic acid"^^xsd:string ; - rdfs:subClassOf CHEBI:38260 ; + rdfs:subClassOf CHEBI:33575, + CHEBI:38260 ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "pyrrolidinecarboxylic acids"^^xsd:string ; oboInOwl:id "CHEBI:46767"^^xsd:string ; @@ -96360,6 +96414,22 @@ CHEBI:78000 a owl:Class ; oboInOwl:id "CHEBI:78000"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . +CHEBI:78006 a owl:Class ; + oboInOwl:hasDbXref "Wikipedia:Colour_retention_agent"^^xsd:string ; + rdfs:label "food colour retention agent"^^xsd:string ; + definition: "A food additive that intensifies, retains or stabilises the colour of a food."^^xsd:string ; + rdfs:subClassOf CHEBI:64047 ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "color retention agent"^^xsd:string, + "color retention agents"^^xsd:string, + "colour retention agent"^^xsd:string, + "colour retention agents"^^xsd:string, + "food color retention agent"^^xsd:string, + "food color retention agents"^^xsd:string, + "food colour retention agents"^^xsd:string ; + oboInOwl:id "CHEBI:78006"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + CHEBI:78016 a owl:Class ; rdfs:label "food gelling agent"^^xsd:string ; definition: "A food additive that enhances the texture of a foodstuff by gel formation."^^xsd:string ; @@ -97515,8 +97585,7 @@ CHEBI:83813 a owl:Class ; oboInOwl:hasDbXref "Wikipedia:Proteinogenic_amino_acid"^^xsd:string ; rdfs:label "proteinogenic amino acid"^^xsd:string ; definition: "Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration."^^xsd:string ; - rdfs:subClassOf CHEBI:33575, - CHEBI:35352 ; + rdfs:subClassOf CHEBI:33709 ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "canonical amino acid"^^xsd:string, "canonical amino acids"^^xsd:string, @@ -98575,11 +98644,10 @@ CHEBI:87635 a owl:Class ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87732 a owl:Class ; - oboInOwl:hasDbXref "LINCS:LSM-1405"^^xsd:string, - "PPDB:681"^^xsd:string ; rdfs:label "4-hydroxy-3-(3-oxo-1-phenylbutyl)-1-benzopyran-2-one"^^xsd:string ; definition: "A member of the class of coumarins that is 4-hydroxycoumarin which is substituted at position 3 by a 1-phenyl-3-oxo-1-butyl group."^^xsd:string ; - rdfs:subClassOf CHEBI:37912, + rdfs:subClassOf CHEBI:22712, + CHEBI:37912, CHEBI:51867 ; chebi:charge "0"^^xsd:string ; chebi:formula "C19H16O4"^^xsd:string ; @@ -98588,13 +98656,25 @@ CHEBI:87732 a owl:Class ; chebi:mass "308.329"^^xsd:string ; chebi:monoisotopicmass "308.10486"^^xsd:string ; chebi:smiles "C1=CC=CC2=C1C(=C(C(O2)=O)C(CC(C)=O)C3=CC=CC=C3)O"^^xsd:string ; - oboInOwl:hasExactSynonym "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string ; + oboInOwl:hasExactSynonym "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, + "2H-1-Benzopyran-2-one, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-"^^xsd:string, + "3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "3-(acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "3-(alpha-phenyl-beta-acetylaethyl)-4-hydroxycumarin"^^xsd:string, + "3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "4-Hydroxy-3-(3-oxo-1-phenyl-butyl)-cumarin"^^xsd:string, + "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, + "4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, + "(Phenyl-1 acetyl-2 ethyl) 3-hydroxy-4 coumarine"^^xsd:string ; oboInOwl:id "CHEBI:87732"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87737 a owl:Class ; oboInOwl:hasDbXref "CAS:5543-58-8"^^xsd:string, + "DrugBank:DB08496"^^xsd:string, "PDBeChem:RWF"^^xsd:string, "PMID:7354137"^^xsd:string, "PMID:21949493"^^xsd:string, @@ -98602,6 +98682,11 @@ CHEBI:87737 a owl:Class ; "PMID:24962085"^^xsd:string, "PMID:26142522"^^xsd:string, "PMID:26161443"^^xsd:string, + "PMID:28735507"^^xsd:string, + "PMID:31608877"^^xsd:string, + "PMID:34579096"^^xsd:string, + "PMID:37122027"^^xsd:string, + "PMID:37598356"^^xsd:string, "Reaxys:4298023"^^xsd:string ; rdfs:label "(R)-warfarin"^^xsd:string ; definition: "A 4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one that has (R)-configuration (the racemate is warfarin, an anticoagulant drug and rodenticide)."^^xsd:string ; @@ -98623,15 +98708,21 @@ CHEBI:87737 a owl:Class ; oboInOwl:hasExactSynonym "4-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, + "(+)-(R)-warfarin"^^xsd:string, "(+)-warfarin"^^xsd:string, - "(R)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, - "(R)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, - "Dextrowarfarin"^^xsd:string ; + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string, + "(R)-(+)-warfarin"^^xsd:string, + "Dextrowarfarin"^^xsd:string, + "R-wafarin"^^xsd:string ; oboInOwl:id "CHEBI:87737"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87738 a owl:Class ; oboInOwl:hasDbXref "CAS:5543-57-7"^^xsd:string, + "DrugBank:DB14055"^^xsd:string, + "KEGG:C20129"^^xsd:string, "LINCS:LSM-5404"^^xsd:string, "PDBeChem:SWF"^^xsd:string, "PMID:7354137"^^xsd:string, @@ -98640,6 +98731,17 @@ CHEBI:87738 a owl:Class ; "PMID:24962085"^^xsd:string, "PMID:26142522"^^xsd:string, "PMID:26161443"^^xsd:string, + "PMID:29433307"^^xsd:string, + "PMID:32601017"^^xsd:string, + "PMID:32680916"^^xsd:string, + "PMID:33341662"^^xsd:string, + "PMID:33754183"^^xsd:string, + "PMID:34579970"^^xsd:string, + "PMID:35426132"^^xsd:string, + "PMID:35699912"^^xsd:string, + "PMID:35798369"^^xsd:string, + "PMID:36914276"^^xsd:string, + "PMID:37598356"^^xsd:string, "Reaxys:4298024"^^xsd:string ; rdfs:label "(S)-warfarin"^^xsd:string ; definition: "A 4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one that has (S)-configuration (the racemate is warfarin, an anticoagulant drug and rodenticide)."^^xsd:string ; @@ -98661,9 +98763,12 @@ CHEBI:87738 a owl:Class ; oboInOwl:hasExactSynonym "4-hydroxy-3-[(1S)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1S)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, - "(-)-Warfarin"^^xsd:string, - "(S)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, - "levrowarfarin"^^xsd:string ; + "(-)-warfarin"^^xsd:string, + "(S)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, + "(S)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string, + "(S)-(-)-warfarin"^^xsd:string, + "levrowarfarin"^^xsd:string, + "S-warfarin"^^xsd:string ; oboInOwl:id "CHEBI:87738"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -99089,9 +99194,11 @@ CHEBI:90709 a owl:Class ; oboInOwl:inSubset chebi3:_STAR . CHEBI:90710 a owl:Class ; + oboInOwl:hasDbXref "Wikipedia:Receptor_modulator"^^xsd:string ; rdfs:label "receptor modulator"^^xsd:string ; definition: "A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors."^^xsd:string ; rdfs:subClassOf CHEBI:23888 ; + oboInOwl:hasAlternativeId "CHEBI:189678"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "receptor modulators"^^xsd:string ; oboInOwl:id "CHEBI:90710"^^xsd:string ; @@ -100315,6 +100422,9 @@ CHEBI:133538 a owl:Class ; rdfs:label "L-lysine zwitterion"^^xsd:string ; definition: "An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-lysine; major species at pH 7.3."^^xsd:string ; rdfs:subClassOf CHEBI:59869, + [ a owl:Restriction ; + owl:onProperty chebi2:is_conjugate_acid_of ; + owl:someValuesFrom CHEBI:32550 ], [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:32551 ], @@ -102628,7 +102738,8 @@ CHEBI:167055 a owl:Class ; CHEBI:167095 a owl:Class ; rdfs:label "secondary fatty alcohol"^^xsd:string ; definition: "A fatty alcohol consisting of a chain of 3 to greater than 27 carbon atoms in which a hydroxy group is attached to a saturated carbon atom different from the terminal carbons. Secondary fatty alcohols may be saturated or unsaturated and may be branched or unbranched."^^xsd:string ; - rdfs:subClassOf CHEBI:24026 ; + rdfs:subClassOf CHEBI:24026, + CHEBI:35681 ; chebi:charge "0"^^xsd:string ; chebi:formula "CH2OR2"^^xsd:string ; chebi:mass "30.026"^^xsd:string ; @@ -103758,6 +103869,64 @@ CHEBI:195233 a owl:Class ; oboInOwl:id "CHEBI:195233"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . +CHEBI:195544 a owl:Class ; + oboInOwl:hasDbXref "MetaCyc:CPD-5583"^^xsd:string ; + rdfs:label "aspartame zwitterion"^^xsd:string ; + definition: "A dipeptide zwitterion resulting from transfer of a proton from the carboxy to the amino group of aspartame; major species at pH 7.3."^^xsd:string ; + rdfs:subClassOf CHEBI:90799, + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:2877 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C14H18N2O5"^^xsd:string ; + chebi:inchi "InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1"^^xsd:string ; + chebi:inchikey "IAOZJIPTCAWIRG-QWRGUYRKSA-N"^^xsd:string ; + chebi:mass "294.307"^^xsd:string ; + chebi:monoisotopicmass "294.12157"^^xsd:string ; + chebi:smiles "COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@@H]([NH3+])CC([O-])=O"^^xsd:string ; + oboInOwl:hasExactSynonym "(3S)-3-azaniumyl-4-{[(2S)-1-methoxy-1-oxo-3-phenylpropan-2-yl]amino}-4-oxobutanoate"^^xsd:string ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "aspartame"^^xsd:string ; + oboInOwl:id "CHEBI:195544"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + +CHEBI:195545 a owl:Class ; + oboInOwl:hasDbXref "MetaCyc:CPD-17700"^^xsd:string ; + rdfs:label "biocytin zwitterion"^^xsd:string ; + definition: "An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of biocytin; major species at pH 7.3."^^xsd:string ; + rdfs:subClassOf CHEBI:59869, + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:27870 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C16H28N4O4S"^^xsd:string ; + chebi:inchi "InChI=1S/C16H28N4O4S/c17-10(15(22)23)5-3-4-8-18-13(21)7-2-1-6-12-14-11(9-25-12)19-16(24)20-14/h10-12,14H,1-9,17H2,(H,18,21)(H,22,23)(H2,19,20,24)/t10-,11-,12-,14-/m0/s1"^^xsd:string ; + chebi:inchikey "BAQMYDQNMFBZNA-MNXVOIDGSA-N"^^xsd:string ; + chebi:mass "372.480"^^xsd:string ; + chebi:monoisotopicmass "372.18313"^^xsd:string ; + chebi:smiles "[H][C@]12CS[C@@H](CCCCC(=O)NCCCC[C@H]([NH3+])C([O-])=O)[C@@]1([H])NC(=O)N2"^^xsd:string ; + oboInOwl:hasExactSynonym "(2S)-2-azaniumyl-6-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoate"^^xsd:string ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "biocytin"^^xsd:string ; + oboInOwl:id "CHEBI:195545"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + +CHEBI:228364 a owl:Class ; + rdfs:label "NMR chemical shift reference compound"^^xsd:string ; + definition: "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing."^^xsd:string ; + rdfs:subClassOf CHEBI:33232, + CHEBI:51086 ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "NMR chemical shift reference compounds"^^xsd:string, + "NMR chemical shift standard"^^xsd:string, + "NMR chemical shift standards"^^xsd:string, + "NMR internal standard"^^xsd:string, + "NMR internal standards"^^xsd:string, + "NMR reference standard"^^xsd:string, + "NMR reference standards"^^xsd:string ; + oboInOwl:id "CHEBI:228364"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + CHEBI:237958 a owl:Class ; rdfs:label "({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(9H-purin-9-yl)oxolan-2-yl]methyl phosphonato}oxy)(phosphonatooxy)phosphinate"^^xsd:string ; rdfs:subClassOf CHEBI:37045, @@ -104273,4 +104442,4 @@ CHEBI:616459 a owl:Class ; oboInOwl:id "CHEBI:616459"^^xsd:string ; oboInOwl:inSubset chebi1:_STAR . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2 diff --git a/ttl/generated/ncbigeneslim.ttl b/ttl/generated/ncbigeneslim.ttl index db72eb68..3b8008a1 100644 --- a/ttl/generated/ncbigeneslim.ttl +++ b/ttl/generated/ncbigeneslim.ttl @@ -12,7 +12,7 @@ rdfs:label "NIF NCBI Gene subset" ; skos:altLabel "ncbigeneslim" ; rdfs:comment "This subset is automatically generated from the NCBI Gene database on a subset of terms listed in /home/tom/git/pyontutils/nifstd/resources/gene-subset-ids.txt." ; - owl:versionInfo "2023-07-26" . + owl:versionInfo "2024-01-26" . ### Classes @@ -2609,6 +2609,7 @@ NCBIGene:13405 a owl:Class ; "dystrophin", "dystrophin delta-E40e", "dystrophin Dp71d(delta71,73-74)", + "dystrophin Dp71f-delta71,74", "dystrophin Dp427-E40e", "dystrophin E40e", "dystrophin E51b", @@ -4435,7 +4436,8 @@ NCBIGene:15242 a owl:Class ; "homeobox protein PRH", "mHex", "Prh", - "Prhx" ; + "Prhx", + "proline-rich homeodomain protein" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -6163,10 +6165,12 @@ NCBIGene:17476 a owl:Class ; skos:prefLabel "macrophage expressed gene 1" ; NIFRID:synonym "macrophage gene 1 protein", "macrophage-expressed gene 1 protein", + "mPFN2", "Mpg-1", "MPS1", "P-2", - "perforin-2" ; + "perforin-2", + "PFN2" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -7711,11 +7715,12 @@ NCBIGene:19141 a owl:Class ; NCBIGene:19142 a owl:Class ; rdfs:label "Prss12" ; - skos:prefLabel "protease, serine 12 neurotrypsin (motopsin)" ; + skos:prefLabel "serine protease 12 neurotrypsin (motopsin)" ; NIFRID:synonym "brain-specific serine protease 3", "Bssp-3", "motopsin", "neurotrypsin", + "protease, serine 12 neurotrypsin (motopsin)", "serine protease 12" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -8181,7 +8186,7 @@ NCBIGene:19701 a owl:Class ; NCBIGene:19704 a owl:Class ; rdfs:label "Upf1" ; - skos:prefLabel "UPF1 regulator of nonsense transcripts homolog (yeast)" ; + skos:prefLabel "UPF1 RNA helicase and ATPase" ; NIFRID:synonym "ATP-dependent helicase RENT1", "B430202H16Rik", "NORF1", @@ -8189,6 +8194,7 @@ NCBIGene:19704 a owl:Class ; "regulator of nonsense transcripts 1", "regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog)", "Rent1", + "UPF1 regulator of nonsense transcripts homolog", "Upflp" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -9098,7 +9104,11 @@ NCBIGene:20670 a owl:Class ; rdfs:label "Sox15" ; skos:prefLabel "SRY (sex determining region Y)-box 15" ; NIFRID:synonym "protein SOX-15", - "SRY-box containing gene 15" ; + "protein SOX-16", + "Sox16", + "SRY (sex determining region Y)-box 16", + "SRY-box containing gene 15", + "SRY-box containing gene 16" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -10032,8 +10042,9 @@ NCBIGene:22139 a owl:Class ; NCBIGene:22158 a owl:Class ; rdfs:label "Tulp3" ; - skos:prefLabel "tubby-like protein 3" ; + skos:prefLabel "TUB like protein 3" ; NIFRID:synonym "2310022L06Rik", + "tubby-like protein 3", "tubby-related protein 3" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -10552,12 +10563,12 @@ NCBIGene:23871 a owl:Class ; ilxtr:definedForTaxon NCBITaxon:10090 . NCBIGene:23880 a owl:Class ; - rdfs:label "Fyb" ; - skos:prefLabel "FYN binding protein" ; + rdfs:label "Fyb1" ; + skos:prefLabel "FYN binding protein 1" ; NIFRID:synonym "ADAP", "adhesion and degranulation promoting adaptor protein", "B630013F22Rik", - "Fyb1", + "Fyb", "FYB-120/130", "FYN binding protein FYB-130", "FYN-binding protein 1", @@ -13077,7 +13088,7 @@ NCBIGene:66700 a owl:Class ; NCBIGene:66713 a owl:Class ; rdfs:label "Actr2" ; - skos:prefLabel "ARP2 actin-related protein 2" ; + skos:prefLabel "actin related protein 2" ; NIFRID:synonym "4921510D23Rik", "actin-like protein 2", "actin-related protein 2", @@ -15533,7 +15544,7 @@ NCBIGene:104681 a owl:Class ; NCBIGene:104759 a owl:Class ; rdfs:label "Pld4" ; - skos:prefLabel "phospholipase D family, member 4" ; + skos:prefLabel "phospholipase D family member 4" ; NIFRID:synonym "5'-3' exonuclease PLD4", "choline phosphatase 4", "phosphatidylcholine-hydrolyzing phospholipase D4", @@ -15550,6 +15561,7 @@ NCBIGene:104776 a owl:Class ; "aldehyde dehydrogenase family 6 member A1", "malonate-semialdehyde dehydrogenase", "methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial", + "methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial", "Mmsdh" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -16862,7 +16874,7 @@ NCBIGene:214855 a owl:Class ; NCBIGene:215819 a owl:Class ; rdfs:label "Nhsl1" ; - skos:prefLabel "NHS-like 1" ; + skos:prefLabel "NHS like 1" ; NIFRID:synonym "5730409E15Rik", "A630035H13Rik", "A730096F01", @@ -17891,7 +17903,8 @@ NCBIGene:242202 a owl:Class ; NCBIGene:242274 a owl:Class ; rdfs:label "Lrrc7" ; skos:prefLabel "leucine rich repeat containing 7" ; - NIFRID:synonym "densin", + NIFRID:synonym "B230334C09Rik", + "densin", "densin 180", "leucine-rich repeat-containing protein 7", "mKIAA1365" ; @@ -18460,4 +18473,4 @@ NCBIGene:102632117 a owl:Class ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2