From 5c46dfc7cc8972c447fed22b4fe4675157161567 Mon Sep 17 00:00:00 2001 From: William Hogan Date: Tue, 20 Feb 2024 17:54:23 -0600 Subject: [PATCH] updating files for release 2024-02-20 --- docs/highest-id-by-release.md | 1 + docs/release-counts.md | 3 +- src/ontology/dron-edit.owl | 97 +++-- src/ontology/imports/apollo_sv_import.owl | 4 +- src/ontology/imports/bfo_import.owl | 4 +- src/ontology/imports/chebi_import.owl | 430 ++++++++++++++++++- src/ontology/imports/go_import.owl | 6 +- src/ontology/imports/obi_import.owl | 6 +- src/ontology/imports/ogms_import.owl | 4 +- src/ontology/imports/omo_import.owl | 4 +- src/ontology/imports/pr_import.owl | 115 ++++- src/ontology/imports/ro_import.owl | 73 +++- src/ontology/mappings/dron-chebi-mapping.csv | 6 +- 13 files changed, 636 insertions(+), 117 deletions(-) diff --git a/docs/highest-id-by-release.md b/docs/highest-id-by-release.md index e3e8def..da27686 100644 --- a/docs/highest-id-by-release.md +++ b/docs/highest-id-by-release.md @@ -1,5 +1,6 @@ | release | highest id | | --- | --- | +| v2024-02-20 | DRON_00996982 | | v2023-08-17 | DRON_00991305 | | v2023-06-11 | DRON_00984401 | | v2023-05-19 | DRON_00984401 | diff --git a/docs/release-counts.md b/docs/release-counts.md index db5be10..2d0faa4 100644 --- a/docs/release-counts.md +++ b/docs/release-counts.md @@ -9,4 +9,5 @@ | v2023-03-09 | 2022-12 | 7295 | 4001 | 89619 | 565361 | | v2023-05-19 | 2023-03 | 7304 | 4017 | 89648 | 571025 | | v2023-06-11 | 2023-03 | 7318 | 3323 | 89648 | 571025 | -| v2023-08-17 | 2023-06 | 7322 | 3333 | 89879 | 577594 | +| v2023-08-17 | 2023-06 | 7322 | 3333 | 89879 | 577594 | +| v2024-02-20 | 2023-09 | 7344 | 4053 | 90155 | 582913 | diff --git a/src/ontology/dron-edit.owl b/src/ontology/dron-edit.owl index 440f893..618ccc0 100644 --- a/src/ontology/dron-edit.owl +++ b/src/ontology/dron-edit.owl @@ -354,7 +354,7 @@ AnnotationAssertion(rdfs:label "has_exact_synonym") -# Annotation Property: (has_narrow_synonym) +# Annotation Property: (has narrow synonym) AnnotationAssertion(rdfs:label "has_narrow_synonym") @@ -458,7 +458,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Nordazepam) +# Class: (nordazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -470,43 +470,43 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Metaclazepam hydrochloride) +# Class: (metaclazepam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Ephedrine) +# Class: ((-)-ephedrine) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Cortisone) +# Class: (cortisone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Hydrocortisone) +# Class: (cortisol) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Alprazolam) +# Class: (alprazolam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Caffeine) +# Class: (caffeine) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Theophylline) +# Class: (theophylline) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Beclomethasone) +# Class: (beclomethasone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Bendroflumethiazide) +# Class: (bendroflumethiazide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Betamethasone) +# Class: (betamethasone) SubClassOf( ObjectSomeValuesFrom( )) @@ -514,11 +514,11 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (brotizolam) +# Class: (Brotizolam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (ciclesonide) +# Class: (Ciclesonide) SubClassOf( ObjectSomeValuesFrom( )) @@ -526,7 +526,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (clotiazepam) +# Class: (Clotiazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -538,7 +538,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Flunitrazepam) +# Class: (flunitrazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -546,11 +546,11 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Budesonide) +# Class: (budesonide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Chlordiazepoxide) +# Class: (chlordiazepoxide) SubClassOf( ObjectSomeValuesFrom( )) @@ -558,35 +558,35 @@ SubClassOf( ObjectSomeValuesFrom( ) -# Class: (Chlorothiazide) +# Class: (chlorothiazide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Chlorthalidone) +# Class: (chlorthalidone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Clonazepam) +# Class: (clonazepam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Dexamethasone) +# Class: (dexamethasone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Dyphylline) +# Class: (dyphylline) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Estazolam) +# Class: (estazolam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Ethacrynate) +# Class: (etacrynic acid) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Diazepam) +# Class: (diazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -598,7 +598,7 @@ SubClassOf( ObjectSomeValuesFrom( ) -# Class: (Flumazenil) +# Class: (flumazenil) SubClassOf( ObjectSomeValuesFrom( )) @@ -606,7 +606,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Flurazepam) +# Class: (flurazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -618,35 +618,35 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Lorazepam) +# Class: (lormetazepam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (halazepam) +# Class: (Halazepam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Hydrochlorothiazide) +# Class: (hydrochlorothiazide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Hydroflumethiazide) +# Class: (hydroflumethiazide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Indapamide) +# Class: (indapamide) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Ipratropium) +# Class: (ipratropium) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (clorazepate) +# Class: (clorazepic acid anion) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Metolazone) +# Class: (metolazone) SubClassOf( ObjectSomeValuesFrom( )) @@ -658,23 +658,23 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Methylprednisolone) +# Class: (6alpha-methylprednisolone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Midazolam) +# Class: (midazolam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Mometasone) +# Class: (mometasone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Meclofenamate) +# Class: (meclofenamic acid(1-)) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Oxazepam) +# Class: (oxazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -686,11 +686,11 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Prednisone) +# Class: (prednisone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (quazepam) +# Class: (Quazepam) SubClassOf( ObjectSomeValuesFrom( )) @@ -698,7 +698,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Levalbuterol) +# Class: ((R)-salbutamol) SubClassOf( ObjectSomeValuesFrom( )) @@ -706,19 +706,19 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) -# Class: (Terbutaline) +# Class: (terbutaline) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Triamcinolone) +# Class: (triamcinolone) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Triazolam) +# Class: (triazolam) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (Trichlormethiazide) +# Class: (trichlormethiazide) SubClassOf( ObjectSomeValuesFrom( )) @@ -1001,7 +1001,6 @@ AnnotationAssertion( "drug product therapeutic function"@en) SubClassOf( ) SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) # Class: (anti-malarial function of a drug product) diff --git a/src/ontology/imports/apollo_sv_import.owl b/src/ontology/imports/apollo_sv_import.owl index 3f80f05..b9bc6a5 100644 --- a/src/ontology/imports/apollo_sv_import.owl +++ b/src/ontology/imports/apollo_sv_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-12-15") +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index 6526f8f..6db0790 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-12-15") +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index 0849a4a..d289758 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-12-15") + +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) @@ -667,6 +667,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1599,6 +1600,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1610,6 +1612,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6630,6 +6637,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13979,6 +13987,7 @@ AnnotationAssertion( "L-lysine zwitterion") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -24378,6 +24387,28 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (neurokinin-3 receptor antagonist) + +AnnotationAssertion( "An antagonist at the neurokinin-3 receptor.") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:25107588") +AnnotationAssertion( "Wikipedia:Tachykinin_receptor_3") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "NK-3 receptor antagonist") +AnnotationAssertion(Annotation( "ChEBI") "NK-3 receptor antagonists") +AnnotationAssertion(Annotation( "ChEBI") "NK3 receptor antagonist") +AnnotationAssertion(Annotation( "ChEBI") "NK3 receptor antagonists") +AnnotationAssertion(Annotation( "ChEBI") "NK3R antagonist") +AnnotationAssertion(Annotation( "ChEBI") "NK3R antagonists") +AnnotationAssertion(Annotation( "ChEBI") "TACR3 antagonist") +AnnotationAssertion(Annotation( "ChEBI") "TACR3 antagonists") +AnnotationAssertion(Annotation( "ChEBI") "neurokinin-3 receptor antagonists") +AnnotationAssertion(Annotation( "ChEBI") "tachykinin receptor 3 antagonist") +AnnotationAssertion(Annotation( "ChEBI") "tachykinin receptor 3 antagonists") +AnnotationAssertion( "CHEBI:140482") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "neurokinin-3 receptor antagonist") +SubClassOf( ) + # Class: (tropomyosin-related kinase B receptor agonist) AnnotationAssertion( "An agonist that binds to and deactivates the tropomyosin-related kinase B (TrkB) receptor, the main signaling receptor of the neurotrophin brain-derived neurotrophic factor (BDNF).") @@ -34516,6 +34547,7 @@ AnnotationAssertion(rdfs:label "amm SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44426,6 +44458,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectin") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50747,14 +50780,13 @@ AnnotationAssertion( "HX") AnnotationAssertion( "1.008") AnnotationAssertion( "1.00783") -AnnotationAssertion( "[F,Cl,Br,I]") +AnnotationAssertion( "*[H]") AnnotationAssertion( "CHEBI:13368") AnnotationAssertion( "CHEBI:37140") AnnotationAssertion( "CHEBI:5599") AnnotationAssertion(Annotation( "IUPAC") "hydrogen halide") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogen halides") AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "UniProt") "HX") AnnotationAssertion(Annotation( "ChEBI") "hydrogen halides") AnnotationAssertion( "CHEBI:18140") AnnotationAssertion( ) @@ -56994,6 +57026,23 @@ AnnotationAssertion(rdfs:label "bet SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (NMR chemical shift reference compound) + +AnnotationAssertion( "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift reference compounds") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standards") +AnnotationAssertion( "CHEBI:228364") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "NMR chemical shift reference compound") +SubClassOf( ) +SubClassOf( ) + # Class: (amino-acid betaine) AnnotationAssertion( "Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries methyl substituents and bears no hydrogen atoms.") @@ -57138,6 +57187,278 @@ AnnotationAssertion(rdfs:label "bra SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (pirtobrutinib) + +AnnotationAssertion( "A secondary carboxamide resulting from the formal condensation of the carboxy group of 5-fluoro-2-methoxybenzoic acid with the amino group of 5-amino-3-[4-(aminomethyl)phenyl]-1-[(2S)-1,1,1-trifluoropropan-2-yl]-1H-pyrazole-4-carboxamide. It is a BTK inhibitor used for the treatment of adult patients with chronic lymphocytic leukemia or small lymphocytic lymphoma.") +AnnotationAssertion( "0") +AnnotationAssertion( "C22H21F4N5O3") +AnnotationAssertion( "InChI=1S/C22H21F4N5O3/c1-11(22(24,25)26)31-19(27)17(20(28)32)18(30-31)13-5-3-12(4-6-13)10-29-21(33)15-9-14(23)7-8-16(15)34-2/h3-9,11H,10,27H2,1-2H3,(H2,28,32)(H,29,33)/t11-/m0/s1") +AnnotationAssertion( "FWZAWAUZXYCBKZ-NSHDSACASA-N") +AnnotationAssertion( "479.436") +AnnotationAssertion( "479.15805") +AnnotationAssertion( "COC1=C(C=C(F)C=C1)C(=O)NCC1=CC=C(C=C1)C1=NN([C@@H](C)C(F)(F)F)C(N)=C1C(N)=O") +AnnotationAssertion(Annotation( "KEGG DRUG") "CAS:2101700-15-4") +AnnotationAssertion( "Chemspider:114875989") +AnnotationAssertion( "DrugBank:DB17472") +AnnotationAssertion( "KEGG:D12050") +AnnotationAssertion( "PDBeChem:Y7W") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10428413") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10429556") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10430907") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10431003") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10431162") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35196427") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35389384") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35747462") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35901282") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36287227") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36475521") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36519322") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36780414") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36796019") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36877244") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36960657") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37004673") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37156004") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37174062") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37192437") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37407001") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37509309") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37530617") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37624619") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37658026") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37818564") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38031799") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38043933") +AnnotationAssertion( "Wikipedia:Pirtobrutinib") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "5-amino-3-{4-[(5-fluoro-2-methoxybenzamido)methyl]phenyl}-1-[(2S)-1,1,1-trifluoropropan-2-yl]-1H-pyrazole-4-carboxamide") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "DrugBank") Annotation( ) "Jaypirca") +AnnotationAssertion(Annotation( "ChEBI") "LOXO 305") +AnnotationAssertion(Annotation( "DrugBank") "LOXO-305") +AnnotationAssertion(Annotation( "ChEBI") "LY 3527727") +AnnotationAssertion(Annotation( "DrugBank") "LY-3527727") +AnnotationAssertion(Annotation( "DrugBank") "LY3527727") +AnnotationAssertion(Annotation( "DrugBank") "RXC-005") +AnnotationAssertion(Annotation( "ChEBI") "RXC005") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "pirtobrutinib") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "pirtobrutinibum") +AnnotationAssertion( "CHEBI:229212") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pirtobrutinib") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (bexagliflozin) + +AnnotationAssertion( "A C-glycosyl comprising of beta-D-glucose in which the anomeric hydroxy group is replaced by a 4-chloro-3-({4-[2-(cyclopropyloxy)ethoxy]phenyl}methyl)phenyl group. It is a sodium-glucose co-transporter 2 (SGLT2) inhibitor indicated as an adjunct to diet and exercise to improve glycemic control in adults with type 2 diabetes mellitus.") +AnnotationAssertion( "0") +AnnotationAssertion( "C24H29ClO7") +AnnotationAssertion( "InChI=1S/C24H29ClO7/c25-19-8-3-15(24-23(29)22(28)21(27)20(13-26)32-24)12-16(19)11-14-1-4-17(5-2-14)30-9-10-31-18-6-7-18/h1-5,8,12,18,20-24,26-29H,6-7,9-11,13H2/t20-,21-,22+,23-,24+/m1/s1") +AnnotationAssertion( "BTCRKOKVYTVOLU-SJSRKZJXSA-N") +AnnotationAssertion( "464.940") +AnnotationAssertion( "464.16018") +AnnotationAssertion( "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)C1=CC=C(Cl)C(CC2=CC=C(OCCOC3CC3)C=C2)=C1") +AnnotationAssertion(Annotation( "KEGG DRUG") "CAS:1118567-05-7") +AnnotationAssertion( "DrugBank:DB12236") +AnnotationAssertion( "KEGG:D10865") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:21215314") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31101403") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31161692") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31297965") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31432741") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31749238") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:34292100") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:34975223") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35773042") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36178197") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36867399") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36929659") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37148170") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37409573") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37509724") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37568270") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37651295") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37748011") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37817422") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38151752") +AnnotationAssertion( "Wikipedia:Bexagliflozin") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "(1S)-1,5-anhydro-1-(4-chloro-3-{4-[2-(cyclopropyloxy)ethoxy]benzyl}phenyl)-D-glucitol") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "(1S)-1,5-anhydro-1-C-[4-chloro-3-[[4-[2-(cyclopropyloxy)ethoxy]phenyl]methyl]phenyl]-D-glucitol") +AnnotationAssertion(Annotation( "IUPAC") "(2S,3R,4R,5S,6R)-2-(4-chloro-3-{4-[2-(cyclopropyloxy)ethoxy]benzyl}phenyl)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol") +AnnotationAssertion(Annotation( "IUPAC") "(2S,3R,4R,5S,6R)-2-[4-chloro-3-({4-[2-(cyclopropyloxy)ethoxy]phenyl}methyl)phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol") +AnnotationAssertion(Annotation( "KEGG_DRUG") Annotation( ) "Brenzavvy") +AnnotationAssertion(Annotation( "ChEBI") "EGT 1442") +AnnotationAssertion(Annotation( "DrugBank") "EGT-1442") +AnnotationAssertion(Annotation( "DrugBank") "EGT0001442") +AnnotationAssertion(Annotation( "DrugBank") "EGT1442") +AnnotationAssertion(Annotation( "ChEBI") "THR 1442") +AnnotationAssertion(Annotation( "DrugBank") "THR-1442") +AnnotationAssertion(Annotation( "DrugBank") "THR1442") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "bexagliflozin") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "bexagliflozina") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "bexagliflozine") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "bexagliflozinum") +AnnotationAssertion( "CHEBI:229225") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "bexagliflozin") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ritlecitinib) + +AnnotationAssertion( "A pyrrolopyrimidine that is 7H-pyrrolo[2,3-d]pyrimidine substituted at position 4 by a [(3R,6S)-6-methyl-1-(prop-2-enoyl)piperidin-3-yl]amino group. It is a dual inhibitor of Janus kinase 3 and the TEC family of tyrosine kinases.") +AnnotationAssertion( "0") +AnnotationAssertion( "C15H19N5O") +AnnotationAssertion( "InChI=1S/C15H19N5O/c1-3-13(21)20-8-11(5-4-10(20)2)19-15-12-6-7-16-14(12)17-9-18-15/h3,6-7,9-11H,1,4-5,8H2,2H3,(H2,16,17,18,19)/t10-,11+/m0/s1") +AnnotationAssertion( "CBRJPFGIXUFMTM-WDEREUQCSA-N") +AnnotationAssertion( "285.351") +AnnotationAssertion( "285.15896") +AnnotationAssertion( "C[C@H]1CC[C@H](CN1C(=O)C=C)NC1=C2C=CNC2=NC=N1") +AnnotationAssertion(Annotation( "DrugBank") "CAS:1792180-81-4") +AnnotationAssertion( "DrugBank:DB14924") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31082193") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:32419304") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:34826225") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35000236") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35210753") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36623678") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36807251") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36808638") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36872080") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36977960") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37062298") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37403610") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37455588") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37521227") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37556041") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37561322") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37691236") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37707764") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37777018") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37812490") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37917289") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38051245") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38051803") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38141256") +AnnotationAssertion( "Wikipedia:Ritlecitinib") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "1-[(2S,5R)-2-methyl-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)piperidin-1-yl]prop-2-en-1-one") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "PF 06651600") +AnnotationAssertion(Annotation( "DrugBank") "PF-06651600") +AnnotationAssertion(Annotation( "ChEBI") "PF06651600") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "ritlecitinib") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "ritlecitinibum") +AnnotationAssertion( "CHEBI:229233") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ritlecitinib") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ritlecitinib(1+)) + +AnnotationAssertion( "An organic cation that is the conjugate acid of ritlecitinib resulting from the protonation of the nitrogen in the pyrrolopyrimidine ring; Major species at pH 7.3.") +AnnotationAssertion( "+1") +AnnotationAssertion( "C15H20N5O") +AnnotationAssertion( "InChI=1S/C15H19N5O/c1-3-13(21)20-8-11(5-4-10(20)2)19-15-12-6-7-16-14(12)17-9-18-15/h3,6-7,9-11H,1,4-5,8H2,2H3,(H2,16,17,18,19)/p+1/t10-,11+/m0/s1") +AnnotationAssertion( "CBRJPFGIXUFMTM-WDEREUQCSA-O") +AnnotationAssertion( "286.358") +AnnotationAssertion( "286.16624") +AnnotationAssertion( "C[C@H]1CC[C@H](CN1C(=O)C=C)NC1=C2C=CNC2=NC=[NH+]1") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "4-{[(3R,6S)-6-methyl-1-(prop-2-enoyl)piperidin-3-yl]amino}-7H-pyrrolo[2,3-d]pyrimidin-3-ium") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "ritlecitinib cation") +AnnotationAssertion( "CHEBI:229235") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ritlecitinib(1+)") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (fezolinetant) + +AnnotationAssertion( "A triazolopyrazine that is 5,6,7,8-tetrahydro[1,2,4]triazolo[4,3-a]pyrazine substituted by 3-methyl-1,2,4-thiadiazol-5-yl, 4-fluorobenzoyl and methyl groups at positions 3, 7, and 8R, respectively. It is a prescription medicine used to reduce moderate to severe vasomotor symptoms due to menopause.") +AnnotationAssertion( "0") +AnnotationAssertion( "C16H15FN6OS") +AnnotationAssertion( "InChI=1S/C16H15FN6OS/c1-9-13-19-20-14(15-18-10(2)21-25-15)23(13)8-7-22(9)16(24)11-3-5-12(17)6-4-11/h3-6,9H,7-8H2,1-2H3/t9-/m1/s1") +AnnotationAssertion( "PPSNFPASKFYPMN-SECBINFHSA-N") +AnnotationAssertion( "358.400") +AnnotationAssertion( "358.10121") +AnnotationAssertion( "C[C@H]1N(CCN2C1=NN=C2C1=NC(C)=NS1)C(=O)C1=CC=C(F)C=C1") +AnnotationAssertion(Annotation( "KEGG DRUG") "CAS:1629229-37-3") +AnnotationAssertion( "DrugBank:DB15669") +AnnotationAssertion( "KEGG:D11976") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC9625322") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:31415087") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:33048862") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:33724119") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:34000049") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:34048742") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36734148") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36897180") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36924778") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37097747") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37276043") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37335635") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37339088") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37343519") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37382493") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37423792") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37442655") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37462862") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37541194") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37808928") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37865107") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37974591") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38016166") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38035319") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38115258") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38161058") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38187079") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38227939") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38231097") +AnnotationAssertion( "Wikipedia:Fezolinetant") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "(4-fluorophenyl)[(8R)-8-methyl-3-(3-methyl-1,2,4-thiadiazol-5-yl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]methanone") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "DrugBank") "ESN 364") +AnnotationAssertion(Annotation( "DrugBank") "ESN-364") +AnnotationAssertion(Annotation( "ChEBI") "ESN364") +AnnotationAssertion(Annotation( "DrugBank") Annotation( ) "Veozah") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "fezolinetant") +AnnotationAssertion(Annotation( "WHO_MedNet") Annotation( ) "fezolinetantum") +AnnotationAssertion( "CHEBI:229236") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "fezolinetant") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (bromohydrocarbon) AnnotationAssertion( "A compound derived from a hydrocarbon by replacing a hydrogen atom with a bromine atom.") @@ -63917,6 +64238,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphoric acid") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -66115,22 +66437,36 @@ AnnotationAssertion( "103.95441") AnnotationAssertion( "[Na+].OS([O-])=O") AnnotationAssertion(Annotation( "Europe PMC") "AGR:IND605265115") -AnnotationAssertion(Annotation( "ChemIDplus") "CAS:7631-90-5") +AnnotationAssertion(Annotation( "NIST Chemistry WebBook") "CAS:7631-90-5") +AnnotationAssertion( "DrugBank:DB14015") +AnnotationAssertion( "FooDB:FDB015420") AnnotationAssertion(Annotation( "Gmelin") "Gmelin:22395") +AnnotationAssertion( "KEGG:D02059") AnnotationAssertion(Annotation( "Europe PMC") "PMID:27905861") AnnotationAssertion(Annotation( "Europe PMC") "PMID:30429859") AnnotationAssertion(Annotation( "Europe PMC") "PMID:32714086") AnnotationAssertion(Annotation( "Europe PMC") "PMID:32785935") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35114314") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:36440381") +AnnotationAssertion( "Wikipedia:Sodium_bisulfite") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "sodium hydrogensulfite") AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "E 222") +AnnotationAssertion(Annotation( "ChEBI") "E222") +AnnotationAssertion(Annotation( "ChEBI") "NaHSO3") AnnotationAssertion(Annotation( "IUPAC") "NaHSO3") AnnotationAssertion(Annotation( "ChEBI") "Natriumbisulfit") AnnotationAssertion(Annotation( "ChEBI") "Natriumhydrogensulfit") +AnnotationAssertion(Annotation( "ChEBI") "hydrogen sulfite sodium") AnnotationAssertion(Annotation( "ChEBI") "primaeres Natriumsulfit") AnnotationAssertion(Annotation( "ChEBI") "saures Natriumsulfit") AnnotationAssertion(Annotation( "ChemIDplus") "sodium bisulfite") AnnotationAssertion(Annotation( "ChemIDplus") "sodium bisulphite") AnnotationAssertion(Annotation( "ChemIDplus") "sodium hydrogen sulfite") +AnnotationAssertion(Annotation( "ChEBI") "sulfurous acid monosodium salt") +AnnotationAssertion(Annotation( "ChEBI") "sulfurous acid sodium salt") +AnnotationAssertion(Annotation( "ChEBI") "sulfurous acid, monosodium salt") +AnnotationAssertion(Annotation( "ChEBI") "sulfurous acid, sodium salt (1:1)") AnnotationAssertion( "CHEBI:26709") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sodium hydrogensulfite") @@ -66139,6 +66475,9 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sodium chloride) @@ -78371,6 +78710,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78977,6 +79317,7 @@ AnnotationAssertion( "hydrogen fluoride") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -93854,6 +94195,7 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -96355,6 +96697,7 @@ AnnotationAssertion( "sodium acetate") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epoxide) @@ -100040,8 +100383,15 @@ SubClassOf( (alpha-amino-acid residue) +AnnotationAssertion( "An amino-acid residue derived from an alpha-amino acid.") +AnnotationAssertion( "0") +AnnotationAssertion( "C2H2NOR") +AnnotationAssertion( "56.043") +AnnotationAssertion( "56.01364") +AnnotationAssertion( "*-NC([*])C(-*)=O") AnnotationAssertion( "chebi_ontology") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid residues") +AnnotationAssertion(Annotation( "UniProt") "an alpha-amino acid residue") AnnotationAssertion( "CHEBI:33710") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alpha-amino-acid residue") @@ -103618,6 +103968,7 @@ AnnotationAssertion( "morpholine") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (N-(30-(9Z,12Z-octadecadienoyloxy)-tricontanoyl)-sphing-4-enine) @@ -114040,6 +114391,7 @@ AnnotationAssertion( "(trifluoromethyl)benzene") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130547,6 +130899,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trifluoroacetic acid") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137757,6 +138110,7 @@ AnnotationAssertion(rdfs:label "tri SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -149297,6 +149651,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "monofluorobenzene") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dipolar compound) @@ -167909,7 +168264,6 @@ AnnotationAssertion( "186.04630") AnnotationAssertion( "CCOC(=O)n1ccn(C)c1=S") AnnotationAssertion( "CHEBI:3397") -AnnotationAssertion(Annotation( "Beilstein") "Beilstein:0144339") AnnotationAssertion(Annotation( "ChemIDplus") "CAS:22232-54-8") AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:22232-54-8") AnnotationAssertion(Annotation( "NIST Chemistry WebBook") "CAS:22232-54-8") @@ -169213,6 +169567,7 @@ AnnotationAssertion( "sodium nitrate") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sodium L-tartrate) @@ -178533,6 +178888,26 @@ AnnotationAssertion( "tocolytic agent") SubClassOf( ) +# Class: (Matrine) + +AnnotationAssertion( "0") +AnnotationAssertion( "C15H24N2O") +AnnotationAssertion( "InChI=1S/C15H24N2O/c18-14-7-1-6-13-12-5-3-9-16-8-2-4-11(15(12)16)10-17(13)14/h11-13,15H,1-10H2/t11-,12+,13+,15-/m0/s1") +AnnotationAssertion( "ZSBXGIUJOOQZMP-JLNYLFASSA-N") +AnnotationAssertion( "248.364") +AnnotationAssertion( "248.18886") +AnnotationAssertion( "O=C1CCC[C@@H]2[C@H]3CCCN4CCC[C@@H](CN12)[C@@H]34") +AnnotationAssertion( "BPDB:3135") +AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:519-02-8") +AnnotationAssertion( "KEGG:C10774") +AnnotationAssertion( "KNApSAcK:C00002227") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Matrine") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:6700") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Matrine") +SubClassOf( ) + # Class: (folates) AnnotationAssertion( "An N-acyl-L-alpha-amino acid anion obtained by deprotonation of any folic acid.") @@ -188711,14 +189086,16 @@ SubClassOf( (sodium-glucose transport protein subtype 2 inhibitor) -AnnotationAssertion( "An inhibitor that interferes with the action of sodium-glucose transport protein subtype 2.") -AnnotationAssertion( "Wikipedia:SLC5A2") +AnnotationAssertion( "Any inhibitor that interferes with the action of sodium-glucose transport protein subtype 2.") +AnnotationAssertion( "Wikipedia:Sodium/glucose_cotransporter_2") AnnotationAssertion( "chebi_ontology") AnnotationAssertion(Annotation( "ChEBI") "SGLT2 inhibitor") AnnotationAssertion(Annotation( "ChEBI") "SGLT2 inhibitors") AnnotationAssertion(Annotation( "ChEBI") "sodium glucose co-transporter 2 inhibitor") AnnotationAssertion(Annotation( "ChEBI") "sodium glucose co-transporter 2 inhibitors") AnnotationAssertion(Annotation( "ChEBI") "sodium-glucose transport protein subtype 2 inhibitors") +AnnotationAssertion(Annotation( "ChEBI") "sodium/glucose cotransporter 2 inhibitor") +AnnotationAssertion(Annotation( "ChEBI") "sodium/glucose cotransporter 2 inhibitors") AnnotationAssertion( "CHEBI:73273") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sodium-glucose transport protein subtype 2 inhibitor") @@ -202233,6 +202610,7 @@ SubClassOf( (food colour retention agent) AnnotationAssertion( "A food additive that intensifies, retains or stabilises the colour of a food.") +AnnotationAssertion( "Wikipedia:Colour_retention_agent") AnnotationAssertion( "chebi_ontology") AnnotationAssertion(Annotation( "ChEBI") "color retention agent") AnnotationAssertion(Annotation( "ChEBI") "color retention agents") @@ -211662,8 +212040,7 @@ AnnotationAssertion(Annotation( "CHEBI:83813") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proteinogenic amino acid") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (morphinane-like compound) @@ -214155,7 +214532,7 @@ SubClassOf( (dapagliflozin) -AnnotationAssertion( "A C-glycosyl comprising beta-D-glucose in which the anomeric hydroxy group is replaced by a 4-chloro-3-(4-ethoxybenzyl)phenyl group. Used (in the formo f its propanediol monohydrate) to improve glycemic control, along with diet and exercise, in adults with type 2 diabetes.") +AnnotationAssertion( "A C-glycosyl comprising beta-D-glucose in which the anomeric hydroxy group is replaced by a 4-chloro-3-(4-ethoxybenzyl)phenyl group. Used (in the form of its propanediol monohydrate) to improve glycemic control, along with diet and exercise, in adults with type 2 diabetes.") AnnotationAssertion( "0") AnnotationAssertion( "C21H25ClO6") AnnotationAssertion( "InChI=1S/C21H25ClO6/c1-2-27-15-6-3-12(4-7-15)9-14-10-13(5-8-16(14)22)21-20(26)19(25)18(24)17(11-23)28-21/h3-8,10,17-21,23-26H,2,9,11H2,1H3/t17-,18-,19+,20-,21+/m1/s1") @@ -214168,6 +214545,8 @@ AnnotationAssertion(Annotation( "DrugBank:DB06292") AnnotationAssertion(Annotation( "DrugCentral") "Drug_Central:4304") AnnotationAssertion( "KEGG:D08897") +AnnotationAssertion(Annotation( "Europe PMC") "PMCID:PMC10706647") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:20509715") AnnotationAssertion(Annotation( "Europe PMC") "PMID:23724409") AnnotationAssertion(Annotation( "Europe PMC") "PMID:24840612") AnnotationAssertion(Annotation( "Europe PMC") "PMID:25200570") @@ -214187,6 +214566,33 @@ AnnotationAssertion(Annotation( "Europe PMC") "PMID:25688893") AnnotationAssertion(Annotation( "Europe PMC") "PMID:25694411") AnnotationAssertion(Annotation( "Europe PMC") "PMID:25710563") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:30000030") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:32454718") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:33859839") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:35272683") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37113469") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37549309") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37664712") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37758208") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37895841") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37931629") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37936747") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:37979161") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38017482") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38031729") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38044448") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38094412") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38097862") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38117458") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38124408") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38128857") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38133155") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38137545") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38170280") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38171497") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38171852") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38185119") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:38220410") AnnotationAssertion(Annotation( "Reaxys") "Reaxys:11966426") AnnotationAssertion( "Wikipedia:Dapagliflozin") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "(1S)-1,5-anhydro-1-[4-chloro-3-(4-ethoxybenzyl)phenyl]-D-glucitol") @@ -214200,7 +214606,7 @@ AnnotationAssertion( "dapagliflozin") SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 4c3f643..2fe7939 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-12-15") + +Annotation( ) +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 83ff481..bc4a0f8 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-12-15") + +Annotation( ) +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ogms_import.owl b/src/ontology/imports/ogms_import.owl index 332be15..097a658 100644 --- a/src/ontology/imports/ogms_import.owl +++ b/src/ontology/imports/ogms_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-12-15") +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(AnnotationProperty()) diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 6639261..e2174b7 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-12-15") +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pr_import.owl b/src/ontology/imports/pr_import.owl index 51c01a0..64fa56e 100644 --- a/src/ontology/imports/pr_import.owl +++ b/src/ontology/imports/pr_import.owl @@ -7,17 +7,34 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-12-15") + +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -26,12 +43,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -39,6 +57,7 @@ Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -68,6 +87,10 @@ Declaration(AnnotationProperty(rdfs:label)) AnnotationAssertion(rdfs:label "definition") +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -132,6 +155,15 @@ AnnotationAssertion( AnnotationAssertion( "participates_in") AnnotationAssertion(rdfs:label "participates_in") +# Object Property: (has_role) + +AnnotationAssertion( "RO:0000087") +AnnotationAssertion( "protein") +AnnotationAssertion( "has_role") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( "has_role") +AnnotationAssertion(rdfs:label "has_role") + # Object Property: (has_component) AnnotationAssertion( "RO:0002180") @@ -194,6 +226,49 @@ AnnotationAssertion( "BFO:0000040") AnnotationAssertion(rdfs:label "material entity") +# Class: (carbon dioxide) + +AnnotationAssertion( "A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.") +AnnotationAssertion(Annotation( "PDBeChem") "CARBON DIOXIDE") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Carbon dioxide") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "carbon dioxide") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dioxidocarbon") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "methanedione") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "CO2") +AnnotationAssertion(Annotation( "UniProt") "CO2") +AnnotationAssertion(Annotation( "ChEBI") "E 290") +AnnotationAssertion(Annotation( "ChEBI") "E-290") +AnnotationAssertion(Annotation( "ChEBI") "E290") +AnnotationAssertion(Annotation( "ChEBI") "R-744") +AnnotationAssertion(Annotation( "MolBase") "[CO2]") +AnnotationAssertion(Annotation( "UM-BBD") "carbonic anhydride") +AnnotationAssertion( "CHEBI:16526") +AnnotationAssertion(rdfs:label "carbon dioxide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbon monoxide) + +AnnotationAssertion( "A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:17245") +AnnotationAssertion(rdfs:label "carbon monoxide") +SubClassOf( ) + # Class: (molecular entity) AnnotationAssertion(Annotation( "fake:2") "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.") @@ -247,11 +322,11 @@ SubClassOf( (biological_process) -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") AnnotationAssertion( "biological process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008150") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological_process") # Class: (Eukaryota) @@ -295,7 +370,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -312,20 +387,20 @@ AnnotationAssertion(rdfs:label "am SubClassOf( ) SubClassOf( ObjectMinCardinality(2 )) -# Class: (protein-containing material entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000050567") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") -AnnotationAssertion(rdfs:label "protein-containing material entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing molecular entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000064867") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") +AnnotationAssertion(rdfs:label "protein-containing molecular entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sequence_feature) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index ea2a8dd..b502e74 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-12-15") + +Annotation( ) +Annotation(owl:versionInfo "2024-02-19") Declaration(Class()) Declaration(Class()) @@ -28,6 +28,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) @@ -471,6 +472,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -497,6 +499,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -581,6 +584,8 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "has characteristic") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -608,7 +613,9 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) @@ -1056,6 +1063,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1686,6 +1694,7 @@ AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -1696,6 +1705,7 @@ DisjointClasses( (realizable entity) AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable"@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1707,13 +1717,17 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (specifically dependent continuant) +# Class: (characteristic) AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "characteristic"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) # Class: (role) @@ -1751,11 +1765,16 @@ AnnotationAssertion(Annotation( "molecular function") AnnotationAssertion( "GO:0003674") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") +AnnotationAssertion(rdfs:label "gene product or complex activity"@en) AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) # Class: (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "Wikipedia:Biological_process") @@ -1764,8 +1783,12 @@ AnnotationAssertion( "single organism process") AnnotationAssertion( "single-organism process") AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "A biological process is an evolved process") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kinase activity) @@ -1791,6 +1814,16 @@ AnnotationAssertion( "curation status specification"@en) EquivalentClasses( ObjectOneOf( )) +# Class: (processed material) + +AnnotationAssertion( "processed material"@en) +AnnotationAssertion( "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Is a material entity that is created or changed during material processing."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "processed material"@en) +SubClassOf( ) + # Class: (organism) AnnotationAssertion( "organism"@en) @@ -1938,30 +1971,30 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) AnnotationAssertion( "## Elucidation diff --git a/src/ontology/mappings/dron-chebi-mapping.csv b/src/ontology/mappings/dron-chebi-mapping.csv index 7a9eb11..0e43ef5 100644 --- a/src/ontology/mappings/dron-chebi-mapping.csv +++ b/src/ontology/mappings/dron-chebi-mapping.csv @@ -310,7 +310,6 @@ http://purl.obolibrary.org/obo/DRON_00012332,http://purl.obolibrary.org/obo/CHEB http://purl.obolibrary.org/obo/DRON_00012398,http://purl.obolibrary.org/obo/CHEBI_23334 http://purl.obolibrary.org/obo/DRON_00012403,http://purl.obolibrary.org/obo/CHEBI_2674 http://purl.obolibrary.org/obo/DRON_00012411,http://purl.obolibrary.org/obo/CHEBI_91090 -http://purl.obolibrary.org/obo/DRON_00012429,http://purl.obolibrary.org/obo/CHEBI_50114 http://purl.obolibrary.org/obo/DRON_00012430,http://purl.obolibrary.org/obo/CHEBI_4882 http://purl.obolibrary.org/obo/DRON_00012431,http://purl.obolibrary.org/obo/CHEBI_134857 http://purl.obolibrary.org/obo/DRON_00012434,http://purl.obolibrary.org/obo/CHEBI_81568 @@ -2155,3 +2154,8 @@ http://purl.obolibrary.org/obo/DRON_00016478,http://purl.obolibrary.org/obo/CHEB http://purl.obolibrary.org/obo/DRON_00973902,http://purl.obolibrary.org/obo/CHEBI_30512 http://purl.obolibrary.org/obo/DRON_00980172,http://purl.obolibrary.org/obo/CHEBI_194186 http://purl.obolibrary.org/obo/DRON_00980177,http://purl.obolibrary.org/obo/CHEBI_86567 +http://purl.obolibrary.org/obo/DRON_00994954,http://purl.obolibrary.org/obo/CHEBI_229233 +http://purl.obolibrary.org/obo/DRON_00994948,http://purl.obolibrary.org/obo/CHEBI_229236 +http://purl.obolibrary.org/obo/DRON_00993044,http://purl.obolibrary.org/obo/CHEBI_229212 +http://purl.obolibrary.org/obo/DRON_00993039,http://purl.obolibrary.org/obo/CHEBI_6700 +http://purl.obolibrary.org/obo/DRON_00994955,http://purl.obolibrary.org/obo/CHEBI_229225 \ No newline at end of file