Skip to content

Commit

Permalink
IDMP-390 - moved certain characteristics of a substance that were ori…
Browse files Browse the repository at this point in the history 
…ginally modeled as properties of molecular structure to being properties of the moiety or chemical substance directly and revised examples accordingly

Signed-off-by: Elisa Kendall <[email protected]>
  • Loading branch information
@ElisaKendall
ElisaKendall committed Dec 29, 2022
1 parent 77fc485 commit b4cc48d
Show file tree
Hide file tree
Showing 3 changed files with 102 additions and 66 deletions.
32 changes: 16 additions & 16 deletions EXT/Examples/AmlodipineExample.rdf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Languages/ISO639-1-LanguageCodes/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Languages/LanguageRepresentation/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/20220901/Examples/AmlodipineExample/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/20221201/Examples/AmlodipineExample/"/>
<idmp-chg:hasMaturityLevel rdf:resource="&idmp-chg;Informative"/>
<cmns-av:copyright>Copyright (c) 2022 EDM Council, Inc.</cmns-av:copyright>
<cmns-av:copyright>Copyright (c) 2022 Pistoia Alliance, Inc.</cmns-av:copyright>
Expand Down Expand Up @@ -137,10 +137,15 @@
<dct:source rdf:resource="https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:2668"/>
<skos:definition>fully substituted dialkyl 1,4-dihydropyridine-3,5-dicarboxylate derivative, which is used for the treatment of hypertension, chronic stable angina and confirmed or suspected vasospastic angina</skos:definition>
<skos:note>It is a long-acting dihydropyridine calcium channel blocker effective in the treatment of angina pectoris and hypertension.</skos:note>
<idmp-sub:hasMolecularFormula>C20H25ClN2O5</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25ClN2O5</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineMolecularWeight"/>
<idmp-sub:hasNumberOfMoieties rdf:datatype="&xsd;integer">1</idmp-sub:hasNumberOfMoieties>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<idmp-sub:hasStructure rdf:resource="&idmp-amp;AmlodipineMolecularStructure"/>
<idmp-sub:isActiveMoietyOf rdf:resource="&idmp-amp;AmlodipineBesylate"/>
<idmp-sub:isActiveMoietyOf rdf:resource="&idmp-amp;AmlodipineMesylateMonohydrate"/>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineAsActiveMoiety">
Expand Down Expand Up @@ -176,8 +181,13 @@
<skos:definition>besylate salt of amlodipine, a long-acting calcium channel blocker</skos:definition>
<skos:note>Amlodipine besylate is chemically described as 3-Ethyl-5-methyl (±)-2-[(2-aminoethoxy)methyl]-4-(2-chlorophenyl)-1,4-dihydro-6-methyl-3,5-pyridinedicarboxylate, monobenzenesulphonate. Amlodipine besylate is a white crystalline powder with a molecular weight of 567.1. It is slightly soluble in water and sparingly soluble in ethanol.</skos:note>
<idmp-sub:hasActiveMoiety rdf:resource="&idmp-amp;Amlodipine"/>
<idmp-sub:hasMolecularFormula>C20H25CIN2O5.C6H6O3S</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25CIN2O5.C6H6O3S</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineBesylateMolecularWeight"/>
<idmp-sub:hasNumberOfMoieties rdf:datatype="&xsd;integer">2</idmp-sub:hasNumberOfMoieties>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<idmp-sub:hasStructure rdf:resource="&idmp-amp;AmlodipineBesylateMolecularStructure"/>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineBesylateAsActiveIngredientInNorvasc">
Expand Down Expand Up @@ -210,12 +220,7 @@
<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineBesylateMolecularStructure">
<rdf:type rdf:resource="&idmp-sub;MolecularStructure"/>
<rdfs:label>amlodipine besylate molecular structure</rdfs:label>
<idmp-sub:hasMolecularFormula>C20H25CIN2O5.C6H6O3S</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25CIN2O5.C6H6O3S</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineBesylateMolecularWeight"/>
<idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>OS(=O)(=O)C1=CC=CC=C1.CCOC(=O)C2=C(COCCN)NC(C)=C(C2C3=C(Cl)C=CC=C3)C(=O)OC</idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineBesylateMolecularWeight">
Expand Down Expand Up @@ -319,9 +324,14 @@
<skos:definition>mesylate salt of amlodipine, a long-acting calcium channel blocker</skos:definition>
<skos:note>Amlodipine mesylate monohydrate is chemically described as 3,5-Pyridinedicarboxylic acid, 2-((2-aminoethoxy)methyl)-4-(2-chlorophenyl)-1,4-dihydro-6-methyl-, 3-ethyl 5-methyl ester, monomethanesulfonate, monohydrate.</skos:note>
<idmp-sub:hasActiveMoiety rdf:resource="&idmp-amp;Amlodipine"/>
<idmp-sub:hasMolecularFormula>C21H31ClN2O9S</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25ClN2O5.CH4O3S.H2O</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineMesylateMonohydrateMolecularWeight"/>
<idmp-sub:hasNumberOfMoieties rdf:datatype="&xsd;integer">3</idmp-sub:hasNumberOfMoieties>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<idmp-sub:hasStructure rdf:resource="&idmp-amp;AmlodipineMesylateMonohydrateMolecularStructure"/>
<cmns-av:synonym>amlodipine mesilate monohydrate</cmns-av:synonym>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineMesylateMonohydrateAsActiveIngredientInAmlodipineEMC">
Expand Down Expand Up @@ -361,12 +371,7 @@
<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineMesylateMonohydrateMolecularStructure">
<rdf:type rdf:resource="&idmp-sub;MolecularStructure"/>
<rdfs:label>amlodipine mesylate monohydrate molecular structure</rdfs:label>
<idmp-sub:hasMolecularFormula>C21H31ClN2O9S</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25ClN2O5.CH4O3S.H2O</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineMesylateMonohydrateMolecularWeight"/>
<idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>O.CS(O)(=O)=O.CCOC(=O)C1=C(COCCN)NC(C)=C(C1C1=C(Cl)C=CC=C1)C(=O)OC</idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineMesylateMonohydrateMolecularWeight">
Expand Down Expand Up @@ -404,11 +409,6 @@
<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineMolecularStructure">
<rdf:type rdf:resource="&idmp-sub;MolecularStructure"/>
<rdfs:label>amlodipine molecular structure</rdfs:label>
<idmp-sub:hasMolecularFormula>C20H25ClN2O5</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C20H25ClN2O5</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-amp;AmlodipineMolecularWeight"/>
<idmp-sub:hasStereochemistry rdf:resource="&idmp-sub;Stereochemistry-Racemic"/>
<cmns-cls:isClassifiedBy rdf:resource="&idmp-sub;OpticalActivity-EitherDirection"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-amp;AmlodipineMolecularWeight">
Expand Down
14 changes: 7 additions & 7 deletions EXT/Examples/TerlipressinExample.rdf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Languages/ISO639-1-LanguageCodes/"/>
<owl:imports rdf:resource="https://www.omg.org/spec/LCC/Languages/LanguageRepresentation/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/20221101/Examples/TerlipressinExample/"/>
<owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/EXT/20221201/Examples/TerlipressinExample/"/>
<idmp-chg:hasMaturityLevel rdf:resource="&idmp-chg;Informative"/>
<cmns-av:copyright>Copyright (c) 2022 EDM Council, Inc.</cmns-av:copyright>
<cmns-av:copyright>Copyright (c) 2022 Pistoia Alliance, Inc.</cmns-av:copyright>
Expand Down Expand Up @@ -143,6 +143,9 @@
<skos:definition>protein that is an analogue of vasopressin used as a vasoactive drug in the management of low blood pressure</skos:definition>
<skos:note>It has been found to be effective when norepinephrine does not help. Indications for use include norepinephrine-resistant septic shock and hepatorenal syndrome. In addition, it is used to treat bleeding esophageal varices.</skos:note>
<skos:note>Terlipressin is currently not available in the United States, or Canada, but it is available in New Zealand, Australia, much of Europe, India, Pakistan and UAE.</skos:note>
<idmp-sub:hasMolecularFormula>C52H75O15N16S2</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C52H75O15N16S2</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-trlp;TerlipressinMolecularWeight"/>
<idmp-sub:hasStructure rdf:resource="&idmp-trlp;TerlipressinMolecularStructure"/>
<idmp-sub:isActiveMoietyOf rdf:resource="&idmp-trlp;TerlipressinAcetate"/>
</owl:NamedIndividual>
Expand All @@ -154,6 +157,9 @@
<skos:definition>analogue of vasopressin used as a vasoactive for proteomics research</skos:definition>
<skos:note>Synonyms for terlipressin acetate include Gly-Gly-Gly-Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Lys-Gly-Nh2 (4-9 Disulfide) Acetate, and as N-(N-(N-Glycylglycyl)Glycyl)-8-L-Lysinevasopressin Acetate.</skos:note>
<idmp-sub:hasActiveMoiety rdf:resource="&idmp-trlp;Terlipressin"/>
<idmp-sub:hasMolecularFormula>C56H92N16O24S2</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C52H74N16O15S2.2C2H4O2.5H2O</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-trlp;TerlipressinAcetateMolecularWeight"/>
<idmp-sub:hasStructure rdf:resource="&idmp-trlp;TerlipressinAcetateMolecularStructure"/>
</owl:NamedIndividual>

Expand Down Expand Up @@ -217,9 +223,6 @@
<rdf:type rdf:resource="&idmp-sub;MolecularStructure"/>
<rdfs:label>terlipressin acetate molecular structure</rdfs:label>
<rdfs:seeAlso rdf:resource="https://go.drugbank.com/salts/DBSALT002332"/>
<idmp-sub:hasMolecularFormula>C56H92N16O24S2</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C52H74N16O15S2.2C2H4O2.5H2O</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-trlp;TerlipressinAcetateMolecularWeight"/>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="&idmp-trlp;TerlipressinAcetateMolecularWeight">
Expand Down Expand Up @@ -376,9 +379,6 @@
<owl:NamedIndividual rdf:about="&idmp-trlp;TerlipressinMolecularStructure">
<rdf:type rdf:resource="&idmp-sub;MolecularStructure"/>
<rdfs:label>terlipressin molecular structure</rdfs:label>
<idmp-sub:hasMolecularFormula>C52H75O15N16S2</idmp-sub:hasMolecularFormula>
<idmp-sub:hasMolecularFormulaByMoiety>C52H75O15N16S2</idmp-sub:hasMolecularFormulaByMoiety>
<idmp-sub:hasMolecularWeight rdf:resource="&idmp-trlp;TerlipressinMolecularWeight"/>
<idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>O=C(N)CNC(=O)[C@@H](NC(=O)[C@H]4N(C(=O)[C@H]1NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)CNC(=O)CNC(=O)CN)CSSC1)Cc2ccc(O)cc2)Cc3ccccc3)CCC(=O)N)CC(=O)N)CCC4)CCCCN</idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification>
</owl:NamedIndividual>

Expand Down
Loading

0 comments on commit b4cc48d

Please sign in to comment.