From b4cc48d7f12f0dcfc99704b2f20a9c95fc4089bc Mon Sep 17 00:00:00 2001 From: Elisa Kendall Date: Wed, 28 Dec 2022 17:56:46 -0800 Subject: [PATCH] IDMP-390 - moved certain characteristics of a substance that were originally 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 --- EXT/Examples/AmlodipineExample.rdf | 32 +++---- EXT/Examples/TerlipressinExample.rdf | 14 +-- ISO/ISO11238-Substances.rdf | 122 +++++++++++++++++---------- 3 files changed, 102 insertions(+), 66 deletions(-) diff --git a/EXT/Examples/AmlodipineExample.rdf b/EXT/Examples/AmlodipineExample.rdf index 7e5e28a0..59245012 100644 --- a/EXT/Examples/AmlodipineExample.rdf +++ b/EXT/Examples/AmlodipineExample.rdf @@ -105,7 +105,7 @@ - + Copyright (c) 2022 EDM Council, Inc. Copyright (c) 2022 Pistoia Alliance, Inc. @@ -137,10 +137,15 @@ 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 It is a long-acting dihydropyridine calcium channel blocker effective in the treatment of angina pectoris and hypertension. + C20H25ClN2O5 + C20H25ClN2O5 + 1 + + @@ -176,8 +181,13 @@ besylate salt of amlodipine, a long-acting calcium channel blocker 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. + C20H25CIN2O5.C6H6O3S + C20H25CIN2O5.C6H6O3S + 2 + + @@ -210,12 +220,7 @@ amlodipine besylate molecular structure - C20H25CIN2O5.C6H6O3S - C20H25CIN2O5.C6H6O3S - OS(=O)(=O)C1=CC=CC=C1.CCOC(=O)C2=C(COCCN)NC(C)=C(C2C3=C(Cl)C=CC=C3)C(=O)OC - - @@ -319,9 +324,14 @@ mesylate salt of amlodipine, a long-acting calcium channel blocker 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. + C21H31ClN2O9S + C20H25ClN2O5.CH4O3S.H2O + 3 + amlodipine mesilate monohydrate + @@ -361,12 +371,7 @@ amlodipine mesylate monohydrate molecular structure - C21H31ClN2O9S - C20H25ClN2O5.CH4O3S.H2O - O.CS(O)(=O)=O.CCOC(=O)C1=C(COCCN)NC(C)=C(C1C1=C(Cl)C=CC=C1)C(=O)OC - - @@ -404,11 +409,6 @@ amlodipine molecular structure - C20H25ClN2O5 - C20H25ClN2O5 - - - diff --git a/EXT/Examples/TerlipressinExample.rdf b/EXT/Examples/TerlipressinExample.rdf index 05042164..d9abda8d 100644 --- a/EXT/Examples/TerlipressinExample.rdf +++ b/EXT/Examples/TerlipressinExample.rdf @@ -105,7 +105,7 @@ - + Copyright (c) 2022 EDM Council, Inc. Copyright (c) 2022 Pistoia Alliance, Inc. @@ -143,6 +143,9 @@ protein that is an analogue of vasopressin used as a vasoactive drug in the management of low blood pressure 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. 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. + C52H75O15N16S2 + C52H75O15N16S2 + @@ -154,6 +157,9 @@ analogue of vasopressin used as a vasoactive for proteomics research 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. + C56H92N16O24S2 + C52H74N16O15S2.2C2H4O2.5H2O + @@ -217,9 +223,6 @@ terlipressin acetate molecular structure - C56H92N16O24S2 - C52H74N16O15S2.2C2H4O2.5H2O - @@ -376,9 +379,6 @@ terlipressin molecular structure - C52H75O15N16S2 - C52H75O15N16S2 - 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 diff --git a/ISO/ISO11238-Substances.rdf b/ISO/ISO11238-Substances.rdf index e9bce1bc..1c7de127 100644 --- a/ISO/ISO11238-Substances.rdf +++ b/ISO/ISO11238-Substances.rdf @@ -85,7 +85,7 @@ - The https://spec.pistoiaalliance.org/idmp/ontology/ISO/20221001/ISO11238-Substances.rdf version of this ontology was modified to rename 'ingredient role' to ingredient for clarification per discussion at the Pistoia Alliance Conference Workshop on 3 November 2022 (IDMP-298). It was also modified to add the concept of matter and to add a specific hasSubstanceName property rather than the more general hasName property in order to accommodate additional semantics. + The https://spec.pistoiaalliance.org/idmp/ontology/ISO/20221001/ISO11238-Substances.rdf version of this ontology was modified to rename 'ingredient role' to ingredient for clarification per discussion at the Pistoia Alliance Conference Workshop on 3 November 2022 (IDMP-298). It was also modified to add the concept of matter and to add a specific hasSubstanceName property rather than the more general hasName property in order to accommodate additional semantics. The relationship between a moiety or substance and some of its characteristics was also revised, including the relationship between a structure and its corresponding representation. The https://spec.pistoiaalliance.org/idmp/ontology/ISO/20221101/ISO11238-Substances.rdf version of this ontology was modified to relax the restriction on the property isStoichiometric with respect to chemical substances to optional from required (IDMP-380), and then reversed per the SME team and to conform with the IDMP standard. Copyright (c) 2022 EDM Council, Inc. @@ -153,6 +153,34 @@ + + + + + 1 + + + + + + + 1 + + + + + + 1 + + + + + + + 1 + + + @@ -436,6 +464,41 @@ 1 + + + + + 1 + + + + + + + 1 + + + + + + 1 + + + + + + + 1 + + + + + + + + 0 + + @@ -512,6 +575,7 @@ molecular graph single chemical structure that is an unambiguous representation of the arrangement of atoms, normalized to conform with the International Union of Pure and Applied Chemistry (IUPAC) specification for drawing chemical structures to the degree possible + @@ -524,45 +588,18 @@ molecular graph identifier unique identifier for a molecular graph representing a single chemical structure + - - - 1 - - - - - - - 1 - - - - - + 1 - - - - 1 - - - - - - - 1 - - - @@ -570,20 +607,15 @@ - - - - - 0 - - molecular structure unambiguous representation of the arrangement of atoms For the purposes of defining substances, the three-dimensional conformations are not captured. Individual conformations or conformers of substances would only be captured in either a general sense for proteins (i.e. denatured) or when a given rotation about a single bond is restricted in such a way that the two different conformers are isolatable from each other and do not interconvert at room temperature (e.g. substituted biphenyls). Structural representations shall include the complete molecular structure with all known stereochemistry indicated. Molecular fragments and moieties shall also contain structural representations. The structure is a defining element for chemicals, polymers and structural modifications. It should be defined in a consistent and unambiguous manner. The Structural Representation can cover complex substances like proteins and nucleic acid by graphical representation. The structure shall contain a sufficient amount of graphical and textual information to define the underlying atoms and the connectivity between atoms as well as the composition ratio of moieties. This representation should be generally translatable into a graphical representation. + ISO 11238:2018 Health informatics - Identification of medicinal products (IDMP) - Data elements and structures for the unique identification and exchange of regulated information on substances, clauses 3.49, 7.2.1 + While certain diagrams, such as Figure 14 in the ISO 11238:2018 show attributes such as stereochemistry, optical activity, and molecular formulas as characteristics of structure, from an ontological perspective these characteristics are actually characteristics of a moiety or chemical substance and are modeled as such herein. @@ -596,6 +628,7 @@ molecular structure identifier unique identifier for the unambiguous representation of the arrangement of atoms for a given substance + @@ -1092,7 +1125,7 @@ - + structural representation ISO 11238:2018 Health informatics - Identification of medicinal products (IDMP) - Data elements and structures for the unique identification and exchange of regulated information on substances, clause 7.3 ISO/TS 19844:2018(E) Health informatics - Identification of medicinal products (IDMP) - Implementation guidelines for ISO 11238 for data elements and structures for the unique identification and exchange of regulated information on substances, clause 6.7.6 @@ -1115,13 +1148,19 @@ arrangement and organization of interrelated elements in a material object or system Material structures include man-made objects such as buildings and machines and natural objects such as biological organisms, minerals and chemicals. - ISO 11238:2018 Health informatics - Identification of medicinal products (IDMP) - Data elements and structures for the unique identification and exchange of regulated information on substances, clauses 3.49, 7.2.1 Note that the term 'structure' is not explicitly defined in the standard, but molecular structure is defined using this concept, and the concept appears in various UML diagrams in the standard. + + + + + 0 + + @@ -1600,7 +1639,6 @@ has molecular formula ISO/TS 19844:2018(E) Health informatics - Identification of medicinal products (IDMP) - Implementation guidelines for ISO 11238 for data elements and structures for the unique identification and exchange of regulated information on substances, clause 6.7.3 - relates a single substance to a formal definition for its molecular formula Molecular formula is written as a sequence of pairs of atom symbol and stoichiometric number (see example below). This formal notation is essentially a code system. Specified according to the Hill system, i.e. first C, then H, then alphabetical. The messaging requirements can dictate a specific electronic format for the molecular formula and the molecular formula by moiety. @@ -1614,7 +1652,6 @@ has molecular formula by moiety ISO/TS 19844:2018(E) Health informatics - Identification of medicinal products (IDMP) - Implementation guidelines for ISO 11238 for data elements and structures for the unique identification and exchange of regulated information on substances, clause 6.7.4 - way of describing of the molecular formula of a stoichiometric or non-stoichiometric substance existing of two or more moieties, the molecular formula of each moiety shall be described separated by a dot In non-cyclic linear structures like sodium nitroprusside: Na2[Fe(CN)5(NO)].2H2O, a non-cyclic structure is constructed in the following order: a) symbol of the central atom placed on the left; b) ionic ligands with cations first then anions; c) neutral ligands. The messaging requirements can dictate a specific electronic format for the molecular formula and the molecular formula by moiety. @@ -1631,7 +1668,7 @@ ISO 11238:2018 Health informatics - Identification of medicinal products (IDMP) - Data elements and structures for the unique identification and exchange of regulated information on substances, clause 7.3 ISO/TS 19844:2018(E) Health informatics - Identification of medicinal products (IDMP) - Implementation guidelines for ISO 11238 for data elements and structures for the unique identification and exchange of regulated information on substances, clause 6.7.5, Figure 10 - relates a substance or its structure to its molecular weight + relates a substance to its molecular weight @@ -1683,7 +1720,6 @@ has stereochemistry ISO 11238:2018 Health informatics - Identification of medicinal products (IDMP) - Data elements and structures for the unique identification and exchange of regulated information on substances, clause 7.2.2 Figure 14 - is classified by the relative spatial arrangement of atoms within molecules When the substance type, as defined in is either chemical or polymer, this class is MANDATORY; for all other cases this class is CONDITIONAL.