Classifying Compounds in Public Databases
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1 Classifying Compounds in Public Databases ACS San Diego, March 15, 2016 OntoChem IT Solutions GmbH Blücherstr Halle (Saale) Germany Tel Fax: mail: info(at)ontochem.com
2 Background Ontology is a formal naming and definition of the types, properties, and relationships of the entities for a particular domain of discourse. William J. Rapaport 2
3 Background Ontology Why in chemistry? Organizing knowledge e.g. terpenes are made of x times 5 carbon isoprene units 3
4 Background Ontology Why in chemistry? Organizing knowledge Conserving old knowledge what are dicarboxylic acids? 4
5 Background Ontology Why in chemistry? Organizing knowledge Conserving old knowledge what are dicarboxylic acids? is_a: dicarboxylic acid ontology 5
6 Background Ontology Why in chemistry? Organizing knowledge Conserving old knowledge what are dicarboxylic acids? is_a: dicarboxylic acid ontology 6
7 Background Ontology Why in chemistry? Organizing knowledge Conserving old knowledge what are dicarboxylic acids? is_a: dicarboxylic acid ontology is_part: 2 carboxylic acid moieties partology (Bolton, Hastings) SSS based 7
8 Background Ontology Why in chemistry? Organizing knowledge Conserving old knowledge Transporting our knowledge e.g. teaching humans and computers Using our knowledge e.g. data mining, property predictions, knowledge inference, creating new products 8
9 need to build on common rules Source: Gardner, S. (2005) Ontologies and semantic data integration. DDT 10(14)
10 SODIAC: Automated Classifications Assignment of organic compounds in structure files, databases, documents Organic Chemistry: 7,916 class concepts 32,469 synonyms 4,698 SMARTS concepts 10
11 SODIAC: Automated Classifications Assignment of compounds in structure files, databases, documents SMARTS based e.g. alkylbromides [C;\!$(C=[O,S,N,P])]Br D. Weininger AND, OR, NOT logic e.g. AND NOT for alkenes: C=C!c:c OR 11
12 SODIAC: Automated Classifications using SMARTS filters with AND, OR & NOT a hierarchical state machine on DB compounds cyclic compounds not cyclohexenes: cycloalkenes NOT cyclohexenes 6-membered carbocycles 12
13 Quality of Classifications? Testing Sodiac by annotating public databases: ChEBI (from E. Bolton, PubChem, March 1, 2016): 42,055 compounds MeSH (from E. Bolton, PubChem, March 1, 2016): 116,542 compounds ChEMBL (from Steve Boyer, IBM, February 2, 2016): 1,456,019 compounds PubChem (downloaded Sept. 2015, PubChem): 68,420,615 compounds performance: takes 6 hours to load db, takes 4h to assign classes Patent full text documents: >90 million full text documents 13
14 ChEBI Classifications ChEBI Manually curated, can we do it automatically? Can we recognize the correct ChEBI parent ID for a compound? 61,904 ChEBI concepts in total, 3,584 ChEBI concepts contain a * in a SMILES 45,748 ChEBI concepts are compounds with SMILES, 44,355 after cleaning Assignment 1,164 ChEBI compounds are present as scaffold concepts in SODIAC as well, e.g. CHEBI:90 (-)-epicatechin 14
15 ChEBI Classifications Assignment of ChEBI concepts CHEBI:90 (-)-epicatechin is_a catechin (CHEBI:23053) is_a polyphenol (CHEBI:26195) has_role antioxidant (CHEBI:22586) is_enantiomer_of (+)-epicatechin (CHEBI:76125) SODIAC: (-)-epicatechin is_a (-)-epicatechin derivatives; alkylarylethers; aromatic compounds; carbon compounds; chromanes; oxacyclic compounds; oxygen compounds; polyols; pyrocatechols; secondary alcohols; triols; 15
16 ChEBI Classifications ChEBI SODIAC (ChEBI) matches: ChEBI 1,888 ChEBI parent concepts have been assigned to the Test Set of 1,164 ChEBI compounds (avg 1.62 parent classes / compound) SODIAC 1,056 ChEBI parents were assigned by SODIAC from 1,888 is_a ChEBI parents = 56% 832 ChEBI concepts not found as they are not represented in SODIAC 29,833 SODIAC classes assigned to 1,164 ChEBI compounds (avg. 26 classes/compound) 14,476 ChEBI concepts found by SODIAC that were not assigned as parents 16
17 ChEBI Classifications ChEBI SODIAC (ChEBI) matches: CHEBI: ent-zingiberene ChEBI: is_a sesquiterpene (CHEBI:35189) SODIAC: 16 new proposals: CHEBI:33654 alicyclic compound CHEBI:33653 aliphatic compound CHEBI:32878 CHEBI:36480 CHEBI:33598 CHEBI:33595 CHEBI:33643 CHEBI:33646 alkadiene CHEBI:24632 CHEBI:18059 CHEBI:33661 CHEBI:35187 CHEBI:50073 p-menthadiene CHEBI:25826 CHEBI:50034 CHEBI:
18 ChEBI Classifications ChEBI SODIAC (ChEBI) cyclobutane (CHEBI:30377) is_a cycloalkane (CHEBI:23453) cyclohexane (CHEBI:29005) is_a cycloalkane (CHEBI:23453) cyclopentane (CHEBI:23492) is_a cycloalkane (CHEBI:23453) cyclopentane (CHEBI:23492) is_a cyclopentanes (CHEBI:23493). automation could help to eliminate human inconsistencies 18
19 Ontology Matching & Merging SODIAC coverage from 7,916 compound class concepts in common: ChEBI: 3,468 (of 16,156) MeSH: 2,570 (of 3,943) ClassyFire: 483 (of 4,832) Next steps: complete overlap with ChEBI and MeSH SODIAC parents SODIAC_xrefs ClassyFire parents ClassyFire_xref pubchem_id ,5:9,10-disecoandrostenes; acyclic ketones; alkene; bicyclic compounds; carbocycles; carbon compounds; carboxylic acids; cyclic ketones; dienes; oxygen compounds; CHEBI:32878; MeSH:D000475; CHEBI:33636; CHEBI:33575; MeSH:D002264; CHEBI:3992; CHEBI:33646; MeSH:D000466; MeSH:D017601; Medium-chain keto acids and derivatives; Hydroxy fatty acids; Branched fatty acids; Unsaturated fatty acids; Alphabranched alpha,beta-unsaturated ketones; Enones; Acryloyl compounds; Cyclic ketones; Monocarboxylic acids and derivatives; Enols; Carboxylic acids; Organic oxides; Hydrocarbon derivatives CHEBI:25754; CHEBI:24654; CHEBI:35819; CHEBI:27208; CHEBI:51689; CHEBI:51689; CHEBI:78840; CHEBI:3992; CHEBI:25384; CHEBI:33823; CHEBI:33575; CHEBI:25701; CHEBI:
20 Ontology Matching & Merging SODIAC / ClassyFire top-bottom statistics SODIAC_ID SODIAC_name count ClassyFire_ID ClassyFire_name count difference OC: alkene 8781 CHEMONTID: Alkenes OC: alkene derivatives 4910 CHEMONTID: Alkenes OC: organic anions 7219 CHEMONTID: Organic anions OC: cyclic ketones 3945 CHEMONTID: Cyclic ketones OC: primary aromatic amines 2606 CHEMONTID: Primary aromatic amines OC: dienes 2487 CHEMONTID: Alkadienes OC: secondary alcohols CHEMONTID: Secondary alcohols OC: phenols 1714 CHEMONTID: Phenols OC: secondary amines 1389 CHEMONTID: Secondary amines OC: inorganic compounds 1251 CHEMONTID: Inorganic compounds OC: thioethers 1132 CHEMONTID: Thioethers OC: pyrocatechols 1642 CHEMONTID: Catechols OC: acetate salts 8 CHEMONTID: Acetate salts OC: carboxylic acid salts 1090 CHEMONTID: Carboxylic acid salts OC: glycosylamines 41 CHEMONTID: Glycosylamines OC: tetrahydropyrans 4079 CHEMONTID: Oxanes OC: primary amines 45 CHEMONTID: Primary amines OC: acetals 1588 CHEMONTID: Acetals OC: carboxylic acids 5969 CHEMONTID: Carboxylic acids OC: azacyclic compounds 6174 CHEMONTID: Azacyclic compounds OC: carbonyl compounds 1335 CHEMONTID: Carbonyl compounds
21 PubChem Classifications 100GB ontology file 21
22 PubChem Classifications Statistics: find missing/wrong definitions / wrong compounds? Concept Aggregated Children Direct Children Concept chemistry 1,242,661,248 chemistry structural classification 1,240,832,811 structural classification compounds 1,227,157,075 compounds organic compounds 574,930,108 52,160 organic compounds cyclic compounds 379,604, ,327 cyclic compounds element compounds 248,665,892 element compounds organic nitrogen compounds 175,349,613 1,083,882 organic nitrogen compounds carbonyl compounds 169,293,274 1,342,539 carbonyl compounds cyclic compounds by element 135,330,213 cyclic compounds by element cyclic compounds by ring size 96,080,495 cyclic compounds by ring size 5-7-membered cyclic compounds 91,681, membered cyclic compounds chalcogen compounds 84,914,021 chalcogen compounds organic halogen compounds 83,842,178 21,610 organic halogen compounds cyclic compounds by number of rings 83,377,605 cyclic compounds by number of rings heterocycles 74,645,912 60,802 heterocycles e.g. organic compound: 2-Benzofuranmethyl [CH2]c1occ2ccccc12 ^1:0 (-)-α-gurjunene radicals? missing scaffold 22
23 PubChem Classifications Statistics: Find missing / wrong definitions Concept Aggregated Children Direct Children Concept iron cyano complex 0 iron cyano complex iron nitroso complex 0 iron nitroso complex 2-exo-hydroxy-1,4-cineole derivatives 0 2-exo-hydroxy-1,4-cineole derivatives Eucarvone derivatives 0 Eucarvone derivatives pinocarvone derivatives 0 pinocarvone derivatives ocimene derivatives 0 ocimene derivatives β-ocimene derivatives 0 β-ocimene derivatives (Z)-β-ocimene derivatives 0 (Z)-β-ocimene derivatives (E)-β-ocimene derivatives 0 (E)-β-ocimene derivatives radium salts 0 radium salts unclassified entities 0 unclassified entities iron cyano complex 0 iron cyano complex iron nitroso complex 0 iron nitroso complex 2-exo-hydroxy-1,4-cineole derivatives 0 2-exo-hydroxy-1,4-cineole derivatives Eucarvone derivatives 0 Eucarvone derivatives 23
24 Patent Classifications: ChemAnalyser ChemAnalyser: searching pinocarvone in patent and non-patent literature: 303 patent hits in total 20 patent hits in 2009 (53 in SciFinder) (1 in SciFinder) 24
25 ChemAnalyser: Cognitive Search Search term tomatidine (a class of natural products for food): ChemAnalyser 664 patent hit documents SciFinder 57 patent hit documents Search term sesquiterpenes (a class of natural products for food): ChemAnalyser 318,707 patent hit documents SciFinder 1,837 patent hit documents Search terms food additives + natural products + triterpenes ChemAnalyser 362,406 patent hit documents SciFinder 33 all hit documents 25
26 ChemAnalyser: Searching Materials Search term neodymium iron boron magnet : ChemAnalyser 25,616 patent hit documents SciFinder 0 patent hit documents Search term NdFeB : ChemAnalyser 25,616 patent hit documents SciFinder 6 patent hit documents Search term 304 stainless steel : ChemAnalyser 14,578 patent hit documents SciFinder 2,487 patent hit documents Search term cosmetic formulation + glyzyrrhizin : ChemAnalyser SciFinder 51,024 patent hit documents No References were found containing all of the concepts "cosmetic", "formulation" and "glyzyrrhizin" 26
27 Thanks! Special thanks to Stephen Evan Yannick Djoumbou Claudia Bobach & Anett please contact us for working on your cognitive Big Data computing project test account to ChemAnalyser supplying you with custom ontologies and tools visit 27
Chemical Ontologies. Chemical Ontologies. ChemAxon UGM May 23, 2012
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