{"id":"https://openalex.org/W2151449987","doi":"https://doi.org/10.1186/1758-2946-3-s1-o4","title":"Chemical ontologies: what are they, what are they for and what are the challenges","display_name":"Chemical ontologies: what are they, what are they for and what are the challenges","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2151449987","doi":"https://doi.org/10.1186/1758-2946-3-s1-o4","mag":"2151449987"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-O4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044072805","display_name":"Janna Hastings","orcid":"https://orcid.org/0000-0002-3469-4923"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Janna Hastings","raw_affiliation_strings":["Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054754797","display_name":"Nico Adams","orcid":"https://orcid.org/0000-0003-3136-1338"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nico Adams","raw_affiliation_strings":["Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002211213","display_name":"Marcus Ennis","orcid":"https://orcid.org/0000-0002-6580-6297"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marcus Ennis","raw_affiliation_strings":["Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014513655","display_name":"Duncan Hull","orcid":"https://orcid.org/0000-0003-2387-503X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Duncan Hull","raw_affiliation_strings":["Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040194803","display_name":"Christoph Steinbeck","orcid":"https://orcid.org/0000-0001-6966-0814"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christoph Steinbeck","raw_affiliation_strings":["Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5044072805"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.133,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.54376028,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8061914443969727},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.703784704208374},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.6563616991043091},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.6411779522895813},{"id":"https://openalex.org/keywords/web-ontology-language","display_name":"Web Ontology Language","score":0.5196048617362976},{"id":"https://openalex.org/keywords/idef5","display_name":"IDEF5","score":0.5027520656585693},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.4819714426994324},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.4614481031894684},{"id":"https://openalex.org/keywords/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.45385584235191345},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.44946202635765076},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.4456360340118408},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.44108515977859497},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4245569109916687},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.4148298501968384},{"id":"https://openalex.org/keywords/chemical-database","display_name":"Chemical database","score":0.41205644607543945},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3969230055809021},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.28071820735931396},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23439452052116394},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.21443617343902588},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17156562209129333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8061914443969727},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.703784704208374},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.6563616991043091},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.6411779522895813},{"id":"https://openalex.org/C101230327","wikidata":"https://www.wikidata.org/wiki/Q826165","display_name":"Web Ontology Language","level":3,"score":0.5196048617362976},{"id":"https://openalex.org/C118248724","wikidata":"https://www.wikidata.org/wiki/Q5969997","display_name":"IDEF5","level":4,"score":0.5027520656585693},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.4819714426994324},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.4614481031894684},{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.45385584235191345},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.44946202635765076},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.4456360340118408},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.44108515977859497},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4245569109916687},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.4148298501968384},{"id":"https://openalex.org/C203394866","wikidata":"https://www.wikidata.org/wiki/Q2881060","display_name":"Chemical database","level":2,"score":0.41205644607543945},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3969230055809021},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.28071820735931396},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23439452052116394},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.21443617343902588},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17156562209129333},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:867ce8f59d6f4df38a9d68171b5fa205","is_oa":true,"landing_page_url":"https://doaj.org/article/867ce8f59d6f4df38a9d68171b5fa205","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss Suppl 1, p O4 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083557","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:researchbank.swinburne.edu.au:e86631b0-72cd-4ebe-a3fa-9c76121fcb87/1","is_oa":false,"landing_page_url":"http://hdl.handle.net/1959.3/452504","pdf_url":null,"source":{"id":"https://openalex.org/S4306401157","display_name":"Swinburne Research Bank (Swinburne University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I57093077","host_organization_name":"Swinburne University of Technology","host_organization_lineage":["https://openalex.org/I57093077"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics: Abstracts of the 6th German Conference on Chemoinformatics, GCC 2010, Vol. 3, no. S1, abstract no. 04","raw_type":""}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2151449987.pdf","grobid_xml":"https://content.openalex.org/works/W2151449987.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W72872960","https://openalex.org/W110386102","https://openalex.org/W1484151351"],"related_works":["https://openalex.org/W2153037537","https://openalex.org/W2317928565","https://openalex.org/W3143892890","https://openalex.org/W2561309435","https://openalex.org/W1801798365","https://openalex.org/W2942194862","https://openalex.org/W1537617436","https://openalex.org/W2133550211","https://openalex.org/W2401209741","https://openalex.org/W184366147"],"abstract_inverted_index":{"Ontologies":[0,183],"encode":[1],"human":[2,19],"knowledge":[3,17,31],"in":[4,25,32,47,150,160,208,222,231],"computationally":[5],"accessible":[6],"forms.":[7],"They":[8],"are":[9,107,115,184],"designed":[10],"to":[11,56,117,138,157],"narrow":[12],"the":[13,16,22,42,74,131,151,169,191,198,209,226,241],"gap":[14],"between":[15],"of":[18,45,102,120,127,130,171,177,197,200,228,243],"experts":[20],"and":[21,38,60,70,89,96,104,122,145,163,176],"functionality":[23],"available":[24],"computer":[26],"systems,":[27],"by":[28,186],"expressing":[29],"expert":[30],"a":[33,123],"manner":[34],"computers":[35],"can":[36],"manipulate":[37],"reason":[39],"over.":[40],"With":[41],"ever-growing":[43],"deluge":[44],"data":[46],"modern":[48],"scientific":[49,152],"domains,":[50],"researchers":[51],"need":[52],"intelligent":[53],"tools":[54,236],"able":[55],"filter":[57],"out":[58],"irrelevant":[59],"automatically":[61],"organise":[62],"relevant":[63],"information":[64,91],"into":[65],"meaningful":[66],"categories.":[67],"The":[68],"Chemoinformatics":[69],"Metabolism":[71],"team":[72],"at":[73],"EBI":[75],"is":[76,203,240],"developing":[77],"chemical":[78,82,87,90,132,201,206,229,238],"ontologies":[79,99,137,149],"for":[80,109,135,142,217],"structure-based":[81],"classification,":[83,88],"role":[84],"or":[85],"bioactivity-based":[86],"entities":[92],"such":[93,136,189],"as":[94,190],"descriptors":[95],"algorithms.":[97],"Our":[98],"provide":[100],"collections":[101],"names":[103],"synonyms":[105],"which":[106,114],"useful":[108,141],"text":[110],"mining,":[111],"stable":[112],"identifiers":[113],"essential":[116],"semantic":[118],"integration":[119],"data,":[121],"semantically":[124],"rich":[125],"encoding":[126],"many":[128],"aspects":[129],"domain.":[133],"But":[134],"be":[139,158],"maximally":[140],"diverse":[143],"users":[144],"interoperable":[146],"with":[147,237],"other":[148],"domain,":[153],"similar-sounding":[154],"things":[155],"have":[156],"disentangled":[159],"our":[161,164,223],"language":[162],"ontology.":[165],"Recent":[166,220],"work":[167],"addresses":[168],"distinguishing":[170],"structures":[172,207,213],"from":[173,179],"chemicals":[174],"[1],":[175],"bioactivity":[178],"drug":[180],"uses":[181],"[2].":[182],"backed":[185],"logical":[187],"formalisms":[188],"Web":[192],"Ontology":[193],"Language,":[194],"OWL.":[195],"One":[196],"challenges":[199],"ontology":[202,239],"representing":[204],"complex":[205],"underlying":[210],"formalism.":[211],"Cyclic":[212],"prove":[214],"particularly":[215],"challenging":[216],"logic-based":[218],"representation.":[219],"research":[221],"group":[224],"investigated":[225],"inclusion":[227],"graphs":[230],"OWL":[232],"[3].":[233],"Integrating":[234],"chemoinformatics":[235],"subject":[242],"ongoing":[244],"research.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
