{"id":"https://openalex.org/W2079898219","doi":"https://doi.org/10.1021/ci900461j","title":"A Semantic Web Ontology for Small Molecules and Their Biological Targets","display_name":"A Semantic Web Ontology for Small Molecules and Their Biological Targets","publication_year":2010,"publication_date":"2010-04-21","ids":{"openalex":"https://openalex.org/W2079898219","doi":"https://doi.org/10.1021/ci900461j","mag":"2079898219","pmid":"https://pubmed.ncbi.nlm.nih.gov/20405959"},"language":"en","primary_location":{"id":"doi:10.1021/ci900461j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900461j","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102345025","display_name":"Jooyoung Choi","orcid":null},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"JooYoung Choi","raw_affiliation_strings":["Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018252802","display_name":"Melissa J. Davis","orcid":"https://orcid.org/0000-0003-4864-7033"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Melissa J. Davis","raw_affiliation_strings":["Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109807677","display_name":"Andrew F. Newman","orcid":null},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew F. Newman","raw_affiliation_strings":["Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023552489","display_name":"Mark A. Ragan","orcid":"https://orcid.org/0000-0003-1672-7020"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Mark A. Ragan","raw_affiliation_strings":["Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102345025"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":null,"apc_paid":null,"fwci":1.3554,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.79810606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"50","issue":"5","first_page":"732","last_page":"741"},"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9950000047683716,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9911999702453613,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/drugbank","display_name":"DrugBank","score":0.8174212574958801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7325370907783508},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.6699616312980652},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6587665677070618},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.6321643590927124},{"id":"https://openalex.org/keywords/pubchem","display_name":"PubChem","score":0.6174808740615845},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.5970766544342041},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4903395175933838},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4328274130821228},{"id":"https://openalex.org/keywords/web-resource","display_name":"Web resource","score":0.41032886505126953},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.37277209758758545},{"id":"https://openalex.org/keywords/social-semantic-web","display_name":"Social Semantic Web","score":0.35498031973838806},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3456175923347473},{"id":"https://openalex.org/keywords/owl-s","display_name":"OWL-S","score":0.33038005232810974},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16193589568138123},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.1483820080757141},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12543326616287231}],"concepts":[{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.8174212574958801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7325370907783508},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.6699616312980652},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6587665677070618},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.6321643590927124},{"id":"https://openalex.org/C158180186","wikidata":"https://www.wikidata.org/wiki/Q278487","display_name":"PubChem","level":2,"score":0.6174808740615845},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.5970766544342041},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4903395175933838},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4328274130821228},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.41032886505126953},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.37277209758758545},{"id":"https://openalex.org/C534406577","wikidata":"https://www.wikidata.org/wiki/Q7550843","display_name":"Social Semantic Web","level":3,"score":0.35498031973838806},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3456175923347473},{"id":"https://openalex.org/C50382505","wikidata":"https://www.wikidata.org/wiki/Q2553356","display_name":"OWL-S","level":4,"score":0.33038005232810974},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16193589568138123},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.1483820080757141},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12543326616287231},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","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/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci900461j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900461j","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:20405959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20405959","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:205897","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W852643139","https://openalex.org/W1480017700","https://openalex.org/W1485209701","https://openalex.org/W1487060125","https://openalex.org/W1523302530","https://openalex.org/W1562643504","https://openalex.org/W1563421732","https://openalex.org/W1577783107","https://openalex.org/W1646048262","https://openalex.org/W1654805921","https://openalex.org/W1665997306","https://openalex.org/W1759440238","https://openalex.org/W1937151504","https://openalex.org/W1972772600","https://openalex.org/W1980352552","https://openalex.org/W1986479479","https://openalex.org/W1990890881","https://openalex.org/W2002043951","https://openalex.org/W2009313526","https://openalex.org/W2025142263","https://openalex.org/W2033377040","https://openalex.org/W2061459648","https://openalex.org/W2063015833","https://openalex.org/W2066024537","https://openalex.org/W2074944495","https://openalex.org/W2076327529","https://openalex.org/W2093410900","https://openalex.org/W2097698606","https://openalex.org/W2108177663","https://openalex.org/W2124957697","https://openalex.org/W2127451705","https://openalex.org/W2127789342","https://openalex.org/W2128966273","https://openalex.org/W2144631782","https://openalex.org/W2147873108","https://openalex.org/W2149963380","https://openalex.org/W2154829072","https://openalex.org/W2156484428","https://openalex.org/W2156779720","https://openalex.org/W2165428180","https://openalex.org/W2170146596","https://openalex.org/W2242459625","https://openalex.org/W2767905780","https://openalex.org/W4230606593"],"related_works":["https://openalex.org/W3066241754","https://openalex.org/W2151971404","https://openalex.org/W2020850455","https://openalex.org/W2170146596","https://openalex.org/W3124354180","https://openalex.org/W3164508606","https://openalex.org/W2029912875","https://openalex.org/W3207789654","https://openalex.org/W2110781397","https://openalex.org/W1993352447"],"abstract_inverted_index":{"A":[0],"wide":[1],"range":[2],"of":[3,11,37,50,65,77,115,147,151,183],"data":[4,29,70,130,134,161,166],"on":[5],"sequences,":[6],"structures,":[7],"pathways,":[8],"and":[9,13,21,25,34,68,75,79,92,107,118,139,141,164,171,190,193],"networks":[10],"genes":[12],"gene":[14],"products":[15],"is":[16],"available":[17],"for":[18,111],"hypothesis":[19],"testing":[20],"discovery":[22],"in":[23,187,194],"biological":[24,35],"biomedical":[26,78],"research.":[27,81],"However,":[28],"describing":[30],"the":[31,59,63,73,84,181],"physical,":[32],"chemical,":[33,188],"properties":[36,114],"small":[38,66,116],"molecules":[39,117],"have":[40,58],"not":[41],"been":[42],"well-integrated":[43],"with":[44,54,121],"these":[45],"resources.":[46],"Semantically":[47],"rich":[48],"representations":[49],"chemical":[51,163],"data,":[52],"combined":[53],"Semantic":[55,85,184],"Web":[56,86,93,185],"technologies,":[57],"potential":[60,182],"to":[61,97,143],"enable":[62],"integration":[64],"molecule":[67],"biomolecular":[69,165],"resources,":[71],"expanding":[72],"scope":[74],"power":[76],"pharmacological":[80,191],"We":[82,126],"employed":[83],"technologies":[87,186],"Resource":[88],"Description":[89],"Framework":[90],"(RDF)":[91],"Ontology":[94,102],"Language":[95],"(OWL)":[96],"generate":[98],"a":[99],"Small":[100],"Molecule":[101],"(SMO)":[103],"that":[104,160,172],"represents":[105],"concepts":[106],"provides":[108],"unique":[109],"identifiers":[110],"biologically":[112],"relevant":[113],"their":[119],"interactions":[120],"biomolecules,":[122],"such":[123],"as":[124,156],"proteins.":[125],"instanced":[127],"SMO":[128,148],"using":[129],"from":[131,162],"three":[132],"public":[133],"sources,":[135],"i.e.,":[136],"DrugBank,":[137],"PubChem":[138],"UniProt,":[140],"converted":[142],"RDF":[144],"triples.":[145],"Evaluation":[146],"by":[149],"use":[150],"predetermined":[152],"competency":[153],"questions":[154],"implemented":[155],"SPARQL":[157],"queries":[158],"demonstrated":[159],"sources":[167],"were":[168],"effectively":[169],"represented":[170],"useful":[173],"knowledge":[174],"can":[175],"be":[176],"extracted.":[177],"These":[178],"results":[179],"illustrate":[180],"biological,":[189],"research":[192],"drug":[195],"discovery.":[196]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
