{"id":"https://openalex.org/W2143916531","doi":"https://doi.org/10.1186/2041-1480-5-17","title":"A rule-based ontological framework for the classification of molecules","display_name":"A rule-based ontological framework for the classification of molecules","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2143916531","doi":"https://doi.org/10.1186/2041-1480-5-17","mag":"2143916531","pmid":"https://pubmed.ncbi.nlm.nih.gov/24735706"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-17","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-17","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-17","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020439365","display_name":"Despoina Magka","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Despoina Magka","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK","Department of Computer Science University of Oxford Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science University of Oxford Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087579719","display_name":"Markus Kr\u00f6tzsch","orcid":"https://orcid.org/0000-0002-9172-2601"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"TU Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Kr\u00f6tzsch","raw_affiliation_strings":["Department of Computer Science, Technical University of Dresden, Dresden, Germany","Department of Computer Science, Technical University of Dresden, Dresden, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Technical University of Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Department of Computer Science, Technical University of Dresden, Dresden, Germany#TAB#","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060350556","display_name":"Ian Horrocks","orcid":"https://orcid.org/0000-0002-2685-7462"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian Horrocks","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK","Department of Computer Science University of Oxford Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science University of Oxford Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020439365"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":1.2685,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.85825522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9995999932289124,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"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":0.9592999815940857,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8628032803535461},{"id":"https://openalex.org/keywords/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.7938532829284668},{"id":"https://openalex.org/keywords/datalog","display_name":"Datalog","score":0.6873841285705566},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6545062065124512},{"id":"https://openalex.org/keywords/web-ontology-language","display_name":"Web Ontology Language","score":0.633599579334259},{"id":"https://openalex.org/keywords/description-logic","display_name":"Description logic","score":0.6147753000259399},{"id":"https://openalex.org/keywords/ontology-language","display_name":"Ontology language","score":0.5542702078819275},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.4769526720046997},{"id":"https://openalex.org/keywords/semantic-reasoner","display_name":"Semantic reasoner","score":0.46006810665130615},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4371912479400635},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.4133504331111908},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3219667673110962},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2832747995853424}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8628032803535461},{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.7938532829284668},{"id":"https://openalex.org/C148230440","wikidata":"https://www.wikidata.org/wiki/Q1172264","display_name":"Datalog","level":2,"score":0.6873841285705566},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6545062065124512},{"id":"https://openalex.org/C101230327","wikidata":"https://www.wikidata.org/wiki/Q826165","display_name":"Web Ontology Language","level":3,"score":0.633599579334259},{"id":"https://openalex.org/C102993220","wikidata":"https://www.wikidata.org/wiki/Q387196","display_name":"Description logic","level":2,"score":0.6147753000259399},{"id":"https://openalex.org/C61673122","wikidata":"https://www.wikidata.org/wiki/Q7095059","display_name":"Ontology language","level":3,"score":0.5542702078819275},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.4769526720046997},{"id":"https://openalex.org/C9616225","wikidata":"https://www.wikidata.org/wiki/Q3929429","display_name":"Semantic reasoner","level":2,"score":0.46006810665130615},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4371912479400635},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.4133504331111908},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3219667673110962},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2832747995853424},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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:10.1186/2041-1480-5-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-17","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-17","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:24735706","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24735706","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 biomedical semantics","raw_type":null},{"id":"pmh:oai:europepmc.org:3030457","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4040517","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:ora.ox.ac.uk:uuid:86b3ef4c-5106-43f6-9814-e83d6ada08c5","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:86b3ef4c-5106-43f6-9814-e83d6ada08c5","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-5-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-17","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-17","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G5128574789","display_name":null,"funder_award_id":"EP/H051511/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G610975920","display_name":"Scalable End-user Access to Big Data","funder_award_id":"318338","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8521439554","display_name":null,"funder_award_id":"EP/L012138/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143916531.pdf","grobid_xml":"https://content.openalex.org/works/W2143916531.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1484151351","https://openalex.org/W1502374275","https://openalex.org/W1503647529","https://openalex.org/W1508604947","https://openalex.org/W1514332291","https://openalex.org/W1539707058","https://openalex.org/W1564494788","https://openalex.org/W1582025563","https://openalex.org/W1601495365","https://openalex.org/W1672891595","https://openalex.org/W1794390359","https://openalex.org/W1806630989","https://openalex.org/W1943070153","https://openalex.org/W1976055110","https://openalex.org/W1976892175","https://openalex.org/W1980352552","https://openalex.org/W1990890881","https://openalex.org/W1996497762","https://openalex.org/W1997201617","https://openalex.org/W2018590585","https://openalex.org/W2028133290","https://openalex.org/W2029380217","https://openalex.org/W2033377040","https://openalex.org/W2038559836","https://openalex.org/W2051810242","https://openalex.org/W2074909362","https://openalex.org/W2098889731","https://openalex.org/W2106350001","https://openalex.org/W2110732896","https://openalex.org/W2114124738","https://openalex.org/W2114940395","https://openalex.org/W2124834853","https://openalex.org/W2130367921","https://openalex.org/W2140611297","https://openalex.org/W2143614763","https://openalex.org/W2148361784","https://openalex.org/W2148797284","https://openalex.org/W2155459813","https://openalex.org/W2156226590","https://openalex.org/W2157058953","https://openalex.org/W2159207970","https://openalex.org/W2161723275","https://openalex.org/W2168356677","https://openalex.org/W2201043149","https://openalex.org/W2216357933","https://openalex.org/W2294320291","https://openalex.org/W2398313167","https://openalex.org/W2400064635","https://openalex.org/W2976869771","https://openalex.org/W3009281336","https://openalex.org/W3102313542","https://openalex.org/W3192290435","https://openalex.org/W4239167359"],"related_works":["https://openalex.org/W2952205895","https://openalex.org/W201976190","https://openalex.org/W2021763726","https://openalex.org/W119226878","https://openalex.org/W2188933543","https://openalex.org/W2398931073","https://openalex.org/W2405742406","https://openalex.org/W1988576567","https://openalex.org/W2542061993","https://openalex.org/W2214104119"],"abstract_inverted_index":{"Our":[0],"proposed":[1],"methodology":[2],"can":[3],"form":[4],"the":[5,15,34,39,42,52,64,89,92],"basis":[6],"of":[7,17,33,41,58,66,94,98],"an":[8],"ontology-mediated":[9],"application":[10],"to":[11,28,38,45,51],"assist":[12],"biocurators":[13],"in":[14],"production":[16],"complete":[18],"and":[19,37,69,79,101],"error-free":[20],"taxonomies.":[21],"Moreover,":[22],"such":[23],"a":[24,29,55,67,95],"tool":[25],"could":[26,62,86],"contribute":[27],"more":[30],"rapid":[31],"development":[32],"ChEBI":[35,43],"ontology":[36],"efforts":[40],"team":[44],"make":[46],"annotated":[47],"chemical":[48],"datasets":[49],"available":[50],"public.":[53],"From":[54],"modelling":[56],"point":[57],"view,":[59],"our":[60],"approach":[61],"stimulate":[63],"adoption":[65],"different":[68],"expressive":[70],"reasoning":[71],"paradigm":[72],"based":[73],"on":[74],"rules":[75],"for":[76,91],"which":[77],"state-of-the-art":[78],"highly":[80],"optimised":[81],"reasoners":[82],"are":[83],"available;":[84],"it":[85],"thus":[87],"pave":[88],"way":[90],"representation":[93],"broader":[96],"spectrum":[97],"life":[99],"sciences":[100],"biomedical":[102],"knowledge.":[103]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
