{"id":"https://openalex.org/W1999773781","doi":"https://doi.org/10.1186/1471-2105-10-125","title":"Survey-based naming conventions for use in OBO Foundry ontology development","display_name":"Survey-based naming conventions for use in OBO Foundry ontology development","publication_year":2009,"publication_date":"2009-04-27","ids":{"openalex":"https://openalex.org/W1999773781","doi":"https://doi.org/10.1186/1471-2105-10-125","mag":"1999773781","pmid":"https://pubmed.ncbi.nlm.nih.gov/19397794"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-125","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-125","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-125","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-125","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049157539","display_name":"Daniel Schober","orcid":"https://orcid.org/0000-0001-8014-6648"},"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"]},{"id":"https://openalex.org/I2801240073","display_name":"University Medical Center Freiburg","ror":"https://ror.org/03vzbgh69","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2801240073"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Daniel Schober","raw_affiliation_strings":["EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. schober@imbi.uni-freiburg.de","EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","Institute of Medical Biometry and Medical Informatics (IMBI), University Medical Center, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. schober@imbi.uni-freiburg.de","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Institute of Medical Biometry and Medical Informatics (IMBI), University Medical Center, Freiburg, Germany","institution_ids":["https://openalex.org/I2801240073"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051216244","display_name":"Barry Smith","orcid":"https://orcid.org/0000-0003-1384-116X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barry Smith","raw_affiliation_strings":["Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, NY, USA","Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076920798","display_name":"Suzanna Lewis","orcid":"https://orcid.org/0000-0002-8343-612X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanna E Lewis","raw_affiliation_strings":["Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA","Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042638083","display_name":"W Ku\u015bnierczyk","orcid":null},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Waclaw Kusnierczyk","raw_affiliation_strings":["Department of Information and Computer Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computer Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069866481","display_name":"Jane Lomax","orcid":"https://orcid.org/0000-0001-8865-4321"},"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"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jane Lomax","raw_affiliation_strings":["EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002223413","display_name":"Chris Mungall","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Mungall","raw_affiliation_strings":["Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA","Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075874654","display_name":"Chris Taylor","orcid":"https://orcid.org/0000-0002-9666-798X"},"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"]},{"id":"https://openalex.org/I131579929","display_name":"Mansfield University","ror":"https://ror.org/01emtgd92","country_code":"US","type":"education","lineage":["https://openalex.org/I131579929"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Chris F Taylor","raw_affiliation_strings":["EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","NERC Environmental Bioinformatics Centre (NEBC), Mansfield Road, Oxford, OX1 3SR, UK","EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","NERC Environmental Bioinformatics Centre (NEBC), Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"NERC Environmental Bioinformatics Centre (NEBC), Mansfield Road, Oxford, OX1 3SR, UK","institution_ids":["https://openalex.org/I131579929"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"NERC Environmental Bioinformatics Centre (NEBC), Oxford, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018395535","display_name":"Philippe Rocca\u2010Serra","orcid":"https://orcid.org/0000-0001-9853-5668"},"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"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Philippe Rocca-Serra","raw_affiliation_strings":["EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008806860","display_name":"Susanna\u2010Assunta Sansone","orcid":"https://orcid.org/0000-0001-5306-5690"},"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"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Susanna-Assunta Sansone","raw_affiliation_strings":["EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5008806860"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.243,"has_fulltext":true,"cited_by_count":86,"citation_normalized_percentile":{"value":0.94802148,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"125","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9824000000953674,"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":0.9824000000953674,"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":0.013500000350177288,"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":0.00039999998989515007,"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/computer-science","display_name":"Computer science","score":0.7893391847610474},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7709949016571045},{"id":"https://openalex.org/keywords/navigability","display_name":"Navigability","score":0.6042422652244568},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5485199689865112},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5471252202987671},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5421276092529297},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4483906626701355},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.44335752725601196},{"id":"https://openalex.org/keywords/readability","display_name":"Readability","score":0.41049593687057495},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4037241041660309},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3347470164299011},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3266749382019043},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.29806679487228394},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22850432991981506},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.1943754255771637},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1029522716999054}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7893391847610474},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7709949016571045},{"id":"https://openalex.org/C2778972660","wikidata":"https://www.wikidata.org/wiki/Q1666353","display_name":"Navigability","level":2,"score":0.6042422652244568},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5485199689865112},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5471252202987671},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5421276092529297},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4483906626701355},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.44335752725601196},{"id":"https://openalex.org/C2778143727","wikidata":"https://www.wikidata.org/wiki/Q1820650","display_name":"Readability","level":2,"score":0.41049593687057495},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4037241041660309},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3347470164299011},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3266749382019043},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.29806679487228394},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22850432991981506},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.1943754255771637},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1029522716999054},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","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},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","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}],"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":"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":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","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":"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":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-10-125","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-125","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-125","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19397794","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19397794","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1626264","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626264","pdf_url":"https://www.osti.gov/servlets/purl/1626264","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:e737a9c987934697883547c5ff1301e1","is_oa":true,"landing_page_url":"https://doaj.org/article/e737a9c987934697883547c5ff1301e1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 125 (2009)","raw_type":"article"},{"id":"pmh:oai:philarchive.org/rec/SCHSNC","is_oa":false,"landing_page_url":"https://philarchive.org/rec/SCHSNC","pdf_url":null,"source":{"id":"https://openalex.org/S4306402130","display_name":"PhilPapers (PhilPapers Foundation)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:philpapers.org/rec/SCHSNC","is_oa":false,"landing_page_url":"https://philpapers.org/rec/SCHSNC","pdf_url":null,"source":{"id":"https://openalex.org/S4306402131","display_name":"PhilPapers (PhilPapers Foundation)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2684543","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2684543","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-125","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-125","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-125","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1770607089","display_name":"Ontology development for the study of metabolism and functional genomics","funder_award_id":"BB/D524283/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7775520706","display_name":null,"funder_award_id":"BB/E025080/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8986954972","display_name":null,"funder_award_id":"BB/D524283/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1999773781.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1490878976","https://openalex.org/W1581987636","https://openalex.org/W1845814381","https://openalex.org/W1871852719","https://openalex.org/W1999773781","https://openalex.org/W2027398710","https://openalex.org/W2089872141","https://openalex.org/W2096704019","https://openalex.org/W2100572047","https://openalex.org/W2103254943","https://openalex.org/W2113142309","https://openalex.org/W2127480960","https://openalex.org/W2128307328","https://openalex.org/W2134418889","https://openalex.org/W2160674432","https://openalex.org/W2163652739","https://openalex.org/W2750987793"],"related_works":["https://openalex.org/W2127299687","https://openalex.org/W1506177826","https://openalex.org/W2532736362","https://openalex.org/W2726617685","https://openalex.org/W1562796463","https://openalex.org/W3135477004","https://openalex.org/W1530162452","https://openalex.org/W2111194626","https://openalex.org/W2008629522","https://openalex.org/W2399880385"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"wide":[2],"variety":[3],"of":[4,27,61,74,84,107,115,137,164,174,199,228,241,247],"ontologies":[5,153,229,242],"relevant":[6],"to":[7,46,125,142,155,189,205,230],"the":[8,16,57,129,135,162,239],"biological":[9,130],"and":[10,20,41,59,65,69,79,105,119,154,177,212,216],"medical":[11],"domains":[12],"are":[13,76,96,147],"available":[14],"through":[15],"OBO":[17,151,184],"Foundry":[18,152,185],"portal,":[19],"their":[21,67,158],"number":[22],"is":[23,34,88,193],"growing":[24],"rapidly.":[25],"Integration":[26],"these":[28],"ontologies,":[29],"while":[30],"requiring":[31],"considerable":[32],"effort,":[33],"extremely":[35],"desirable.":[36],"However,":[37],"heterogeneities":[38],"in":[39,52,128,183,244],"format":[40],"style":[42],"pose":[43],"serious":[44],"obstacles":[45],"such":[47],"integration.":[48,70],"In":[49],"particular,":[50],"inconsistencies":[51],"naming":[53,86,117,145,163,191,222],"conventions":[54,87,95,118,146,179,192,202,223],"can":[55],"impair":[56],"readability":[58],"navigability":[60],"ontology":[62,206],"class":[63],"hierarchies,":[64],"hinder":[66],"alignment":[68],"While":[71],"other":[72],"sources":[73],"diversity":[75],"tremendously":[77],"complex":[78],"challenging,":[80],"agreeing":[81],"a":[82,113,138,197],"set":[83,173],"common":[85,190],"an":[89,171],"achievable":[90],"goal,":[91],"particularly":[92],"if":[93],"those":[94],"based":[97],"on":[98],"lessons":[99],"drawn":[100],"from":[101],"pooled":[102],"practical":[103],"experience":[104],"surveys":[106],"community":[108],"opinion.":[109],"RESULTS:":[110],"We":[111,132],"summarize":[112],"review":[114],"existing":[116],"highlight":[120],"certain":[121],"disadvantages":[122],"with":[123],"respect":[124],"general":[126],"applicability":[127],"domain.":[131],"also":[133,225],"present":[134],"results":[136],"survey":[139],"carried":[140],"out":[141],"establish":[143],"which":[144],"currently":[148],"employed":[149],"by":[150,238],"determine":[156],"what":[157,234],"special":[159],"requirements":[160],"regarding":[161],"entities":[165],"might":[166],"be.":[167],"Lastly,":[168],"we":[169],"propose":[170],"initial":[172],"typographic,":[175],"syntactic":[176],"semantic":[178],"for":[180],"labelling":[181],"classes":[182],"ontologies.":[186,220],"CONCLUSION:":[187],"Adherence":[188],"more":[194,231],"than":[195],"just":[196],"matter":[198],"aesthetics.":[200],"Such":[201],"provide":[203],"guidance":[204],"creators,":[207],"help":[208],"developers":[209],"avoid":[210],"flaws":[211],"inaccuracies":[213],"when":[214,218],"editing,":[215],"especially":[217],"interlinking,":[219],"Common":[221],"will":[224],"assist":[226],"consumers":[227],"readily":[232],"understand":[233],"meanings":[235],"were":[236],"intended":[237],"authors":[240],"used":[243],"annotating":[245],"bodies":[246],"data.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":12}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
