{"id":"https://openalex.org/W2099100406","doi":"https://doi.org/10.1186/1471-2105-6-s1-s21","title":"Finding genomic ontology terms in text using evidence content","display_name":"Finding genomic ontology terms in text using evidence content","publication_year":2005,"publication_date":"2005-05-01","ids":{"openalex":"https://openalex.org/W2099100406","doi":"https://doi.org/10.1186/1471-2105-6-s1-s21","mag":"2099100406","pmid":"https://pubmed.ncbi.nlm.nih.gov/15960834"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-s1-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s21","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-S21","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/10.1186/1471-2105-6-S1-S21","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014333753","display_name":"Francisco M. Couto","orcid":"https://orcid.org/0000-0003-0627-1496"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Francisco M Couto","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, Portugal. fcouto@di.fc.ul.pt","Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, , Portugal"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, Portugal. fcouto@di.fc.ul.pt","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, , Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043057704","display_name":"M\u00e1rio J. Silva","orcid":"https://orcid.org/0000-0002-5452-6185"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"M\u00e1rio J Silva","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, Portugal","Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, , Portugal"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias da Universidade de Lisboa, , Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102987146","display_name":"Pedro M. Coutinho","orcid":"https://orcid.org/0000-0003-3992-0384"},"institutions":[{"id":"https://openalex.org/I4210146787","display_name":"Architecture et Fonction des Macromol\u00e9cules Biologiques","ror":"https://ror.org/04jm8zw14","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210146787"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pedro M Coutinho","raw_affiliation_strings":["Architecture et Fonction des Macromol\u00e9cules Biologiques, CNRS, Marseille, France","Architecture et Fonction des Macromolecules Biologiques, CNRS, Marseille, France"],"affiliations":[{"raw_affiliation_string":"Architecture et Fonction des Macromol\u00e9cules Biologiques, CNRS, Marseille, France","institution_ids":["https://openalex.org/I4210146787","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Architecture et Fonction des Macromolecules Biologiques, CNRS, Marseille, France","institution_ids":["https://openalex.org/I4210146787","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014333753"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.6583,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.89901408,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"S1","first_page":"S21","last_page":"S21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9783999919891357,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9692999720573425,"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":0.8018302321434021},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6931065320968628},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6911234855651855},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6511549353599548},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6195892691612244},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5171448588371277},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5024433135986328},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.4184423089027405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3428501486778259},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.0963386595249176},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08048182725906372},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07652944326400757}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8018302321434021},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6931065320968628},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6911234855651855},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6511549353599548},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6195892691612244},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5171448588371277},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5024433135986328},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4184423089027405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3428501486778259},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0963386595249176},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08048182725906372},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07652944326400757},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013782","descriptor_name":"Textbooks as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013782","descriptor_name":"Textbooks as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013782","descriptor_name":"Textbooks as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-6-s1-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s21","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-S21","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:15960834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15960834","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:europepmc.org:1423895","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1869014","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:repositorio.ul.pt:10451/14991","is_oa":true,"landing_page_url":"http://hdl.handle.net/10451/14991","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-6-s1-s21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s21","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-S21","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099100406.pdf","grobid_xml":"https://content.openalex.org/works/W2099100406.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1659833910","https://openalex.org/W1967376701","https://openalex.org/W2097106271","https://openalex.org/W2108491719","https://openalex.org/W2112441656","https://openalex.org/W2134226301","https://openalex.org/W2151598682","https://openalex.org/W2152183901"],"related_works":["https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W1999129612","https://openalex.org/W2009940763","https://openalex.org/W4361192415","https://openalex.org/W2126804125","https://openalex.org/W2946410450","https://openalex.org/W2162782320","https://openalex.org/W2137318037","https://openalex.org/W4386637333"],"abstract_inverted_index":{"From":[0],"the":[1],"performance":[2],"obtained":[3],"in":[4,22],"BioCreative,":[5],"we":[6],"concluded":[7],"that":[8],"an":[9],"automatic":[10],"annotation":[11],"system":[12],"can":[13],"effectively":[14],"use":[15],"our":[16],"method":[17],"to":[18],"identify":[19],"biological":[20],"properties":[21],"unstructured":[23],"text.":[24]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
