{"id":"https://openalex.org/W2136437513","doi":"https://doi.org/10.1186/s12859-015-0472-9","title":"Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research","display_name":"Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research","publication_year":2015,"publication_date":"2015-02-20","ids":{"openalex":"https://openalex.org/W2136437513","doi":"https://doi.org/10.1186/s12859-015-0472-9","mag":"2136437513","pmid":"https://pubmed.ncbi.nlm.nih.gov/25886734"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0472-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0472-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0472-9","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/s12859-015-0472-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072446636","display_name":"\u00c1lex Bravo","orcid":"https://orcid.org/0000-0001-5999-6269"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"\u00c0lex Bravo","raw_affiliation_strings":["Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. abravo@imim.es","Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. abravo@imim.es","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054199754","display_name":"Janet Pi\u00f1ero","orcid":"https://orcid.org/0000-0003-1244-7654"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Janet Pi\u00f1ero","raw_affiliation_strings":["Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. jpinero@imim.es","Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. jpinero@imim.es","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080481806","display_name":"N\u00faria Queralt-Rosi\u00f1ach","orcid":"https://orcid.org/0000-0003-0169-8159"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"N\u00faria Queralt-Rosinach","raw_affiliation_strings":["Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. nqueralt@imim.es","Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. nqueralt@imim.es","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010193662","display_name":"Michael Rautschka","orcid":null},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Michael Rautschka","raw_affiliation_strings":["Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. rautschy@gmail.com","Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. rautschy@gmail.com","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028427590","display_name":"Laura I. Furlong","orcid":"https://orcid.org/0000-0002-9383-528X"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Laura I Furlong","raw_affiliation_strings":["Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. lfurlong@imim.es","Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain. lfurlong@imim.es","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028427590"],"corresponding_institution_ids":["https://openalex.org/I170486558"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":7.3798,"has_fulltext":true,"cited_by_count":253,"citation_normalized_percentile":{"value":0.97863849,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"1","first_page":"55","last_page":"55"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9961000084877014,"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":0.9961000084877014,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.000699999975040555,"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/T10028","display_name":"Topic Modeling","score":0.00039999998989515007,"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/dna-microarray","display_name":"DNA microarray","score":0.6353024244308472},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5689140558242798},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5570839643478394},{"id":"https://openalex.org/keywords/translational-research","display_name":"Translational research","score":0.518650233745575},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5017514228820801},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.47246694564819336},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44065237045288086},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41538673639297485},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.385865181684494},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.371127724647522},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.346590131521225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3304404020309448},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27377891540527344},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.2535143494606018},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2083895206451416},{"id":"https://openalex.org/keywords/biotechnology","display_name":"Biotechnology","score":0.12111163139343262},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09715601801872253}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6353024244308472},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5689140558242798},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5570839643478394},{"id":"https://openalex.org/C128544194","wikidata":"https://www.wikidata.org/wiki/Q474859","display_name":"Translational research","level":2,"score":0.518650233745575},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5017514228820801},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.47246694564819336},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44065237045288086},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41538673639297485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.385865181684494},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.371127724647522},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.346590131521225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3304404020309448},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27377891540527344},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.2535143494606018},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2083895206451416},{"id":"https://openalex.org/C150903083","wikidata":"https://www.wikidata.org/wiki/Q7108","display_name":"Biotechnology","level":1,"score":0.12111163139343262},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09715601801872253},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003863","descriptor_name":"Depression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003863","descriptor_name":"Depression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003863","descriptor_name":"Depression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057170","descriptor_name":"Translational Research, Biomedical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057170","descriptor_name":"Translational Research, Biomedical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057170","descriptor_name":"Translational Research, Biomedical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0472-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0472-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0472-9","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:25886734","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25886734","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:repositori.upf.edu:10230/23654","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/23654","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3430079","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4466840","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0472-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0472-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0472-9","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":[{"score":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2759350490","display_name":null,"funder_award_id":"115191","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G3222439407","display_name":null,"funder_award_id":"PI13/00082","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G3829048491","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3848063861","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4108925770","display_name":null,"funder_award_id":"115002","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4439374236","display_name":null,"funder_award_id":"115002","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G5161020159","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5440316326","display_name":null,"funder_award_id":"CP10/00524","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G5593277320","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5702163051","display_name":null,"funder_award_id":"FP7/2007","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6104069830","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G6456714180","display_name":"The Open Pharmacological Concepts Triple Store","funder_award_id":"115191","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G659062546","display_name":null,"funder_award_id":"115002","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"},{"id":"https://openalex.org/G7195248210","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"},{"id":"https://openalex.org/G7364720146","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G8646936266","display_name":null,"funder_award_id":"115002","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"}],"funders":[{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320326631","display_name":"Innovative Medicines Initiative","ror":"https://ror.org/019af4n30"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136437513.pdf","grobid_xml":"https://content.openalex.org/works/W2136437513.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W113629972","https://openalex.org/W1493270114","https://openalex.org/W1577541759","https://openalex.org/W1966615318","https://openalex.org/W1971048089","https://openalex.org/W1982464493","https://openalex.org/W1983766967","https://openalex.org/W1986463049","https://openalex.org/W1986704581","https://openalex.org/W1989217037","https://openalex.org/W1990794790","https://openalex.org/W1997680883","https://openalex.org/W2004536774","https://openalex.org/W2030390110","https://openalex.org/W2030531674","https://openalex.org/W2032566933","https://openalex.org/W2033237963","https://openalex.org/W2036935277","https://openalex.org/W2044420612","https://openalex.org/W2046747418","https://openalex.org/W2052217781","https://openalex.org/W2064299012","https://openalex.org/W2084292968","https://openalex.org/W2085860988","https://openalex.org/W2097960255","https://openalex.org/W2098201295","https://openalex.org/W2105440823","https://openalex.org/W2106921868","https://openalex.org/W2114348990","https://openalex.org/W2115203342","https://openalex.org/W2116947789","https://openalex.org/W2119091936","https://openalex.org/W2120814856","https://openalex.org/W2122683221","https://openalex.org/W2129038679","https://openalex.org/W2133683801","https://openalex.org/W2136775759","https://openalex.org/W2138768461","https://openalex.org/W2141605886","https://openalex.org/W2147418473","https://openalex.org/W2148395543","https://openalex.org/W2150288223","https://openalex.org/W2154142897","https://openalex.org/W2159203162","https://openalex.org/W2159230276","https://openalex.org/W2160194473","https://openalex.org/W2161604082","https://openalex.org/W4240689716"],"related_works":["https://openalex.org/W4310075773","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W1802639773","https://openalex.org/W2118505788","https://openalex.org/W4323018902","https://openalex.org/W4254166511","https://openalex.org/W2560183138","https://openalex.org/W2150084125","https://openalex.org/W1542823905"],"abstract_inverted_index":{"BACKGROUND:":[0],"Current":[1],"biomedical":[2,52,158,244],"research":[3,245],"needs":[4],"to":[5,75,89,130,209,213,218,329],"leverage":[6],"and":[7,60,79,118,149,154,175,181,221,225,238,246,265,287,308,334,337],"exploit":[8],"the":[9,44,70,104,107,164,173,191,260],"large":[10,282],"amount":[11],"of":[12,35,69,87,106,116,134,151,166,190,262,277,284,292,315],"information":[13,68,97,167],"reported":[14],"in":[15,22,95,126,142,172,200,216,280,298],"scientific":[16],"publications.":[17],"Automated":[18],"text":[19,40,253,316],"mining":[20,254,272],"approaches,":[21],"particular":[23],"those":[24],"aimed":[25,47],"at":[26,48],"finding":[27],"relationships":[28,50],"between":[29,51],"entities,":[30],"are":[31,139],"key":[32],"for":[33,99,235,242,259],"identification":[34,261],"actionable":[36],"knowledge":[37],"from":[38],"free":[39],"repositories.":[41],"We":[42,102,183,231,310],"present":[43,141,232],"BeFree":[45,72,88,112,124,197,249],"system":[46,255],"identifying":[49,127],"entities":[53],"with":[54,82,120,156,319],"a":[55,114,131,187,206,251,274,281,289,326],"special":[56],"focus":[57],"on":[58,163,305],"genes":[59,128],"their":[61],"associated":[62,129],"diseases.":[63],"RESULTS:":[64],"By":[65],"exploiting":[66],"morpho-syntactic":[67],"text,":[71],"is":[73,198,205,250,295],"able":[74],"identify":[76],"gene-disease,":[77,263],"drug-disease":[78,264],"drug-target":[80,266],"associations":[81,109,193],"state-of-the-art":[83],"performance.":[84],"The":[85],"application":[86],"real-case":[90],"scenarios":[91],"shows":[92],"its":[93,240],"effectiveness":[94],"extracting":[96],"relevant":[98],"translational":[100],"research.":[101],"show":[103,270],"value":[105],"gene-disease":[108,152,192,285],"extracted":[110],"by":[111,195,322],"through":[113],"number":[115],"analyses":[117,269],"integration":[119,155],"other":[121,143],"data":[122,179,224,236,306,318,320,332],"sources.":[123],"succeeds":[125],"major":[132],"cause":[133],"morbidity":[135],"worldwide,":[136],"depression,":[137],"which":[138],"not":[140],"public":[144],"resources.":[145],"Moreover,":[146],"large-scale":[147],"extraction":[148],"analysis":[150,314],"associations,":[153,286],"current":[157],"knowledge,":[159],"provided":[160],"interesting":[161,338],"insights":[162],"kind":[165],"that":[168,185,256,271,312],"can":[169],"be":[170],"found":[171,184],"literature,":[174],"raised":[176],"challenges":[177],"regarding":[178],"prioritization":[180,237,307],"curation.":[182,309],"only":[186,273,288],"small":[188,275,290],"proportion":[189,291],"discovered":[194],"using":[196],"collected":[199],"expert-curated":[201],"databases.":[202,230],"Thus,":[203],"there":[204],"pressing":[207],"need":[208],"find":[210],"alternative":[211],"strategies":[212],"manual":[214],"curation,":[215],"order":[217],"review,":[219],"prioritize":[220],"curate":[222],"text-mining":[223],"incorporate":[226],"it":[227],"into":[228],"domain-specific":[229],"our":[233],"strategy":[234],"discuss":[239],"implications":[241],"supporting":[243],"applications.":[247],"CONCLUSIONS:":[248],"novel":[252,336],"performs":[257],"competitively":[258],"associations.":[267],"Our":[268],"fraction":[276],"MEDLINE":[278],"results":[279],"dataset":[283,294],"this":[293],"actually":[296],"recorded":[297],"curated":[299,321],"resources":[300],"(2%),":[301],"raising":[302],"several":[303],"issues":[304],"propose":[311],"joint":[313],"mined":[317],"experts":[323],"appears":[324],"as":[325],"suitable":[327],"approach":[328],"both":[330],"assess":[331],"quality":[333],"highlight":[335],"information.":[339]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":40},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":34},{"year":2020,"cited_by_count":32},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
