{"id":"https://openalex.org/W2061327015","doi":"https://doi.org/10.1089/106652703322756104","title":"Mining the Biomedical Literature in the Genomic Era: An Overview","display_name":"Mining the Biomedical Literature in the Genomic Era: An Overview","publication_year":2003,"publication_date":"2003-12-01","ids":{"openalex":"https://openalex.org/W2061327015","doi":"https://doi.org/10.1089/106652703322756104","mag":"2061327015","pmid":"https://pubmed.ncbi.nlm.nih.gov/14980013"},"language":"en","primary_location":{"id":"doi:10.1089/106652703322756104","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652703322756104","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043310715","display_name":"Hagit Shatkay","orcid":"https://orcid.org/0000-0001-6953-3970"},"institutions":[{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hagit Shatkay","raw_affiliation_strings":["School of Computing, Queen's University, Kingston, Ontario, Canada K7L3N6","School of Computing, Queen's University, Kingston, Ontario, Canada K7L3N6. shatkay@cs.queensu.ca"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Queen's University, Kingston, Ontario, Canada K7L3N6","institution_ids":["https://openalex.org/I204722609"]},{"raw_affiliation_string":"School of Computing, Queen's University, Kingston, Ontario, Canada K7L3N6. shatkay@cs.queensu.ca","institution_ids":["https://openalex.org/I204722609"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111407570","display_name":"Ronen Feldman","orcid":null},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ronen Feldman","raw_affiliation_strings":["Department of Computer Science, Bar Ilan University, Ramat Gan 52900, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Bar Ilan University, Ramat Gan 52900, Israel","institution_ids":["https://openalex.org/I13955877"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":9.4102,"has_fulltext":false,"cited_by_count":265,"citation_normalized_percentile":{"value":0.98849323,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"6","first_page":"821","last_page":"855"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9995999932289124,"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":0.9995999932289124,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.993399977684021,"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":0.9904000163078308,"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/data-science","display_name":"Data science","score":0.789218544960022},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.548789918422699},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5058503150939941},{"id":"https://openalex.org/keywords/sort","display_name":"sort","score":0.49249133467674255},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46309661865234375},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2587473690509796},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2554885745048523},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.22922301292419434},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.22476673126220703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21486207842826843}],"concepts":[{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.789218544960022},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.548789918422699},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5058503150939941},{"id":"https://openalex.org/C88548561","wikidata":"https://www.wikidata.org/wiki/Q347599","display_name":"sort","level":2,"score":0.49249133467674255},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46309661865234375},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2587473690509796},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2554885745048523},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.22922301292419434},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.22476673126220703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21486207842826843},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1089/106652703322756104","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652703322756104","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:14980013","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14980013","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 computational biology : a journal of computational molecular cell biology","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.2.2061","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.2.2061","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.shatkay.org/papers/JCB03.ps","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.85.6049","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.85.6049","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.queensu.ca/~shatkay/papers/JCB03.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6899999976158142,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":140,"referenced_works":["https://openalex.org/W740415","https://openalex.org/W138910040","https://openalex.org/W167149422","https://openalex.org/W316834394","https://openalex.org/W1500752107","https://openalex.org/W1504993955","https://openalex.org/W1509769683","https://openalex.org/W1518149811","https://openalex.org/W1519945466","https://openalex.org/W1541931954","https://openalex.org/W1546654380","https://openalex.org/W1549026077","https://openalex.org/W1566012138","https://openalex.org/W1570542661","https://openalex.org/W1588806355","https://openalex.org/W1592053870","https://openalex.org/W1601529450","https://openalex.org/W1602918385","https://openalex.org/W1604959358","https://openalex.org/W1617571838","https://openalex.org/W1625807337","https://openalex.org/W1663435917","https://openalex.org/W1718065290","https://openalex.org/W1769049279","https://openalex.org/W1920003194","https://openalex.org/W1954715867","https://openalex.org/W1965708122","https://openalex.org/W1967080262","https://openalex.org/W1968953480","https://openalex.org/W1969572066","https://openalex.org/W1970156673","https://openalex.org/W1970761617","https://openalex.org/W1981933378","https://openalex.org/W1983453172","https://openalex.org/W1984581259","https://openalex.org/W1986913017","https://openalex.org/W1987146951","https://openalex.org/W1988001261","https://openalex.org/W1989568037","https://openalex.org/W1994301758","https://openalex.org/W1994851566","https://openalex.org/W1998154529","https://openalex.org/W1999117234","https://openalex.org/W2000390755","https://openalex.org/W2004620268","https://openalex.org/W2004652662","https://openalex.org/W2005422315","https://openalex.org/W2009341227","https://openalex.org/W2011726136","https://openalex.org/W2023736097","https://openalex.org/W2027356109","https://openalex.org/W2036136590","https://openalex.org/W2043887901","https://openalex.org/W2050071812","https://openalex.org/W2058616517","https://openalex.org/W2060216474","https://openalex.org/W2061310592","https://openalex.org/W2067096102","https://openalex.org/W2069334446","https://openalex.org/W2080667183","https://openalex.org/W2081687495","https://openalex.org/W2088468751","https://openalex.org/W2089933214","https://openalex.org/W2091273188","https://openalex.org/W2093390569","https://openalex.org/W2093432797","https://openalex.org/W2093618552","https://openalex.org/W2093723065","https://openalex.org/W2096411881","https://openalex.org/W2097847889","https://openalex.org/W2100176599","https://openalex.org/W2100796029","https://openalex.org/W2103017472","https://openalex.org/W2103090613","https://openalex.org/W2103370600","https://openalex.org/W2103453943","https://openalex.org/W2104768328","https://openalex.org/W2107499729","https://openalex.org/W2107743791","https://openalex.org/W2112861996","https://openalex.org/W2114083522","https://openalex.org/W2114535528","https://openalex.org/W2114565252","https://openalex.org/W2115159360","https://openalex.org/W2115603438","https://openalex.org/W2115880858","https://openalex.org/W2118020653","https://openalex.org/W2121407024","https://openalex.org/W2121940249","https://openalex.org/W2123280311","https://openalex.org/W2126185232","https://openalex.org/W2127071136","https://openalex.org/W2127230663","https://openalex.org/W2129706127","https://openalex.org/W2130494035","https://openalex.org/W2130851608","https://openalex.org/W2131630280","https://openalex.org/W2131826878","https://openalex.org/W2135187880","https://openalex.org/W2135937947","https://openalex.org/W2138548161","https://openalex.org/W2139259976","https://openalex.org/W2142418779","https://openalex.org/W2144212226","https://openalex.org/W2147152072","https://openalex.org/W2148853951","https://openalex.org/W2149684865","https://openalex.org/W2149887408","https://openalex.org/W2149942697","https://openalex.org/W2152458080","https://openalex.org/W2152698860","https://openalex.org/W2153962014","https://openalex.org/W2155042162","https://openalex.org/W2156909104","https://openalex.org/W2158120166","https://openalex.org/W2158505321","https://openalex.org/W2158714788","https://openalex.org/W2159203162","https://openalex.org/W2160484851","https://openalex.org/W2161377381","https://openalex.org/W2162311237","https://openalex.org/W2163085258","https://openalex.org/W2163107094","https://openalex.org/W2163514362","https://openalex.org/W2165011536","https://openalex.org/W2165270659","https://openalex.org/W2168808732","https://openalex.org/W2169974160","https://openalex.org/W2170654002","https://openalex.org/W2217772701","https://openalex.org/W2283504545","https://openalex.org/W2314420468","https://openalex.org/W2341078838","https://openalex.org/W2611831635","https://openalex.org/W2937343401","https://openalex.org/W3152337545","https://openalex.org/W4231741839","https://openalex.org/W4247420482","https://openalex.org/W4251507866","https://openalex.org/W4255855797"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2361805396","https://openalex.org/W2972254340","https://openalex.org/W2887358545","https://openalex.org/W2022231341","https://openalex.org/W2390279801","https://openalex.org/W1805912688","https://openalex.org/W2358668433","https://openalex.org/W4241083716","https://openalex.org/W2061327015"],"abstract_inverted_index":{"The":[0],"past":[1],"decade":[2],"has":[3,48],"seen":[4],"a":[5,50,86],"tremendous":[6],"growth":[7,26],"in":[8,18,33,58,95,105,111,135],"the":[9,19,34,40,43,55,71,90,102,132],"amount":[10],"of":[11,21,36,52,67,73,123,131],"experimental":[12],"and":[13,23,69,77,97,120],"computational":[14],"biomedical":[15,37,112],"data,":[16],"specifically":[17],"areas":[20],"genomics":[22],"proteomics.":[24],"This":[25,83],"is":[27],"accompanied":[28],"by":[29],"an":[30],"accelerated":[31],"increase":[32],"number":[35],"publications":[38],"discussing":[39],"findings.":[41],"In":[42],"last":[44],"few":[45],"years,":[46],"there":[47],"been":[49],"lot":[51],"interest":[53],"within":[54,98],"scientific":[56],"community":[57],"literature-mining":[59,92],"tools":[60],"to":[61,89,117],"help":[62],"sort":[63],"through":[64],"this":[65],"abundance":[66],"literature":[68,113],"find":[70],"nuggets":[72],"information":[74],"most":[75],"relevant":[76],"useful":[78],"for":[79],"specific":[80],"analysis":[81,125],"tasks.":[82],"paper":[84],"provides":[85,121],"road":[87],"map":[88],"various":[91],"methods,":[93],"both":[94],"general":[96],"bioinformatics.":[99,136],"It":[100],"surveys":[101],"disciplines":[103],"involved":[104],"unstructured-text":[106],"analysis,":[107],"categorizes":[108],"current":[109,133],"work":[110],"mining":[114],"with":[115],"respect":[116],"these":[118],"disciplines,":[119],"examples":[122],"text":[124],"methods":[126],"applied":[127],"towards":[128],"meeting":[129],"some":[130],"challenges":[134]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":10}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
