{"id":"https://openalex.org/W2120535580","doi":"https://doi.org/10.1093/bioinformatics/btp049","title":"SciMiner: web-based literature mining tool for target identification and functional enrichment analysis","display_name":"SciMiner: web-based literature mining tool for target identification and functional enrichment analysis","publication_year":2009,"publication_date":"2009-02-02","ids":{"openalex":"https://openalex.org/W2120535580","doi":"https://doi.org/10.1093/bioinformatics/btp049","mag":"2120535580","pmid":"https://pubmed.ncbi.nlm.nih.gov/19188191"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp049","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/838/50286504/bioinformatics_25_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/838/50286504/bioinformatics_25_6_838.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068376728","display_name":"Junguk Hur","orcid":"https://orcid.org/0000-0002-0736-2149"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Junguk Hur","raw_affiliation_strings":["1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012731226","display_name":"Adam D. Schuyler","orcid":"https://orcid.org/0000-0001-7583-899X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam D. Schuyler","raw_affiliation_strings":["1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111548295","display_name":"David J. States","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J. States","raw_affiliation_strings":["1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056304003","display_name":"Eva L. Feldman","orcid":"https://orcid.org/0000-0002-9162-2694"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eva L. Feldman","raw_affiliation_strings":["1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Program, 2Department of Neurology, University of Michigan, Ann Arbor, MI 48109 and 3School of Health Information Science, University of Texas at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5068376728"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I919571938"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.8971,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.94311242,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"6","first_page":"838","last_page":"840"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.996399998664856,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9807999730110168,"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":0.7375733256340027},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6830404996871948},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6264091730117798},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.6259035468101501},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.557064414024353},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5111668705940247},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4857509732246399},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.47012007236480713},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.3930639624595642},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34970468282699585},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3394710421562195},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22678449749946594},{"id":"https://openalex.org/keywords/nomenclature","display_name":"Nomenclature","score":0.1378462016582489},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12014055252075195},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.09799504280090332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7375733256340027},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6830404996871948},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6264091730117798},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.6259035468101501},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.557064414024353},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5111668705940247},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4857509732246399},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.47012007236480713},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.3930639624595642},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34970468282699585},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3394710421562195},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22678449749946594},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"score":0.1378462016582489},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12014055252075195},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.09799504280090332},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","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":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","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":false},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","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":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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp049","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/838/50286504/bioinformatics_25_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19188191","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19188191","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2654801","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2654801","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp049","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/838/50286504/bioinformatics_25_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120535580.pdf","grobid_xml":"https://content.openalex.org/works/W2120535580.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2031950862","https://openalex.org/W2110601338","https://openalex.org/W2120736575","https://openalex.org/W2129113459","https://openalex.org/W2141869602","https://openalex.org/W2159335058","https://openalex.org/W2159675211","https://openalex.org/W2290195878"],"related_works":["https://openalex.org/W2116726748","https://openalex.org/W2098932404","https://openalex.org/W2291669096","https://openalex.org/W2605215238","https://openalex.org/W2371635796","https://openalex.org/W2404565489","https://openalex.org/W3185751515","https://openalex.org/W2121234677","https://openalex.org/W1479703980","https://openalex.org/W2951946877"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":17}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
