{"id":"https://openalex.org/W2147585745","doi":"https://doi.org/10.1093/bioinformatics/btq221","title":"PathText: a text mining integrator for biological pathway visualizations","display_name":"PathText: a text mining integrator for biological pathway visualizations","publication_year":2010,"publication_date":"2010-06-01","ids":{"openalex":"https://openalex.org/W2147585745","doi":"https://doi.org/10.1093/bioinformatics/btq221","mag":"2147585745","pmid":"https://pubmed.ncbi.nlm.nih.gov/20529930"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i374/48859502/bioinformatics_26_12_i374.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/26/12/i374/48859502/bioinformatics_26_12_i374.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090700011","display_name":"Brian Kemper","orcid":null},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Brian Kemper","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016823828","display_name":"Takuya Matsuzaki","orcid":"https://orcid.org/0000-0002-7425-4914"},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]},{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takuya Matsuzaki","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101616697","display_name":"Yukiko Matsuoka","orcid":"https://orcid.org/0000-0002-5171-9096"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yukiko Matsuoka","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064113904","display_name":"Yoshimasa Tsuruoka","orcid":"https://orcid.org/0000-0002-0707-1077"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshimasa Tsuruoka","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086835862","display_name":"Hiroaki Kitano","orcid":"https://orcid.org/0000-0002-3589-1953"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Kitano","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077976343","display_name":"Sophia Ananiadou","orcid":"https://orcid.org/0000-0002-4097-9191"},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sophia Ananiadou","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112241147","display_name":"Jun\u2019ichi Tsujii","orcid":null},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Jun'ichi Tsujii","raw_affiliation_strings":["1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Tokyo, 2 The Systems Biology Institute, Tokyo, 3 JST ERATO Kawaoka Infection-induced Host-Response Network Project, Tokyo, Japan, 4 National Centre for Text Mining, UK, 5 School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa, 6 Okinawa Institute of Science and Technology, Okinawa, Japan and 7 School of Computer Science, University of Manchester, UK","institution_ids":["https://openalex.org/I4210118579","https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5112241147"],"corresponding_institution_ids":["https://openalex.org/I142637625","https://openalex.org/I161296585","https://openalex.org/I177738480","https://openalex.org/I4210118579"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.3885,"has_fulltext":true,"cited_by_count":64,"citation_normalized_percentile":{"value":0.92945345,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"12","first_page":"i374","last_page":"i381"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9700000286102295,"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":0.6895604729652405},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6713531613349915},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.623991072177887},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5989168882369995},{"id":"https://openalex.org/keywords/reading","display_name":"Reading (process)","score":0.5800029039382935},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4924114942550659},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4410414397716522},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35993653535842896},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3412250578403473},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.255093514919281},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.21076488494873047},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1849135160446167},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15012356638908386},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09674111008644104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6895604729652405},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6713531613349915},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.623991072177887},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5989168882369995},{"id":"https://openalex.org/C554936623","wikidata":"https://www.wikidata.org/wiki/Q199657","display_name":"Reading (process)","level":2,"score":0.5800029039382935},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4924114942550659},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4410414397716522},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35993653535842896},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3412250578403473},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.255093514919281},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21076488494873047},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1849135160446167},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15012356638908386},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09674111008644104},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btq221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i374/48859502/bioinformatics_26_12_i374.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:20529930","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20529930","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:pure.atira.dk:openaire_cris_publications/0ef7f56e-d0ad-49e3-8e03-250e5ca01813","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/0ef7f56e-d0ad-49e3-8e03-250e5ca01813","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Kemper, B, Matsuzaki, T, Matsuoka, Y, Tsuruoka, Y, Kitano, H, Ananiadou, S & Tsujii, J 2010, 'PathText: A text mining integrator for biological pathway visualizations', Bioinformatics, vol. 26, no. 12, btq221, pp. 374-381. https://doi.org/10.1093/bioinformatics/btq221","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:2881405","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2881405","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/btq221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i374/48859502/bioinformatics_26_12_i374.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":[{"display_name":"Quality Education","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G4655000275","display_name":null,"funder_award_id":"BB/E004431/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4793955247","display_name":null,"funder_award_id":"BB/G53025X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320324799","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147585745.pdf","grobid_xml":"https://content.openalex.org/works/W2147585745.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W13703775","https://openalex.org/W1523095068","https://openalex.org/W1965893653","https://openalex.org/W1967225297","https://openalex.org/W1976522393","https://openalex.org/W1977781366","https://openalex.org/W1994086054","https://openalex.org/W2010502047","https://openalex.org/W2020561965","https://openalex.org/W2038248725","https://openalex.org/W2045478141","https://openalex.org/W2047632644","https://openalex.org/W2065807795","https://openalex.org/W2066024537","https://openalex.org/W2069157810","https://openalex.org/W2077631777","https://openalex.org/W2082621456","https://openalex.org/W2103017472","https://openalex.org/W2103397879","https://openalex.org/W2109252435","https://openalex.org/W2109368679","https://openalex.org/W2110025254","https://openalex.org/W2110280725","https://openalex.org/W2117364474","https://openalex.org/W2120609672","https://openalex.org/W2128276963","https://openalex.org/W2132288458","https://openalex.org/W2143969914","https://openalex.org/W2144896636","https://openalex.org/W2147558260","https://openalex.org/W2149803936","https://openalex.org/W2150908245","https://openalex.org/W2155967165","https://openalex.org/W2160238006","https://openalex.org/W2160317546","https://openalex.org/W2169810918","https://openalex.org/W3149154678","https://openalex.org/W6600552100","https://openalex.org/W6644632210","https://openalex.org/W6676824183","https://openalex.org/W6821143472"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2366107444","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2371223562"],"abstract_inverted_index":{"Metabolic":[0],"and":[1,37,76,121,140,168,178,183],"signaling":[2],"pathways":[3],"are":[4],"an":[5],"increasingly":[6],"important":[7],"part":[8],"of":[9,21,35,46,70,137,143,166,176,181,189],"organizing":[10],"knowledge":[11],"in":[12],"systems":[13,120],"biology.":[14],"They":[15],"serve":[16],"to":[17,54,60,66,72,81,113,132],"integrate":[18,114],"collective":[19],"interpretations":[20],"facts":[22],"scattered":[23],"throughout":[24],"literature.":[25],"Biologists":[26,57],"construct":[27],"a":[28,32,41,97,101,110,115,125,138],"pathway":[29,116,139],"by":[30,90,160,187],"reading":[31],"large":[33,152],"number":[34],"articles":[36,64,75],"interpreting":[38],"them":[39],"as":[40,145,147],"consistent":[42],"network,":[43],"but":[44],"most":[45],"the":[47,62,78,82,86,179],"models":[48],"constructed":[49],"currently":[50],"lack":[51],"direct":[52],"links":[53],"those":[55],"articles.":[56],"who":[58],"want":[59],"check":[61],"original":[63],"have":[65],"spend":[67],"substantial":[68],"amounts":[69],"time":[71],"collect":[73],"relevant":[74,80,99,141,149],"identify":[77,148],"sections":[79,142],"pathway.":[83],"Furthermore,":[84],"with":[85],"scientific":[87],"literature":[88],"expanding":[89],"several":[91],"thousand":[92],"papers":[93,150],"per":[94],"week,":[95],"keeping":[96],"model":[98],"requires":[100],"continuous":[102],"curation":[103],"effort.":[104],"In":[105],"this":[106],"article,":[107],"we":[108],"present":[109],"system":[111],"designed":[112],"visualizer,":[117],"text":[118,153],"mining":[119],"annotation":[122],"tools":[123],"into":[124],"seamless":[126],"environment.":[127],"This":[128],"will":[129],"enable":[130],"biologists":[131,190],"freely":[133],"move":[134],"between":[135],"parts":[136],"articles,":[144],"well":[146],"from":[151,191],"bases.":[154],"The":[155],"system,":[156],"PathText,":[157],"is":[158,184],"developed":[159],"Systems":[161],"Biology":[162],"Institute,":[163],"Okinawa":[164],"Institute":[165],"Science":[167],"Technology,":[169],"National":[170],"Centre":[171],"for":[172],"Text":[173],"Mining":[174],"(University":[175],"Manchester)":[177],"University":[180],"Tokyo,":[182],"being":[185],"used":[186],"groups":[188],"these":[192],"locations.":[193]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
