{"id":"https://openalex.org/W2065807795","doi":"https://doi.org/10.1186/1471-2105-9-s3-s5","title":"New challenges for text mining: mapping between text and manually curated pathways","display_name":"New challenges for text mining: mapping between text and manually curated pathways","publication_year":2008,"publication_date":"2008-04-01","ids":{"openalex":"https://openalex.org/W2065807795","doi":"https://doi.org/10.1186/1471-2105-9-s3-s5","mag":"2065807795","pmid":"https://pubmed.ncbi.nlm.nih.gov/18426550"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-s3-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s3-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S3-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S3-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109319551","display_name":"Kanae Oda","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kanae Oda","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. k.oda@is.s.u-tokyo.ac.jp","Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. k.oda@is.s.u-tokyo.ac.jp","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063923711","display_name":"Jin-Dong Kim","orcid":"https://orcid.org/0000-0001-9660-6303"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jin-Dong Kim","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007825608","display_name":"Tomoko Ohta","orcid":"https://orcid.org/0000-0002-9418-8352"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomoko Ohta","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056883370","display_name":"Daisuke Okanohara","orcid":"https://orcid.org/0000-0001-5969-587X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Daisuke Okanohara","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"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/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takuya Matsuzaki","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068056695","display_name":"Yuka Tateisi","orcid":"https://orcid.org/0000-0002-3813-5782"},"institutions":[{"id":"https://openalex.org/I116465919","display_name":"Kogakuin University","ror":"https://ror.org/01wc2tq75","country_code":"JP","type":"education","lineage":["https://openalex.org/I116465919"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuka Tateisi","raw_affiliation_strings":["Faculty of Informatics, Kogakuin University, 1-24-2 Nishi-shinjuku, Shinjuku-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Informatics, Kogakuin University, 1-24-2 Nishi-shinjuku, Shinjuku-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I116465919"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112241147","display_name":"Jun\u2019ichi Tsujii","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["GB","JP"],"is_corresponding":true,"raw_author_name":"Jun'ichi Tsujii","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","National Centre for Text Mining, 131 Princess Street, Manchester, M1 7DN, UK","School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"National Centre for Text Mining, 131 Princess Street, Manchester, M1 7DN, UK","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5112241147"],"corresponding_institution_ids":["https://openalex.org/I28407311","https://openalex.org/I74801974"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.9303,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.94127881,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"S3","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9574999809265137,"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":0.9574999809265137,"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":0.006300000008195639,"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":0.0038999998942017555,"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":0.5914015769958496},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.512915849685669},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.48558610677719116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46344709396362305},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4223648011684418},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3828449249267578},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.36281442642211914},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2608090043067932},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23816078901290894},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12951511144638062},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09874436259269714}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5914015769958496},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.512915849685669},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.48558610677719116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46344709396362305},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4223648011684418},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3828449249267578},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36281442642211914},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2608090043067932},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23816078901290894},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12951511144638062},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09874436259269714},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004014","descriptor_name":"Dictionaries as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004014","descriptor_name":"Dictionaries as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004014","descriptor_name":"Dictionaries as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-s3-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s3-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S3-S5","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:18426550","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18426550","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:doaj.org/article:ccc52d64c9b14db7a6def2fa3646a065","is_oa":true,"landing_page_url":"https://doaj.org/article/ccc52d64c9b14db7a6def2fa3646a065","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss Suppl 3, p S5 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2352872","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2352872","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-s3-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s3-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S3-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065807795.pdf","grobid_xml":"https://content.openalex.org/works/W2065807795.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1482328859","https://openalex.org/W1517476684","https://openalex.org/W1755219215","https://openalex.org/W1965893653","https://openalex.org/W2005966091","https://openalex.org/W2018389597","https://openalex.org/W2034646855","https://openalex.org/W2048786492","https://openalex.org/W2093618552","https://openalex.org/W2100592161","https://openalex.org/W2109368679","https://openalex.org/W2110025254","https://openalex.org/W2114090586","https://openalex.org/W2120433106","https://openalex.org/W2129113459","https://openalex.org/W2137881949","https://openalex.org/W2143969914","https://openalex.org/W2149803936","https://openalex.org/W2153258203","https://openalex.org/W2160238006","https://openalex.org/W2161682775","https://openalex.org/W2162243457","https://openalex.org/W2395624811","https://openalex.org/W2760751490","https://openalex.org/W3147442204","https://openalex.org/W4300022934","https://openalex.org/W4360598533"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237","https://openalex.org/W2990314835","https://openalex.org/W2131319730","https://openalex.org/W2059850119"],"abstract_inverted_index":{"BACKGROUND:":[0],"Associating":[1],"literature":[2],"with":[3,76,86],"pathways":[4],"poses":[5],"new":[6,70],"challenges":[7,18],"to":[8,19,72],"the":[9,23,26,40,43,51,74,82,98,105,115,122,130,137,148,154,157],"Text":[10],"Mining":[11],"(TM)":[12],"community.":[13],"There":[14],"are":[15],"three":[16],"main":[17],"this":[20],"task:":[21],"(1)":[22],"identification":[24],"of":[25,29,42,55,118,125,139,156,160],"mapping":[27],"position":[28],"a":[30,36,77],"specific":[31],"entity":[32],"or":[33],"reaction":[34],"in":[35,129],"given":[37],"pathway,":[38],"(2)":[39],"recognition":[41],"causal":[44],"relationships":[45],"among":[46],"multiple":[47],"reactions,":[48],"and":[49,53,89,109,121,143],"(3)":[50],"formulation":[52],"implementation":[54],"required":[56],"inferences":[57],"based":[58],"on":[59],"biological":[60],"domain":[61],"knowledge.":[62],"RESULTS:":[63],"To":[64],"address":[65,97],"these":[66],"challenges,":[67],"we":[68,96,113],"constructed":[69],"resources":[71,142],"link":[73],"text":[75,108],"model":[78],"pathway;":[79],"they":[80],"are:":[81],"GENIA":[83],"pathway":[84,110,131,161],"corpus":[85],"event":[87],"annotation":[88],"NF-kB":[90],"pathway.":[91],"Through":[92],"their":[93,119,144],"detailed":[94,145],"analysis,":[95],"untapped":[99],"resource,":[100],"'bio-inference,'":[101],"as":[102,104],"well":[103],"differences":[106],"between":[107],"representation.":[111],"Here,":[112],"show":[114],"precise":[116],"comparisons":[117],"representations":[120],"nine":[123],"classes":[124],"'bio-inference'":[126],"schemes":[127],"observed":[128],"corpus.":[132],"CONCLUSIONS:":[133],"We":[134],"believe":[135],"that":[136],"creation":[138],"such":[140],"rich":[141],"analysis":[146],"is":[147],"significant":[149],"first":[150],"step":[151],"for":[152],"accelerating":[153],"research":[155],"automatic":[158],"construction":[159],"from":[162],"text.":[163]},"counts_by_year":[{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":9}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
