{"id":"https://openalex.org/W2147154106","doi":"https://doi.org/10.1093/bioinformatics/bts332","title":"BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events","display_name":"BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events","publication_year":2012,"publication_date":"2012-06-17","ids":{"openalex":"https://openalex.org/W2147154106","doi":"https://doi.org/10.1093/bioinformatics/bts332","mag":"2147154106","pmid":"https://pubmed.ncbi.nlm.nih.gov/22711795"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts332","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts332","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2154/48869938/bioinformatics_28_16_2154.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/28/16/2154/48869938/bioinformatics_28_16_2154.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013526527","display_name":"Martin Gerner","orcid":"https://orcid.org/0000-0002-9439-1879"},"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"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Martin Gerner","raw_affiliation_strings":["1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052182084","display_name":"Farzaneh Sarafraz","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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Farzaneh Sarafraz","raw_affiliation_strings":["1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079037577","display_name":"Casey Bergman","orcid":"https://orcid.org/0000-0002-5462-9854"},"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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Casey M. Bergman","raw_affiliation_strings":["1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005912060","display_name":"Goran Nenadi\u0107","orcid":"https://orcid.org/0000-0003-0795-5363"},"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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Goran Nenadic","raw_affiliation_strings":["1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT and 2School of Computer Science, University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013526527"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.1781,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.92678054,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"16","first_page":"2154","last_page":"2161"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9968000054359436,"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":0.9968000054359436,"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":0.0013000000035390258,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.6829771399497986},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.6524152755737305},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6201207637786865},{"id":"https://openalex.org/keywords/contextualization","display_name":"Contextualization","score":0.6188721656799316},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5598210096359253},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5522284507751465},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5250794291496277},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4231155812740326},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.41559910774230957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40309107303619385},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32679951190948486},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20138204097747803},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.08260565996170044}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6829771399497986},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.6524152755737305},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6201207637786865},{"id":"https://openalex.org/C2780712339","wikidata":"https://www.wikidata.org/wiki/Q5165204","display_name":"Contextualization","level":3,"score":0.6188721656799316},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5598210096359253},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5522284507751465},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5250794291496277},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4231155812740326},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.41559910774230957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40309107303619385},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32679951190948486},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20138204097747803},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.08260565996170044},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"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":"D039781","descriptor_name":"PubMed","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":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/bts332","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts332","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2154/48869938/bioinformatics_28_16_2154.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:22711795","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22711795","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:CiteSeerX.psu:10.1.1.1018.193","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1018.193","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/28/16/2154.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.805.1993","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.805.1993","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/31/bts332.PMC3413385.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2418714","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3413385","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/b06cad03-baf4-43d8-8de1-d4491a004881","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/b06cad03-baf4-43d8-8de1-d4491a004881","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Gerner, M, Sarafraz, F, Bergman, C M & Nenadic, G 2012, 'BioContext: An integrated text mining system for large-scale extraction and contextualization of biomolecular events', Bioinformatics, vol. 28, no. 16, bts332, pp. 2154-2161. https://doi.org/10.1093/bioinformatics/bts332","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:publications/b06cad03-baf4-43d8-8de1-d4491a004881","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/biocontext-an-integrated-text-mining-system-for-largescale-extraction-and-contextualization-of-biomolecular-events(b06cad03-baf4-43d8-8de1-d4491a004881).html","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Gerner, M, Sarafraz, F, Bergman, C M & Nenadic, G 2012, 'BioContext: An integrated text mining system for large-scale extraction and contextualization of biomolecular events', Bioinformatics, vol. 28, no. 16, bts332, pp. 2154-2161. https://doi.org/10.1093/bioinformatics/bts332","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts332","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts332","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2154/48869938/bioinformatics_28_16_2154.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":[],"awards":[{"id":"https://openalex.org/G3622200210","display_name":"A Multi-Processor Linux Farm for Bioinformatics and Functional Genomics","funder_award_id":"BB/E012868/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4262708766","display_name":null,"funder_award_id":"BB/E012868/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320291","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"},{"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/W2147154106.pdf","grobid_xml":"https://content.openalex.org/works/W2147154106.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W154351976","https://openalex.org/W174568167","https://openalex.org/W1590479039","https://openalex.org/W1786456657","https://openalex.org/W1977748891","https://openalex.org/W2005958938","https://openalex.org/W2006566482","https://openalex.org/W2032566933","https://openalex.org/W2035574008","https://openalex.org/W2037442572","https://openalex.org/W2057545775","https://openalex.org/W2064030835","https://openalex.org/W2075655036","https://openalex.org/W2098332568","https://openalex.org/W2100627415","https://openalex.org/W2101265630","https://openalex.org/W2102563561","https://openalex.org/W2103320915","https://openalex.org/W2107005506","https://openalex.org/W2108706252","https://openalex.org/W2109487646","https://openalex.org/W2111044246","https://openalex.org/W2124772738","https://openalex.org/W2127603354","https://openalex.org/W2131520733","https://openalex.org/W2132186707","https://openalex.org/W2145428772","https://openalex.org/W2149803936","https://openalex.org/W2154599958","https://openalex.org/W2162965868","https://openalex.org/W2163568299","https://openalex.org/W2169918010","https://openalex.org/W2170953709","https://openalex.org/W2793614157","https://openalex.org/W2916138694","https://openalex.org/W2916767477","https://openalex.org/W6606243021","https://openalex.org/W6638185459","https://openalex.org/W6644678941","https://openalex.org/W6674840050","https://openalex.org/W6675420493","https://openalex.org/W6675914680","https://openalex.org/W6678739045","https://openalex.org/W6679427128","https://openalex.org/W6684115428"],"related_works":["https://openalex.org/W1788528807","https://openalex.org/W104581431","https://openalex.org/W2725657302","https://openalex.org/W2407111306","https://openalex.org/W1975174578","https://openalex.org/W2393978999","https://openalex.org/W1548492051","https://openalex.org/W2364610604","https://openalex.org/W1546263170","https://openalex.org/W2105217514"],"abstract_inverted_index":{"MOTIVATION:":[0],"Although":[1],"the":[2,25,150,154,159,176,183],"amount":[3],"of":[4,78,89,143,153],"data":[5,49,185],"in":[6,24],"biology":[7],"is":[8,161,171,187],"rapidly":[9],"increasing,":[10],"critical":[11],"information":[12,36,147],"for":[13,173,190],"understanding":[14],"biological":[15,38],"events":[16,39,144],"like":[17],"phosphorylation":[18],"or":[19,157,165],"gene":[20],"expression":[21],"remains":[22],"locked":[23],"biomedical":[26],"literature.":[27],"Most":[28],"current":[29],"text":[30],"mining":[31],"(TM)":[32],"approaches":[33],"to":[34,56,92,136],"extract":[35],"about":[37],"are":[40,125],"focused":[41],"on":[42],"either":[43],"limited-scale":[44],"studies":[45],"and/or":[46],"abstracts,":[47],"with":[48,182],"extracted":[50,184],"lacking":[51],"context":[52],"and":[53,72,86,97,132],"rarely":[54],"available":[55,172,189],"support":[57],"further":[58],"research.":[59],"RESULTS:":[60],"Here":[61],"we":[62],"present":[63],"BioContext,":[64],"an":[65],"integrated":[66],"TM":[67],"system":[68,91],"which":[69,186],"extracts,":[70],"extends":[71],"integrates":[73],"results":[74],"from":[75,103],"a":[76,141],"number":[77],"tools":[79],"performing":[80],"entity":[81],"recognition,":[82],"biomolecular":[83],"event":[84,155,160],"extraction":[85],"contextualization.":[87],"Application":[88],"our":[90],"10.9":[93],"million":[94,109,113,130],"MEDLINE":[95],"abstracts":[96],"234":[98],"000":[99,121],"open-access":[100],"full-text":[101],"articles":[102],"PubMed":[104],"Central":[105],"yielded":[106],"over":[107,119],"36":[108],"mentions":[110],"representing":[111],"11.4":[112],"distinct":[114,122],"events.":[115],"Event":[116],"participants":[117],"included":[118],"290":[120],"genes/proteins":[123],"that":[124],"mentioned":[126],"more":[127],"than":[128],"80":[129],"times":[131],"linked":[133],"where":[134],"possible":[135],"Entrez":[137],"Gene":[138],"identifiers.":[139],"Over":[140],"third":[142],"contain":[145],"contextual":[146],"such":[148],"as":[149,163],"anatomical":[151],"location":[152],"occurrence":[156],"whether":[158],"reported":[162],"negated":[164],"speculative.":[166],"AVAILABILITY:":[167],"The":[168],"BioContext":[169],"pipeline":[170],"download":[174],"(under":[175],"BSD":[177],"license)":[178],"at":[179],"http://www.biocontext.org,":[180],"along":[181],"also":[188],"online":[191],"browsing.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":9}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
