{"id":"https://openalex.org/W2133601033","doi":"https://doi.org/10.1093/bioinformatics/btp602","title":"Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D","display_name":"Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D","publication_year":2009,"publication_date":"2009-10-22","ids":{"openalex":"https://openalex.org/W2133601033","doi":"https://doi.org/10.1093/bioinformatics/btp602","mag":"2133601033","pmid":"https://pubmed.ncbi.nlm.nih.gov/19850753"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp602","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/1/111/48852286/bioinformatics_26_1_111.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/1/111/48852286/bioinformatics_26_1_111.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100770856","display_name":"Yun Niu","orcid":"https://orcid.org/0000-0002-6841-3659"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Yun Niu","raw_affiliation_strings":["1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I9842412","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004895270","display_name":"David Otasek","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"David Otasek","raw_affiliation_strings":["1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I9842412","https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055656807","display_name":"Igor Juri\u0161ica","orcid":"https://orcid.org/0000-0002-2507-946X"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Igor Jurisica","raw_affiliation_strings":["1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"1 Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, 2 Nanjing University of Aeronautics and Astronautics, Nanjing, China, 3 Department of Computer Science and 4 Department of Medical Biophysics, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I9842412","https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100770856"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I9842412"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.1005,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.92025121,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"26","issue":"1","first_page":"111","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9923999905586243,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9496999979019165,"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":0.7987378835678101},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.582764208316803},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5712932348251343},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.530281126499176},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.5100839734077454},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49826884269714355},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4647967219352722},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4451679289340973},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44463494420051575},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.418300986289978},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.417550265789032},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3623356819152832},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1092749536037445},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07900750637054443}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7987378835678101},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.582764208316803},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5712932348251343},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.530281126499176},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.5100839734077454},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49826884269714355},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4647967219352722},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4451679289340973},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44463494420051575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.418300986289978},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.417550265789032},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3623356819152832},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1092749536037445},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07900750637054443},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":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/btp602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp602","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/1/111/48852286/bioinformatics_26_1_111.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19850753","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19850753","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:2796811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2796811","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":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/btp602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp602","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/1/111/48852286/bioinformatics_26_1_111.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":null,"license_id":null,"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","score":0.8100000023841858,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320314024","display_name":"Ontario Genomics","ror":null},{"id":"https://openalex.org/F4320319905","display_name":"Ontario Genomics Institute","ror":"https://ror.org/00c68jz96"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2133601033.pdf","grobid_xml":"https://content.openalex.org/works/W2133601033.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W137105571","https://openalex.org/W1518780818","https://openalex.org/W1968920591","https://openalex.org/W1982428412","https://openalex.org/W1986967481","https://openalex.org/W1991983805","https://openalex.org/W1994803330","https://openalex.org/W2006566482","https://openalex.org/W2033384218","https://openalex.org/W2037036397","https://openalex.org/W2040734632","https://openalex.org/W2044514479","https://openalex.org/W2052852434","https://openalex.org/W2053238041","https://openalex.org/W2064030835","https://openalex.org/W2069185229","https://openalex.org/W2077550665","https://openalex.org/W2084619201","https://openalex.org/W2085577304","https://openalex.org/W2097698606","https://openalex.org/W2097960255","https://openalex.org/W2101181377","https://openalex.org/W2104315543","https://openalex.org/W2113019448","https://openalex.org/W2113654464","https://openalex.org/W2120433106","https://openalex.org/W2123280311","https://openalex.org/W2128165179","https://openalex.org/W2132178599","https://openalex.org/W2132180308","https://openalex.org/W2134672568","https://openalex.org/W2135197754","https://openalex.org/W2137786672","https://openalex.org/W2139259976","https://openalex.org/W2144014661","https://openalex.org/W2148866736","https://openalex.org/W2155320925","https://openalex.org/W2158256570","https://openalex.org/W2163362093","https://openalex.org/W2163980860","https://openalex.org/W2166474856","https://openalex.org/W2166558964","https://openalex.org/W2167566248","https://openalex.org/W2169628276","https://openalex.org/W2601748485","https://openalex.org/W2785349534","https://openalex.org/W3147442204","https://openalex.org/W4236956086","https://openalex.org/W4301424533","https://openalex.org/W6605596884","https://openalex.org/W6646873156","https://openalex.org/W6658966837","https://openalex.org/W6663603978","https://openalex.org/W6667202976","https://openalex.org/W6672018611","https://openalex.org/W6747435310"],"related_works":["https://openalex.org/W159132833","https://openalex.org/W83344948","https://openalex.org/W2536723159","https://openalex.org/W2041190900","https://openalex.org/W2001121861","https://openalex.org/W2897178939","https://openalex.org/W2886703719","https://openalex.org/W2282329238","https://openalex.org/W1522545030","https://openalex.org/W3189089173"],"abstract_inverted_index":{"The":[0],"data":[1],"and":[2],"software":[3],"are":[4],"available":[5],"at:":[6],"http://www.cs.utoronto.ca/":[7],"approximately":[8],"juris/data/BI09/.":[9]},"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":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
