{"id":"https://openalex.org/W2512456704","doi":"https://doi.org/10.1093/database/baw101","title":"PIPE: a protein\u2013protein interaction passage extraction module for BioCreative challenge","display_name":"PIPE: a protein\u2013protein interaction passage extraction module for BioCreative challenge","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2512456704","doi":"https://doi.org/10.1093/database/baw101","mag":"2512456704","pmid":"https://pubmed.ncbi.nlm.nih.gov/27524807"},"language":"en","primary_location":{"id":"doi:10.1093/database/baw101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw101","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw101/17474307/baw101.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw101/17474307/baw101.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018928362","display_name":"Yung\u2010Chun Chang","orcid":"https://orcid.org/0000-0002-9634-8380"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yung-Chun Chang","raw_affiliation_strings":["Institute of Information Science, Academia Sinica, Taipei, Taiwan Department of Information Management, National Taiwan University, Taipei, Taiwan hsu@iis.sinica.edu.tw changyc@iis.sinica.edu.tw","Department of Information Management, National Taiwan University, Taipei, Taiwan","Institute of Information Science, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan Department of Information Management, National Taiwan University, Taipei, Taiwan hsu@iis.sinica.edu.tw changyc@iis.sinica.edu.tw","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"Department of Information Management, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112209175","display_name":"Chun-Han Chu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chun-Han Chu","raw_affiliation_strings":["Institute of Information Science, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110439340","display_name":"Yu-Chen Su","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yu-Chen Su","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101806372","display_name":"Chien Chin Chen","orcid":"https://orcid.org/0000-0002-8357-1305"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chien Chin Chen","raw_affiliation_strings":["Department of Information Management, National Taiwan University, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Management, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112054430","display_name":"Wen-Lian Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Wen-Lian Hsu","raw_affiliation_strings":["Institute of Information Science, Academia Sinica, Taipei, Taiwan hsu@iis.sinica.edu.tw","Institute of Information Science, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan hsu@iis.sinica.edu.tw","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5112054430"],"corresponding_institution_ids":["https://openalex.org/I4210098366"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":2.6112,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.89908954,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"2016","issue":null,"first_page":"baw101","last_page":"baw101"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9729999899864197,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9677000045776367,"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":0.819183349609375},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.6621535420417786},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5866995453834534},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5716925859451294},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.497163325548172},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.48658549785614014},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.41624388098716736},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38717520236968994},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37886881828308105},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37396514415740967},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35556793212890625}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.819183349609375},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.6621535420417786},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5866995453834534},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5716925859451294},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.497163325548172},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.48658549785614014},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.41624388098716736},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38717520236968994},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37886881828308105},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37396514415740967},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35556793212890625},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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/database/baw101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw101","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw101/17474307/baw101.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:27524807","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27524807","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:databa:2016/0/baw101","is_oa":false,"landing_page_url":"http://database.oxfordjournals.org/cgi/content/short/2016/0/baw101","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4983456","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4983456","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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baw101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw101","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw101/17474307/baw101.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W151685798","https://openalex.org/W1493270114","https://openalex.org/W1497603085","https://openalex.org/W1508977358","https://openalex.org/W1514107797","https://openalex.org/W1553682320","https://openalex.org/W1563088657","https://openalex.org/W1574901103","https://openalex.org/W1587871245","https://openalex.org/W1604685658","https://openalex.org/W1850865022","https://openalex.org/W1965756895","https://openalex.org/W1969114498","https://openalex.org/W1971886065","https://openalex.org/W1987818105","https://openalex.org/W1990794790","https://openalex.org/W1994392346","https://openalex.org/W2027424931","https://openalex.org/W2032566933","https://openalex.org/W2048059249","https://openalex.org/W2097960255","https://openalex.org/W2098162425","https://openalex.org/W2098551466","https://openalex.org/W2104148262","https://openalex.org/W2108010925","https://openalex.org/W2116786260","https://openalex.org/W2121844933","https://openalex.org/W2124225821","https://openalex.org/W2127713198","https://openalex.org/W2130687290","https://openalex.org/W2130832525","https://openalex.org/W2131859788","https://openalex.org/W2134488721","https://openalex.org/W2140190241","https://openalex.org/W2141869602","https://openalex.org/W2143954109","https://openalex.org/W2152269015","https://openalex.org/W2166111585","https://openalex.org/W2166474856","https://openalex.org/W2186428165","https://openalex.org/W2296755350","https://openalex.org/W2342313026","https://openalex.org/W2509885322","https://openalex.org/W4254630790","https://openalex.org/W4256647194","https://openalex.org/W4285719527","https://openalex.org/W6679272186","https://openalex.org/W6681287948"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4224009465","https://openalex.org/W4306674287","https://openalex.org/W4286629047","https://openalex.org/W4205958290","https://openalex.org/W4384212932","https://openalex.org/W2548721895","https://openalex.org/W2373456246","https://openalex.org/W1493568480","https://openalex.org/W4390590544"],"abstract_inverted_index":{"Identifying":[0],"the":[1,12,20,37,67],"interactions":[2],"between":[3],"proteins":[4],"mentioned":[5],"in":[6,19,36],"biomedical":[7],"literatures":[8],"is":[9,101],"one":[10],"of":[11,16],"frequently":[13],"discussed":[14],"topics":[15],"text":[17],"mining":[18],"life":[21],"science":[22],"field.":[23],"In":[24],"this":[25],"article,":[26],"we":[27],"propose":[28],"PIPE,":[29],"an":[30,58],"interaction":[31,50,59],"pattern":[32,60],"generation":[33],"module":[34],"used":[35],"Collaborative":[38],"Biocurator":[39],"Assistant":[40],"Task":[41],"at":[42],"BioCreative":[43],"V":[44],"(http://www.biocreative.org/)":[45],"to":[46,75],"capture":[47],"frequent":[48],"protein-protein":[49],"(PPI)":[51],"patterns":[52,69],"within":[53],"text.":[54],"We":[55],"also":[56],"present":[57],"tree":[61,72],"(IPT)":[62],"kernel":[63,73],"method":[64,100],"that":[65,98],"integrates":[66],"PPI":[68,107],"with":[70],"convolution":[71],"(CTK)":[74],"extract":[76],"PPIs.":[77],"Methods":[78],"were":[79],"evaluated":[80],"on":[81],"LLL,":[82],"IEPA,":[83],"HPRD50,":[84],"AIMed":[85],"and":[86,92,103],"BioInfer":[87],"corpora":[88],"using":[89],"cross-validation,":[90],"cross-learning":[91],"cross-corpus":[93],"evaluation.":[94],"Empirical":[95],"evaluations":[96],"demonstrate":[97],"our":[99],"effective":[102],"outperforms":[104],"several":[105],"well-known":[106],"extraction":[108],"methods.":[109],"DATABASE":[110],"URL.":[111]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}
