{"id":"https://openalex.org/W2123651477","doi":"https://doi.org/10.1186/1471-2105-10-s11-s18","title":"PathBinder \u2013 text empirics and automatic extraction of biomolecular interactions","display_name":"PathBinder \u2013 text empirics and automatic extraction of biomolecular interactions","publication_year":2009,"publication_date":"2009-10-01","ids":{"openalex":"https://openalex.org/W2123651477","doi":"https://doi.org/10.1186/1471-2105-10-s11-s18","mag":"2123651477","pmid":"https://pubmed.ncbi.nlm.nih.gov/19811683"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s11-s18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S18","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/10.1186/1471-2105-10-S11-S18","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003556201","display_name":"Lifeng Zhang","orcid":"https://orcid.org/0000-0001-5431-6084"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lifeng Zhang","raw_affiliation_strings":["Iowa State University, Ames, Iowa, USA","Iowa State University Ames, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, Iowa, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Iowa State University Ames, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108822086","display_name":"Daniel Berleant","orcid":null},"institutions":[{"id":"https://openalex.org/I102401767","display_name":"University of Arkansas at Little Rock","ror":"https://ror.org/04fttyv97","country_code":"US","type":"education","lineage":["https://openalex.org/I102401767"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Berleant","raw_affiliation_strings":["University of Arkansas at Little Rock, Little Rock, Arkansas, USA","University of Arkansas At Little Rock, Little Rock, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Arkansas at Little Rock, Little Rock, Arkansas, USA","institution_ids":["https://openalex.org/I102401767"]},{"raw_affiliation_string":"University of Arkansas At Little Rock, Little Rock, USA","institution_ids":["https://openalex.org/I102401767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101503403","display_name":"Jing Ding","orcid":"https://orcid.org/0000-0002-5893-4207"},"institutions":[{"id":"https://openalex.org/I2802841970","display_name":"The Ohio State University Wexner Medical Center","ror":"https://ror.org/00c01js51","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2802841970"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Ding","raw_affiliation_strings":["Ohio State University Medical Center, Columbus, Ohio, USA","Ohio State University Medical Center, Columbus, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ohio State University Medical Center, Columbus, Ohio, USA","institution_ids":["https://openalex.org/I2802841970","https://openalex.org/I52357470"]},{"raw_affiliation_string":"Ohio State University Medical Center, Columbus, USA","institution_ids":["https://openalex.org/I2802841970","https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110459984","display_name":"Tuan Dung Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tuan Cao","raw_affiliation_strings":["Iowa State University, Ames, Iowa, USA","Iowa State University Ames, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, Iowa, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Iowa State University Ames, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054812749","display_name":"Eve Syrkin Wurtele","orcid":"https://orcid.org/0000-0003-1552-9495"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eve Syrkin Wurtele","raw_affiliation_strings":["Iowa State University, Ames, Iowa, USA","Iowa State University Ames, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, Iowa, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Iowa State University Ames, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5108822086"],"corresponding_institution_ids":["https://openalex.org/I102401767"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.7555,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.70455288,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"S11","first_page":"S18","last_page":"S18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9961000084877014,"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":0.9961000084877014,"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":0.0007999999797903001,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.7910257577896118},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5659838318824768},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5310324430465698},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4899732172489166},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34668731689453125},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.33793139457702637}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7910257577896118},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5659838318824768},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5310324430465698},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4899732172489166},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34668731689453125},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.33793139457702637}],"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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":5,"locations":[{"id":"doi:10.1186/1471-2105-10-s11-s18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S18","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:19811683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19811683","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:lib.dr.iastate.edu:gdcb_las_conf-1002","is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/gdcb_las_conf/2","pdf_url":null,"source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genetics, Development and Cell Biology Presentations, Posters and Proceedings","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:f36b2fbeaeab4c6bac59152f6ceffe79","is_oa":false,"landing_page_url":"https://doaj.org/article/f36b2fbeaeab4c6bac59152f6ceffe79","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 11, p S18 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3226189","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3226189","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:10.1186/1471-2105-10-s11-s18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S18","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":[{"id":"https://openalex.org/G490571479","display_name":"Arabidopsis 2010: MetNet: Integrated Software for Arabidopsis Systems Biology Research","funder_award_id":"0520267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123651477.pdf","grobid_xml":"https://content.openalex.org/works/W2123651477.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W111301558","https://openalex.org/W1483118642","https://openalex.org/W1489127507","https://openalex.org/W1492581928","https://openalex.org/W1532325895","https://openalex.org/W1623698862","https://openalex.org/W1999117234","https://openalex.org/W2000678571","https://openalex.org/W2016928406","https://openalex.org/W2025538594","https://openalex.org/W2033853342","https://openalex.org/W2044514479","https://openalex.org/W2097960255","https://openalex.org/W2098910027","https://openalex.org/W2099794271","https://openalex.org/W2100592161","https://openalex.org/W2100857018","https://openalex.org/W2102064386","https://openalex.org/W2104768328","https://openalex.org/W2107344625","https://openalex.org/W2109070394","https://openalex.org/W2115936127","https://openalex.org/W2120361304","https://openalex.org/W2123112337","https://openalex.org/W2123280311","https://openalex.org/W2130687290","https://openalex.org/W2130748131","https://openalex.org/W2132288458","https://openalex.org/W2146116329","https://openalex.org/W2153438709","https://openalex.org/W2155331065","https://openalex.org/W2158505321","https://openalex.org/W2158796363","https://openalex.org/W2160238006","https://openalex.org/W2165674132","https://openalex.org/W2166043581","https://openalex.org/W2167289895","https://openalex.org/W2169974160","https://openalex.org/W2171623083","https://openalex.org/W2394552777","https://openalex.org/W4213009331","https://openalex.org/W4255855797","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4312192474","https://openalex.org/W4210805261"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,131,198],"increasingly":[2],"large":[3],"amount":[4],"of":[5,50,66,72,83,96,123,181,211],"free,":[6],"online":[7],"biological":[8,51],"text":[9,52,67,199],"makes":[10],"automatic":[11,209],"interaction":[12,182,189],"extraction":[13,210],"correspondingly":[14],"attractive.":[15],"Machine":[16],"learning":[17],"is":[18],"one":[19],"strategy":[20],"that":[21,29],"works":[22],"by":[23],"uncovering":[24],"and":[25,86,120],"using":[26],"useful":[27,101],"properties":[28,37,49,112,122],"are":[30,38],"implicit":[31],"in":[32,42,54,174],"the":[33,43,64,110,142,178],"text.":[34],"However":[35],"these":[36],"usually":[39],"not":[40],"reported":[41],"literature":[44],"explicitly.":[45],"By":[46],"investigating":[47],"specific":[48],"passages":[53],"this":[55,84],"paper,":[56],"we":[57,113],"aim":[58],"to":[59,69,102,108,126,137,145,167,176],"facilitate":[60],"an":[61,93,139],"alternative":[62],"strategy,":[63],"use":[65,109],"empirics,":[68],"support":[70],"mining":[71],"biomedical":[73],"texts":[74],"for":[75,141,154],"biomolecular":[76,147,188,212],"interactions.":[77],"We":[78,116],"report":[79,88],"on":[80,194],"our":[81],"application":[82],"approach,":[85],"also":[87,106],"some":[89],"empirical":[90,111,133],"findings":[91],"about":[92],"important":[94],"class":[95],"passages.":[97],"These":[98],"may":[99,105],"be":[100],"others":[103],"who":[104],"wish":[107],"describe.":[114],"RESULTS:":[115],"manually":[117],"analyzed":[118],"syntactic":[119],"semantic":[121],"sentences":[124,155,173],"likely":[125],"describe":[127],"interactions":[128,148,157,213],"between":[129,158,183],"biomolecules.":[130,161,186],"resulting":[132],"data":[134],"were":[135],"used":[136,202],"design":[138],"algorithm":[140],"PathBinder":[143,151,162],"system":[144],"extract":[146],"from":[149,170,214],"texts.":[150,215],"searches":[152],"PubMed":[153,175],"describing":[156],"two":[159,184],"given":[160],"then":[163],"uses":[164],"probabilistic":[165],"methods":[166],"combine":[168],"evidence":[169],"multiple":[171],"relevant":[172],"assess":[177],"relative":[179],"likelihood":[180],"arbitrary":[185],"A":[187],"network":[190],"was":[191],"constructed":[192],"based":[193],"those":[195],"likelihoods.":[196],"CONCLUSION:":[197],"empirics":[200],"approach":[201],"here":[203],"supports":[204],"computationally":[205],"friendly,":[206],"performance":[207],"competitive,":[208],"AVAILABILITY:":[216],"http://www.metnetdb.org/pathbinder.":[217]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
