{"id":"https://openalex.org/W4255154157","doi":"https://doi.org/10.12688/f1000research.11389.1","title":"PubRunner: A light-weight framework for updating text mining results","display_name":"PubRunner: A light-weight framework for updating text mining results","publication_year":2017,"publication_date":"2017-05-02","ids":{"openalex":"https://openalex.org/W4255154157","doi":"https://doi.org/10.12688/f1000research.11389.1"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.11389.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.11389.1","pdf_url":"https://f1000research.com/articles/6-612/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/6-612/v1/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026721445","display_name":"Kishore R. Anekalla","orcid":"https://orcid.org/0000-0002-8366-5782"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kishore R. Anekalla","raw_affiliation_strings":["Northwestern University, Chicago, IL, 60611, USA","Northwestern University, Chicago, IL, 60611"],"raw_orcid":"https://orcid.org/0000-0002-8366-5782","affiliations":[{"raw_affiliation_string":"Northwestern University, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Northwestern University, Chicago, IL, 60611","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035654499","display_name":"Jean-Paul Courneya","orcid":"https://orcid.org/0000-0001-9014-649X"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I6059380","display_name":"University of Baltimore","ror":"https://ror.org/024gw2733","country_code":"US","type":"education","lineage":["https://openalex.org/I6059380"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J.P. Courneya","raw_affiliation_strings":["Health Sciences and Human Services Library, University of Maryland, Baltimore, MD, 21201, USA","Health Sciences and Human Services Library, University of Maryland, Baltimore, MD, 21201"],"raw_orcid":"https://orcid.org/0000-0001-9014-649X","affiliations":[{"raw_affiliation_string":"Health Sciences and Human Services Library, University of Maryland, Baltimore, MD, 21201, USA","institution_ids":["https://openalex.org/I6059380","https://openalex.org/I126744593"]},{"raw_affiliation_string":"Health Sciences and Human Services Library, University of Maryland, Baltimore, MD, 21201","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075746125","display_name":"Nicolas Fiorini","orcid":"https://orcid.org/0000-0002-9260-1326"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicolas Fiorini","raw_affiliation_strings":["National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA","National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894"],"raw_orcid":"https://orcid.org/0000-0002-9260-1326","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088887674","display_name":"Jake Lever","orcid":"https://orcid.org/0000-0001-8198-2939"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jake Lever","raw_affiliation_strings":["Canada's Michael Smith Genome Sciences Centre, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada","Canada's Michael Smith Genome Sciences Centre, University of British Columbia, Vancouver, BC, V5Z 4S6"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canada's Michael Smith Genome Sciences Centre, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada","institution_ids":["https://openalex.org/I4210133112"]},{"raw_affiliation_string":"Canada's Michael Smith Genome Sciences Centre, University of British Columbia, Vancouver, BC, V5Z 4S6","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086745995","display_name":"Michael Muchow","orcid":"https://orcid.org/0000-0002-2825-4120"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Muchow","raw_affiliation_strings":["National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA","National Institute of Standards and Technology, Gaithersburg, MD, 20899"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA","institution_ids":["https://openalex.org/I1321296531"]},{"raw_affiliation_string":"National Institute of Standards and Technology, Gaithersburg, MD, 20899","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070603357","display_name":"Ben Busby","orcid":"https://orcid.org/0000-0001-5267-4988"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Busby","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894"],"raw_orcid":"https://orcid.org/0000-0001-5267-4988","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5026721445"],"corresponding_institution_ids":["https://openalex.org/I111979921"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.8984,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7459394,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"6","issue":null,"first_page":"612","last_page":"612"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9793999791145325,"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":0.9628000259399414,"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/upload","display_name":"Upload","score":0.7673819065093994},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7109917402267456},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6184287667274475},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5975739359855652},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5367568135261536},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.49726322293281555},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.47581392526626587},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.43329381942749023},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3801257312297821},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.30706334114074707},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2817087173461914},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.08773472905158997}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.7673819065093994},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7109917402267456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6184287667274475},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5975739359855652},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5367568135261536},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.49726322293281555},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.47581392526626587},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.43329381942749023},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3801257312297821},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.30706334114074707},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2817087173461914},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.08773472905158997},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.12688/f1000research.11389.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.11389.1","pdf_url":"https://f1000research.com/articles/6-612/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.11389.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.11389.1","pdf_url":"https://f1000research.com/articles/6-612/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4255154157.pdf","grobid_xml":"https://content.openalex.org/works/W4255154157.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2103151642","https://openalex.org/W2112723752","https://openalex.org/W2118806902","https://openalex.org/W2132812398","https://openalex.org/W2162965868","https://openalex.org/W2515582862","https://openalex.org/W3210198983"],"related_works":["https://openalex.org/W3185751515","https://openalex.org/W1479703980","https://openalex.org/W2749535755","https://openalex.org/W1553529581","https://openalex.org/W4206039273","https://openalex.org/W4232119327","https://openalex.org/W2911489562","https://openalex.org/W2134429551","https://openalex.org/W3183808544","https://openalex.org/W2188854577"],"abstract_inverted_index":{"<ns4:p>":[0],"Biomedical":[1],"text":[2,41,56,81,107,127,178],"mining":[3,42,57,82,108,128,179],"promises":[4],"to":[5,83,118,147,181],"assist":[6],"biologists":[7,188],"in":[8,14,74,189],"quickly":[9],"navigating":[10],"the":[11,23,49,70,75,111,134,144,153,159,191],"combined":[12],"knowledge":[13,73],"their":[15,62],"domain.":[16],"This":[17,167],"would":[18],"allow":[19],"improved":[20],"understanding":[21],"of":[22,155,171],"complex":[24],"interactions":[25],"within":[26],"biological":[27],"systems":[28],"and":[29,40,66,120,151],"faster":[30],"hypothesis":[31],"generation.":[32],"New":[33],"biomedical":[34,80],"research":[35],"articles":[36],"are":[37,44,59,64],"published":[38],"daily":[39],"tools":[43,58,109,183],"only":[45],"as":[46,48],"good":[47],"corpus":[50],"from":[51,137],"which":[52],"they":[53],"work.":[54],"Many":[55],"underused":[60],"because":[61],"results":[63,157],"static":[65],"do":[67],"not":[68],"reflect":[69],"constantly":[71],"expanding":[72],"field.":[76],"In":[77],"order":[78],"for":[79,104],"become":[84],"an":[85,125],"indispensable":[86],"tool":[87],"used":[88],"by":[89],"researchers,":[90],"this":[91,97],"problem":[92],"must":[93],"be":[94,122],"addressed.":[95],"To":[96],"end,":[98],"we":[99,174],"present":[100],"PubRunner,":[101],"a":[102,140,148,169],"framework":[103],"regularly":[105],"running":[106],"on":[110,158],"latest":[112,135,192],"publications.":[113,193],"PubRunner":[114],"is":[115],"lightweight,":[116],"simple":[117],"use,":[119],"can":[121],"integrated":[123],"with":[124],"existing":[126],"tool.":[129],"The":[130],"workflow":[131],"involves":[132],"downloading":[133],"abstracts":[136],"PubMed,":[138],"executing":[139],"user-defined":[141],"tool,":[142],"pushing":[143],"resulting":[145],"data":[146],"public":[149,160],"FTP,":[150],"publicizing":[152],"location":[154],"these":[156],"<ns4:ext-link":[161],"xmlns:ns3=\"http://www.w3.org/1999/xlink\"":[162],"ext-link-type=\"uri\"":[163],"ns3:href=\"http://www.pubrunner.org/\">PubRunner":[164],"website</ns4:ext-link>":[165],".":[166],"shows":[168],"proof":[170],"concept":[172],"that":[173,184],"hope":[175],"will":[176,186],"encourage":[177],"developers":[180],"build":[182],"truly":[185],"aid":[187],"exploring":[190],"</ns4:p>":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
