{"id":"https://openalex.org/W2940618253","doi":"https://doi.org/10.2478/dim-2019-0003","title":"Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service","display_name":"Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W2940618253","doi":"https://doi.org/10.2478/dim-2019-0003","mag":"2940618253"},"language":"en","primary_location":{"id":"doi:10.2478/dim-2019-0003","is_oa":true,"landing_page_url":"https://doi.org/10.2478/dim-2019-0003","pdf_url":"https://content.sciendo.com/downloadpdf/journals/dim/3/1/article-p3.pdf","source":{"id":"https://openalex.org/S4210174804","display_name":"Data and Information Management","issn_l":"2543-9251","issn":["2543-9251"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data and Information Management","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://content.sciendo.com/downloadpdf/journals/dim/3/1/article-p3.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101883722","display_name":"Weijia Xu","orcid":"https://orcid.org/0000-0002-5134-6381"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Weijia Xu","raw_affiliation_strings":["Texas Advanced Computing Center, University of Texas, Austin, USA"],"affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, University of Texas, Austin, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058405202","display_name":"Amit Gupta","orcid":"https://orcid.org/0000-0002-3109-4949"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amit Gupta","raw_affiliation_strings":["Texas Advanced Computing Center, University of Texas, Austin, USA"],"affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, University of Texas, Austin, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049418039","display_name":"Pankaj Jaiswal","orcid":"https://orcid.org/0000-0002-1005-8383"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pankaj Jaiswal","raw_affiliation_strings":["Oregon State University, Corvallis, Oregon, USA"],"affiliations":[{"raw_affiliation_string":"Oregon State University, Corvallis, Oregon, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063231330","display_name":"Crispin B. Taylor","orcid":"https://orcid.org/0000-0002-4669-3215"},"institutions":[{"id":"https://openalex.org/I2799982318","display_name":"American Society of Plant Biologists","ror":"https://ror.org/04f49a463","country_code":"US","type":"other","lineage":["https://openalex.org/I2799982318"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Crispin Taylor","raw_affiliation_strings":["American Society of Plant Biologists, Rockville, Maryland, USA"],"affiliations":[{"raw_affiliation_string":"American Society of Plant Biologists, Rockville, Maryland, USA","institution_ids":["https://openalex.org/I2799982318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059629158","display_name":"Patti Lockhart","orcid":"https://orcid.org/0000-0002-9573-8520"},"institutions":[{"id":"https://openalex.org/I2799982318","display_name":"American Society of Plant Biologists","ror":"https://ror.org/04f49a463","country_code":"US","type":"other","lineage":["https://openalex.org/I2799982318"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patti Lockhart","raw_affiliation_strings":["American Society of Plant Biologists, Rockville, Maryland, USA"],"affiliations":[{"raw_affiliation_string":"American Society of Plant Biologists, Rockville, Maryland, USA","institution_ids":["https://openalex.org/I2799982318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072714322","display_name":"Jennifer Regala","orcid":"https://orcid.org/0000-0002-4078-0692"},"institutions":[{"id":"https://openalex.org/I2799982318","display_name":"American Society of Plant Biologists","ror":"https://ror.org/04f49a463","country_code":"US","type":"other","lineage":["https://openalex.org/I2799982318"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer Regala","raw_affiliation_strings":["American Society of Plant Biologists, Rockville, Maryland, USA"],"affiliations":[{"raw_affiliation_string":"American Society of Plant Biologists, Rockville, Maryland, USA","institution_ids":["https://openalex.org/I2799982318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101883722"],"corresponding_institution_ids":["https://openalex.org/I4388891828"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.0859,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.46246542,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"3","issue":"1","first_page":"3","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9980000257492065,"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/T10028","display_name":"Topic Modeling","score":0.9922999739646912,"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/pipeline","display_name":"Pipeline (software)","score":0.6809738874435425},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5866259932518005},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.4857766926288605},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41658177971839905},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33050113916397095},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.12725785374641418},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10787627100944519}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6809738874435425},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5866259932518005},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.4857766926288605},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41658177971839905},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33050113916397095},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.12725785374641418},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10787627100944519},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.2478/dim-2019-0003","is_oa":true,"landing_page_url":"https://doi.org/10.2478/dim-2019-0003","pdf_url":"https://content.sciendo.com/downloadpdf/journals/dim/3/1/article-p3.pdf","source":{"id":"https://openalex.org/S4210174804","display_name":"Data and Information Management","issn_l":"2543-9251","issn":["2543-9251"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data and Information Management","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.2478/dim-2019-0003","is_oa":true,"landing_page_url":"https://doi.org/10.2478/dim-2019-0003","pdf_url":"https://content.sciendo.com/downloadpdf/journals/dim/3/1/article-p3.pdf","source":{"id":"https://openalex.org/S4210174804","display_name":"Data and Information Management","issn_l":"2543-9251","issn":["2543-9251"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data and Information Management","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2974868206","display_name":null,"funder_award_id":"IOS-1127112","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G694679094","display_name":null,"funder_award_id":"DBI-0735191","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8445956669","display_name":null,"funder_award_id":"DBI-1265383","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2940618253.pdf","grobid_xml":"https://content.openalex.org/works/W2940618253.grobid-xml"},"referenced_works_count":104,"referenced_works":["https://openalex.org/W167355512","https://openalex.org/W188433705","https://openalex.org/W1540449438","https://openalex.org/W1547556487","https://openalex.org/W1547612978","https://openalex.org/W1697079089","https://openalex.org/W1850865022","https://openalex.org/W1974839435","https://openalex.org/W1981590391","https://openalex.org/W1981797826","https://openalex.org/W1990028388","https://openalex.org/W1995099886","https://openalex.org/W2004890010","https://openalex.org/W2015079391","https://openalex.org/W2017102965","https://openalex.org/W2018874418","https://openalex.org/W2020278455","https://openalex.org/W2033377040","https://openalex.org/W2043089011","https://openalex.org/W2047782770","https://openalex.org/W2048140075","https://openalex.org/W2050626994","https://openalex.org/W2061834489","https://openalex.org/W2064199746","https://openalex.org/W2065963191","https://openalex.org/W2068882115","https://openalex.org/W2071797522","https://openalex.org/W2090950329","https://openalex.org/W2096413109","https://openalex.org/W2096951189","https://openalex.org/W2097716833","https://openalex.org/W2100672227","https://openalex.org/W2103017472","https://openalex.org/W2108991785","https://openalex.org/W2119130230","https://openalex.org/W2123556395","https://openalex.org/W2124147474","https://openalex.org/W2129999749","https://openalex.org/W2130292407","https://openalex.org/W2134429551","https://openalex.org/W2141099517","https://openalex.org/W2144578941","https://openalex.org/W2147880316","https://openalex.org/W2148019918","https://openalex.org/W2148540243","https://openalex.org/W2151690004","https://openalex.org/W2153078783","https://openalex.org/W2154129128","https://openalex.org/W2159640576","https://openalex.org/W2161741964","https://openalex.org/W2167243426","https://openalex.org/W2167865654","https://openalex.org/W2168340032","https://openalex.org/W2169918010","https://openalex.org/W2235409271","https://openalex.org/W2250861254","https://openalex.org/W2301095666","https://openalex.org/W2301623411","https://openalex.org/W2336067426","https://openalex.org/W2407338347","https://openalex.org/W2411190207","https://openalex.org/W2415816939","https://openalex.org/W2515248967","https://openalex.org/W2589050661","https://openalex.org/W2734608416","https://openalex.org/W2768308516","https://openalex.org/W2769436351","https://openalex.org/W2807800730","https://openalex.org/W2912026815","https://openalex.org/W2913201579","https://openalex.org/W2963738950","https://openalex.org/W3146259567","https://openalex.org/W3147597245","https://openalex.org/W4206192903","https://openalex.org/W4235399338","https://openalex.org/W4238213357","https://openalex.org/W4240505079","https://openalex.org/W4244203596","https://openalex.org/W4255196843","https://openalex.org/W4302802341","https://openalex.org/W4365799834","https://openalex.org/W6606991246","https://openalex.org/W6607626469","https://openalex.org/W6632404493","https://openalex.org/W6644181178","https://openalex.org/W6645769393","https://openalex.org/W6651468824","https://openalex.org/W6662590293","https://openalex.org/W6673382958","https://openalex.org/W6674623038","https://openalex.org/W6679081091","https://openalex.org/W6680215324","https://openalex.org/W6681095162","https://openalex.org/W6682072402","https://openalex.org/W6682452302","https://openalex.org/W6682520957","https://openalex.org/W6683666313","https://openalex.org/W6684580497","https://openalex.org/W6691486186","https://openalex.org/W6714112401","https://openalex.org/W6714775741","https://openalex.org/W6716509343","https://openalex.org/W6725658358","https://openalex.org/W6764288440"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"With":[0],"the":[1,51,103,107,115,164,167,176,187,195,212,222,232,265],"increasing":[2],"amount":[3],"of":[4,50,56,78,92,102,215,235],"digital":[5,74],"journal":[6,38,108],"submissions,":[7],"there":[8,42],"is":[9,25],"a":[10,90,137,147,206,218,285,298],"need":[11],"to":[12,18,26,47,72,95,175,185,243],"deploy":[13],"new":[14],"scalable":[15],"computational":[16],"methods":[17,53],"improve":[19,186],"information":[20,29],"accessibilities.":[21],"One":[22],"common":[23],"task":[24],"identify":[27],"useful":[28],"and":[30,54,80,84,106,118,136,149,159,173,201,226,263,272,296],"named":[31,287],"entity":[32,79,128,188,282,288],"from":[33,256,260],"text":[34],"documents":[35],"such":[36],"as":[37,217],"article":[39],"submission.":[40],"However,":[41],"are":[43,143],"many":[44],"technical":[45],"challenges":[46],"limit":[48],"applicability":[49],"general":[52,57],"lack":[55],"tools.":[58],"In":[59,89,205,277],"this":[60],"paper,":[61],"we":[62,209],"present":[63,240],"domain":[64],"informational":[65,82],"vocabulary":[66],"extraction":[67,283],"(DIVE)":[68],"project,":[69],"which":[70],"aims":[71],"enrich":[73],"publications":[75],"through":[76,152],"detection":[77,189],"key":[81],"words":[83],"by":[85,110,161,231],"adding":[86],"additional":[87,171],"annotations.":[88],"first":[91,213],"its":[93,246],"kind":[94],"our":[96,98,199],"knowledge,":[97],"system":[99,122],"engages":[100],"authors":[101,168],"peer-reviewed":[104],"articles":[105,193],"publishers":[109],"integrating":[111],"DIVE":[112,257],"implementation":[113],"in":[114,146,190,194,203],"manuscript":[116],"proofing":[117],"publication":[119],"process.":[120],"The":[121,179,227],"implements":[123],"multiple":[124],"strategies":[125],"for":[126,157],"biological":[127,281],"detection,":[129],"including":[130],"using":[131],"regular":[132],"expression":[133],"rules,":[134],"ontology,":[135],"keyword":[138],"dictionary.":[139],"These":[140],"extracted":[141],"entities":[142],"then":[144,182],"stored":[145],"database":[148],"made":[150],"accessible":[151],"an":[153,279],"interactive":[154],"web":[155,165],"application":[156],"curation":[158,262],"evaluation":[160],"authors.":[162],"Through":[163],"interface,":[166],"can":[169,181,291],"make":[170],"annotations":[172],"corrections":[174],"current":[177],"results.":[178],"updates":[180],"be":[183],"used":[184],"subsequent":[191],"processed":[192],"future.":[196],"We":[197,239,251],"describe":[198],"framework":[200],"deployment":[202],"details.":[204],"pilot":[207],"program,":[208],"have":[210],"deployed":[211],"phase":[214],"development":[216],"service":[219,266],"integrated":[220],"with":[221,258],"journals":[223],"Plant":[224,228,236],"Physiology":[225],"cell":[229],"published":[230],"American":[233],"Society":[234],"Biologists":[237],"(ASPB).":[238],"usage":[241],"statistics":[242],"date":[244],"since":[245],"production":[247],"on":[248,268],"April":[249],"2018.":[250],"compare":[252],"automated":[253],"recognition":[254],"results":[255,259],"author":[261],"show":[264],"achieved":[267],"average":[269],"80%":[270],"recall":[271,295],"70%":[273],"precision":[274],"per":[275],"article.":[276],"contrast,":[278],"existing":[280],"tool,":[284],"biomedical":[286],"recognizer":[289],"(ABNER),":[290],"only":[292],"achieve":[293],"47%":[294],"return":[297],"much":[299],"larger":[300],"candidate":[301],"set.":[302]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
