{"id":"https://openalex.org/W3006574710","doi":"https://doi.org/10.1093/bioinformatics/btaa095","title":"ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes","display_name":"ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes","publication_year":2020,"publication_date":"2020-02-08","ids":{"openalex":"https://openalex.org/W3006574710","doi":"https://doi.org/10.1093/bioinformatics/btaa095","mag":"3006574710","pmid":"https://pubmed.ncbi.nlm.nih.gov/32058567"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2966/33180946/btaa095.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/36/9/2966/33180946/btaa095.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110787381","display_name":"Gustavo Arango-Argoty","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G A Arango-Argoty","raw_affiliation_strings":["Department of Computer Science"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011964563","display_name":"Giselle K. P. Guron","orcid":"https://orcid.org/0000-0002-2009-5807"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G K P Guron","raw_affiliation_strings":["Department of Civil and Environmental Engineering","Department of Food Science and Technology , Virginia Tech, Blacksburg, VA 24061 - 0217, USA"],"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering","institution_ids":[]},{"raw_affiliation_string":"Department of Food Science and Technology , Virginia Tech, Blacksburg, VA 24061 - 0217, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017041972","display_name":"Emily Garner","orcid":"https://orcid.org/0000-0002-1579-155X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E Garner","raw_affiliation_strings":["Department of Civil and Environmental Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063743396","display_name":"Maria V. Riquelme","orcid":"https://orcid.org/0000-0003-1142-109X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M V Riquelme","raw_affiliation_strings":["Department of Civil and Environmental Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057291575","display_name":"Lenwood S. Heath","orcid":"https://orcid.org/0000-0003-1608-431X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L S Heath","raw_affiliation_strings":["Department of Computer Science"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046181665","display_name":"Amy Pruden","orcid":"https://orcid.org/0000-0002-3191-6244"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A Pruden","raw_affiliation_strings":["Department of Civil and Environmental Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075592885","display_name":"Peter J. Vikesland","orcid":"https://orcid.org/0000-0003-2654-5132"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P J Vikesland","raw_affiliation_strings":["Department of Civil and Environmental Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062532274","display_name":"Luyao Zhang","orcid":"https://orcid.org/0000-0001-9165-0436"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"L Zhang","raw_affiliation_strings":["Department of Computer Science"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5062532274"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8115,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.91907514,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"9","first_page":"2966","last_page":"2973"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/T10419","display_name":"Pharmaceutical and Antibiotic Environmental Impacts","score":0.9858999848365784,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crowdsourcing","display_name":"Crowdsourcing","score":0.8623497486114502},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.75743567943573},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.7469921112060547},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6884379386901855},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4724457859992981},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4700906276702881},{"id":"https://openalex.org/keywords/web-resource","display_name":"Web resource","score":0.4665650427341461},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42993253469467163},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40360933542251587},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3494427800178528},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34501004219055176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12883207201957703}],"concepts":[{"id":"https://openalex.org/C62230096","wikidata":"https://www.wikidata.org/wiki/Q275969","display_name":"Crowdsourcing","level":2,"score":0.8623497486114502},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.75743567943573},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7469921112060547},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6884379386901855},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4724457859992981},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4700906276702881},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.4665650427341461},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42993253469467163},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40360933542251587},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3494427800178528},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34501004219055176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12883207201957703},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063045","descriptor_name":"Crowdsourcing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063045","descriptor_name":"Crowdsourcing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063045","descriptor_name":"Crowdsourcing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2966/33180946/btaa095.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:32058567","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32058567","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2966/33180946/btaa095.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/8","display_name":"Decent work and economic growth","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G3239519503","display_name":null,"funder_award_id":"2015-68003-2305","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G8652598970","display_name":null,"funder_award_id":"1545756","funder_id":"https://openalex.org/F4320306468","funder_display_name":"Pacific Institute for Research and Evaluation"},{"id":"https://openalex.org/G8919468226","display_name":null,"funder_award_id":"2017-68003-26498","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320306468","display_name":"Pacific Institute for Research and Evaluation","ror":"https://ror.org/01jfr3w16"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3006574710.pdf","grobid_xml":"https://content.openalex.org/works/W3006574710.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1964071916","https://openalex.org/W1964640602","https://openalex.org/W1964670939","https://openalex.org/W1969605785","https://openalex.org/W1986708244","https://openalex.org/W1990524884","https://openalex.org/W1995008770","https://openalex.org/W2006611385","https://openalex.org/W2008274231","https://openalex.org/W2012365024","https://openalex.org/W2014101418","https://openalex.org/W2037900484","https://openalex.org/W2044986849","https://openalex.org/W2045204781","https://openalex.org/W2054762659","https://openalex.org/W2098420525","https://openalex.org/W2099837668","https://openalex.org/W2116744776","https://openalex.org/W2116947789","https://openalex.org/W2118582067","https://openalex.org/W2118688136","https://openalex.org/W2123579157","https://openalex.org/W2129113812","https://openalex.org/W2134852597","https://openalex.org/W2139531859","https://openalex.org/W2140275799","https://openalex.org/W2152127318","https://openalex.org/W2160244074","https://openalex.org/W2163303745","https://openalex.org/W2166240318","https://openalex.org/W2168156515","https://openalex.org/W2173622648","https://openalex.org/W2380447136","https://openalex.org/W2419548415","https://openalex.org/W2493916176","https://openalex.org/W2509476196","https://openalex.org/W2528511189","https://openalex.org/W2557776122","https://openalex.org/W2560622971","https://openalex.org/W2563315795","https://openalex.org/W2611303477","https://openalex.org/W2728028487","https://openalex.org/W2739999456","https://openalex.org/W2761788747","https://openalex.org/W2766807003","https://openalex.org/W2884849385","https://openalex.org/W2900984733","https://openalex.org/W2951274106","https://openalex.org/W7043590196"],"related_works":["https://openalex.org/W3032998312","https://openalex.org/W135177976","https://openalex.org/W4384486036","https://openalex.org/W1503094549","https://openalex.org/W2337920774","https://openalex.org/W4286908577","https://openalex.org/W2886410948","https://openalex.org/W2025875869","https://openalex.org/W4318823662","https://openalex.org/W2356472869"],"abstract_inverted_index":{"Curation":[0],"of":[1,43,45,57,80,94,119,150,153,158,180,210,215],"antibiotic":[2,102],"resistance":[3,104],"gene":[4,100],"(ARG)":[5],"databases":[6,27,51],"is":[7,65,163],"a":[8,54,69,77,85,126,135,181,211,219],"labor-intensive":[9],"process":[10],"that":[11,161],"requires":[12],"expert":[13,173,201],"knowledge":[14],"to":[15,25,29,67,171,196],"manually":[16],"collect,":[17],"correct,":[18],"and/or":[19],"annotate":[20],"individual":[21],"genes.":[22],"Correspondingly,":[23],"updates":[24],"existing":[26,49],"tend":[28],"be":[30,197],"infrequent,":[31],"commonly":[32],"requiring":[33],"years":[34],"for":[35,108,129,185,207],"completion":[36],"and":[37,106,110,143,167,222],"often":[38],"containing":[39],"inconsistences.":[40],"Further,":[41],"because":[42],"limitations":[44,118],"manual":[46,120],"curation,":[47,121],"most":[48],"ARG":[50,72],"contain":[52],"only":[53],"small":[55],"proportion":[56],"known":[58],"ARGs":[59,95],"(~5k":[60],"genes).":[61],"A":[62],"new":[63,86],"approach":[64,146],"needed":[66],"achieve":[68],"truly":[70,136],"comprehensive":[71],"database,":[73],"while":[74],"also":[75],"maintaining":[76],"high":[78],"level":[79],"accuracy.":[81],"Here":[82],"we":[83,122],"propose":[84],"web-based":[87],"curation":[88,131],"system,":[89],"ARG-miner,":[90],"which":[91],"supports":[92],"annotation":[93,209],"at":[96,225],"multiple":[97,151],"levels,":[98],"including:":[99],"name,":[101],"category,":[103],"mechanism,":[105],"evidence":[107],"mobility":[109],"occurrence":[111],"in":[112],"clinically-important":[113],"bacterial":[114],"strains.":[115],"To":[116],"overcome":[117],"employ":[123],"crowdsourcing":[124],"as":[125,198,200],"novel":[127],"strategy":[128],"expanding":[130],"capacity":[132],"towards":[133],"achieving":[134],"comprehensive,":[137],"up-to-date":[138],"database.":[139],"We":[141,175],"develop":[142],"validate":[144],"the":[145,178,208],"by":[147,190],"comparing":[148],"performance":[149],"cohorts":[152],"curators":[154],"with":[155,203],"varying":[156],"levels":[157],"expertise,":[159],"demonstrating":[160],"ARG-miner":[162,217],"more":[164],"cost":[165],"effective":[166],"less":[168],"time-consuming":[169],"relative":[170],"traditional":[172],"curation.":[174],"further":[176],"demonstrate":[177],"reliability":[179],"trust":[182],"validation":[183],"filter":[184],"rejecting":[186],"confounding":[187],"input":[188],"generated":[189],"spammers.":[191],"Crowdsourcing":[193],"was":[194],"found":[195],"accurate":[199],"annotation,":[202],"an":[204],"accuracy":[205],">90%":[206],"diverse":[212],"test":[213],"set":[214],"ARGs.":[216],"provides":[218],"public":[220],"API":[221],"database":[223],"available":[224],"http://bench.cs.vt.edu/argminer.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
