{"id":"https://openalex.org/W1972171558","doi":"https://doi.org/10.1093/nar/gkr286","title":"The BioExtract Server: a web-based bioinformatic workflow platform","display_name":"The BioExtract Server: a web-based bioinformatic workflow platform","publication_year":2011,"publication_date":"2011-05-05","ids":{"openalex":"https://openalex.org/W1972171558","doi":"https://doi.org/10.1093/nar/gkr286","mag":"1972171558","pmid":"https://pubmed.ncbi.nlm.nih.gov/21546552"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr286","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W528/7624226/gkr286.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","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/nar/article-pdf/39/suppl_2/W528/7624226/gkr286.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108466260","display_name":"C. M. Lushbough","orcid":null},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"C. M. Lushbough","raw_affiliation_strings":["Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA. clushbou@usd.edu","Department of Computer Science, University of South Dakota, Vermillion, SD, 57069, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA. clushbou@usd.edu","institution_ids":["https://openalex.org/I189957204"]},{"raw_affiliation_string":"Department of Computer Science, University of South Dakota, Vermillion, SD, 57069, USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028414609","display_name":"Douglas M. Jennewein","orcid":"https://orcid.org/0000-0002-8361-8361"},"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"]},{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. M. Jennewein","raw_affiliation_strings":["Department of Computer Science, University of South Dakota, Vermillion, SD 57069 USA and 2 Department of Genetics, Development and Cell Biology and 3 Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of South Dakota, Vermillion, SD 57069 USA and 2 Department of Genetics, Development and Cell Biology and 3 Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA","institution_ids":["https://openalex.org/I189957204","https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033118239","display_name":"Volker Brendel","orcid":"https://orcid.org/0000-0002-8055-7508"},"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"]},{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. P. Brendel","raw_affiliation_strings":["Department of Computer Science, University of South Dakota, Vermillion, SD 57069 USA and 2 Department of Genetics, Development and Cell Biology and 3 Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of South Dakota, Vermillion, SD 57069 USA and 2 Department of Genetics, Development and Cell Biology and 3 Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA","institution_ids":["https://openalex.org/I189957204","https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5108466260"],"corresponding_institution_ids":["https://openalex.org/I189957204"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":6.7711,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.96093367,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"39","issue":"suppl","first_page":"W528","last_page":"W532"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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":0.9930999875068665,"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/workflow","display_name":"Workflow","score":0.8282182216644287},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.7215498685836792},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6166675686836243},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5341094732284546},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.513340413570404},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4975757896900177},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4790709912776947},{"id":"https://openalex.org/keywords/java-applet","display_name":"Java applet","score":0.4753113389015198},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.45342516899108887},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.43891435861587524},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.42458558082580566},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.41686737537384033},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3971789479255676},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3278771638870239},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.29611313343048096},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2251075804233551},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.15659460425376892},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12068066000938416}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8282182216644287},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7215498685836792},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6166675686836243},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5341094732284546},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.513340413570404},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4975757896900177},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4790709912776947},{"id":"https://openalex.org/C15524039","wikidata":"https://www.wikidata.org/wiki/Q865817","display_name":"Java applet","level":3,"score":0.4753113389015198},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.45342516899108887},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.43891435861587524},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.42458558082580566},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.41686737537384033},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3971789479255676},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3278771638870239},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29611313343048096},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2251075804233551},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.15659460425376892},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12068066000938416},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkr286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr286","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W528/7624226/gkr286.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:21546552","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21546552","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3125737","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3125737","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr286","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W528/7624226/gkr286.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6006204460","display_name":"Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB","funder_award_id":"0606909","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/W1972171558.pdf","grobid_xml":"https://content.openalex.org/works/W1972171558.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1527878510","https://openalex.org/W1598163061","https://openalex.org/W1977859620","https://openalex.org/W1983833794","https://openalex.org/W2066972244","https://openalex.org/W2077215938","https://openalex.org/W2095724872","https://openalex.org/W2096435507","https://openalex.org/W2101108147","https://openalex.org/W2105550995","https://openalex.org/W2115570304","https://openalex.org/W2134283755","https://openalex.org/W2136482257","https://openalex.org/W2137653635","https://openalex.org/W2140157849","https://openalex.org/W2145550746","https://openalex.org/W2158714788","https://openalex.org/W2160943260","https://openalex.org/W2161427213"],"related_works":["https://openalex.org/W4255811401","https://openalex.org/W1936400974","https://openalex.org/W2111842914","https://openalex.org/W2797581729","https://openalex.org/W2543547881","https://openalex.org/W1634075213","https://openalex.org/W2387535791","https://openalex.org/W2476641826","https://openalex.org/W2373899618","https://openalex.org/W1972171558"],"abstract_inverted_index":{"The":[0,66,131,178],"BioExtract":[1],"Server":[2],"(bioextract.org)":[3],"is":[4],"an":[5],"open,":[6],"web-based":[7],"system":[8,35,132,179],"designed":[9],"to":[10,98,135,183],"aid":[11],"researchers":[12,144],"in":[13],"the":[14,24,34,41,85,99,110,119,125,146,160,170],"analysis":[15],"of":[16,26,68,148,156,173],"genomic":[17],"data":[18,50,57,94],"by":[19,36,40],"providing":[20],"a":[21,76,153,195],"platform":[22],"for":[23,81,102],"creation":[25],"bioinformatic":[27],"workflows.":[28],"Scientific":[29],"workflows":[30],"are":[31],"created":[32],"within":[33],"recording":[37],"tasks":[38,44,70],"performed":[39],"user.":[42],"These":[43],"may":[45],"include":[46,96],"querying":[47],"multiple,":[48],"distributed":[49],"sources,":[51],"saving":[52],"query":[53],"results":[54],"as":[55,75],"searchable":[56],"extracts,":[58],"and":[59,62,90,107,124,141,169,175],"executing":[60],"local":[61,185],"web-accessible":[63],"analytic":[64,139],"tools.":[65],"series":[67],"recorded":[69],"can":[71],"then":[72],"be":[73],"saved":[74],"reproducible,":[77],"sharable":[78],"workflow":[79],"available":[80],"subsequent":[82],"execution":[83],"with":[84,145],"original":[86],"or":[87],"modified":[88],"inputs":[89],"parameter":[91],"settings.":[92],"Integrated":[93],"resources":[95],"interfaces":[97],"National":[100],"Center":[101],"Biotechnology":[103],"Information":[104],"(NCBI)":[105],"nucleotide":[106,117],"protein":[108],"databases,":[109],"European":[111,161],"Molecular":[112,162],"Biology":[113,163],"Laboratory":[114],"(EMBL-Bank)":[115],"non-redundant":[116],"database,":[118],"Universal":[120],"Protein":[121],"Resource":[122],"(UniProt),":[123],"UniProt":[126],"Reference":[127],"Clusters":[128],"(UniRef)":[129],"database.":[130],"offers":[133],"access":[134],"numerous":[136],"preinstalled,":[137],"curated":[138],"tools":[140,151,188],"also":[142],"provides":[143],"option":[147],"selecting":[149],"computational":[150],"from":[152],"large":[154],"list":[155],"web":[157],"services":[158],"including":[159],"Open":[164],"Software":[165],"Suite":[166],"(EMBOSS),":[167],"BioMoby,":[168],"Kyoto":[171],"Encyclopedia":[172],"Genes":[174],"Genomes":[176],"(KEGG).":[177],"further":[180],"allows":[181],"users":[182],"integrate":[184],"command":[186],"line":[187],"residing":[189],"on":[190],"their":[191],"own":[192],"computers":[193],"through":[194],"client-side":[196],"Java":[197],"applet.":[198]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}
