{"id":"https://openalex.org/W2773303631","doi":"https://doi.org/10.12688/f1000research.12974.1","title":"Using bio.tools to generate and annotate workbench tool descriptions","display_name":"Using bio.tools to generate and annotate workbench tool descriptions","publication_year":2017,"publication_date":"2017-11-30","ids":{"openalex":"https://openalex.org/W2773303631","doi":"https://doi.org/10.12688/f1000research.12974.1","mag":"2773303631","pmid":"https://pubmed.ncbi.nlm.nih.gov/29333231","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5747335"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.12974.1","doi":"https://doi.org/10.12688/f1000research.12974.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.12974.1","pdf_url":"https://f1000research.com/articles/6-2074/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,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/6-2074/v1/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036639871","display_name":"Kenzo-Hugo Hillion","orcid":"https://orcid.org/0000-0002-6517-6934","observed_orcids":["https://orcid.org/0000-0002-6517-6934"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Kenzo-Hugo Hillion","raw_affiliation_strings":["Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris, France","Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"]},{"raw_affiliation_string":"Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090064487","display_name":"Ivan Kuzmin","orcid":"https://orcid.org/0000-0001-9138-9901","observed_orcids":["https://orcid.org/0000-0001-9138-9901"]},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Ivan Kuzmin","raw_affiliation_strings":["Institute of Computer Science, University of Tartu, Tartu, Estonia","Institute of Computer Science, University of Tartu, Tartu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, University of Tartu, Tartu, Estonia","institution_ids":["https://openalex.org/I56085075"]},{"raw_affiliation_string":"Institute of Computer Science, University of Tartu, Tartu","institution_ids":["https://openalex.org/I56085075"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001310798","display_name":"Anton Khodak","orcid":"https://orcid.org/0000-0003-3263-4553","observed_orcids":["https://orcid.org/0000-0003-3263-4553"]},"institutions":[{"id":"https://openalex.org/I202483615","display_name":"National Technical University of Ukraine \u201cIgor Sikorsky Kyiv Polytechnic Institute\u201d","ror":"https://ror.org/00syn5v21","country_code":"UA","type":"education","lineage":["https://openalex.org/I202483615"]}],"countries":["UA"],"is_corresponding":false,"raw_author_name":"Anton Khodak","raw_affiliation_strings":["Igor Sikorsky Kyiv Polytechnic Institute, National Technical University of Ukraine, Kyiv, Ukraine","Igor Sikorsky Kyiv Polytechnic Institute, National Technical University of Ukraine, Kyiv"],"raw_orcid":"https://orcid.org/0000-0003-3263-4553","affiliations":[{"raw_affiliation_string":"Igor Sikorsky Kyiv Polytechnic Institute, National Technical University of Ukraine, Kyiv, Ukraine","institution_ids":["https://openalex.org/I202483615"]},{"raw_affiliation_string":"Igor Sikorsky Kyiv Polytechnic Institute, National Technical University of Ukraine, Kyiv","institution_ids":["https://openalex.org/I202483615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017588251","display_name":"Eric S. Rasche","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Eric Rasche","raw_affiliation_strings":["Lehrstuhl f\u00fcr Bioinformatik, Institut f\u00fcr Informatik, Albert-Ludwigs-Universit\u00e4t Freiburg, Freiburg, Germany","Lehrstuhl f\u00fcr Bioinformatik, Institut f\u00fcr Informatik, Albert-Ludwigs-Universit\u00e4t Freiburg, Freiburg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lehrstuhl f\u00fcr Bioinformatik, Institut f\u00fcr Informatik, Albert-Ludwigs-Universit\u00e4t Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Lehrstuhl f\u00fcr Bioinformatik, Institut f\u00fcr Informatik, Albert-Ludwigs-Universit\u00e4t Freiburg, Freiburg","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020288899","display_name":"Michael Robin Crusoe","orcid":"https://orcid.org/0000-0002-2961-9670","observed_orcids":["https://orcid.org/0000-0002-2961-9670"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael Crusoe","raw_affiliation_strings":["Common Workflow Language Project, Vilnius, Lithuania","Common Workflow Language Project, Vilnius"],"raw_orcid":"https://orcid.org/0000-0002-2961-9670","affiliations":[{"raw_affiliation_string":"Common Workflow Language Project, Vilnius, Lithuania","institution_ids":[]},{"raw_affiliation_string":"Common Workflow Language Project, Vilnius","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089890429","display_name":"Hedi Peterson","orcid":"https://orcid.org/0000-0001-9951-5116","observed_orcids":["https://orcid.org/0000-0001-9951-5116"]},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Hedi Peterson","raw_affiliation_strings":["Institute of Computer Science, University of Tartu, Tartu, Estonia","Institute of Computer Science, University of Tartu, Tartu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, University of Tartu, Tartu, Estonia","institution_ids":["https://openalex.org/I56085075"]},{"raw_affiliation_string":"Institute of Computer Science, University of Tartu, Tartu","institution_ids":["https://openalex.org/I56085075"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080837511","display_name":"Jon Ison","orcid":"https://orcid.org/0000-0001-6666-1520","observed_orcids":["https://orcid.org/0000-0001-6666-1520"]},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jon Ison","raw_affiliation_strings":["DTU Bioinformatics, Technical University of Denmark, Copenhagen, Denmark","DTU Bioinformatics, Technical University of Denmark, Copenhagen"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DTU Bioinformatics, Technical University of Denmark, Copenhagen, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"DTU Bioinformatics, Technical University of Denmark, Copenhagen","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057666741","display_name":"Herv\u00e9 M\u00e9nager","orcid":"https://orcid.org/0000-0002-7552-1009","observed_orcids":["https://orcid.org/0000-0002-7552-1009"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Herv\u00e9 M\u00e9nager","raw_affiliation_strings":["Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris, France","Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"]},{"raw_affiliation_string":"Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Int\u00e9grative (C3BI, USR 3756 Institut Pasteur et CNRS), Paris","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5036639871","https://openalex.org/A5057666741"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":2.3302,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.90262889,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"6","issue":null,"first_page":"2074","last_page":"2074"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9976000189781189,"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":0.9976000189781189,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.000699999975040555,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0006000000284984708,"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/bio-tools","display_name":"bio.tools","score":0.9100000262260437},{"id":"https://openalex.org/keywords/common-workflow-language","display_name":"Common Workflow Language","score":0.9829999804496765},{"id":"https://openalex.org/keywords/source-code-analysis","display_name":"source code analysis","score":0.7419999837875366}],"concepts":[{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.8728331327438354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7796252965927124},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7501505613327026},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6871631145477295},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.5727236866950989},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5625600218772888},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.5582465529441833},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.4987938404083252},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4641351103782654},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4407278299331665},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.42162394523620605},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.41067296266555786},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.32131317257881165},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23186638951301575},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.1853632628917694},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.15891361236572266}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.12688/f1000research.12974.1","doi":"https://doi.org/10.12688/f1000research.12974.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.12974.1","pdf_url":"https://f1000research.com/articles/6-2074/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,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"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"},{"id":"pmh:oai:europepmc.org:4675122","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5747335","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5747335","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5747335","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Res","raw_type":"Text"},{"id":"pmid:29333231","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29333231","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,"listed_in":[],"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":"F1000Research","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:8920f2ec64124dd89edb749617f54e9d","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/8920f2ec64124dd89edb749617f54e9d","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"F1000Research, Vol 6 (2017)","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/b89863a8-c458-4114-b235-5d3dc1333fd2","doi":null,"is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/b89863a8-c458-4114-b235-5d3dc1333fd2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Hillion , K-H , Kuzmin , I , Khodak , A , Rasche , E , Crusoe , M , Peterson , H , Ison , J & M\u00e9nager , H 2017 , ' Using bio.tools to generate and annotate workbench tool descriptions ' , F1000Research , vol. 6 , 2074 . https://doi.org/10.12688/f1000research.12974.1","raw_type":"article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.12974.1","doi":"https://doi.org/10.12688/f1000research.12974.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.12974.1","pdf_url":"https://f1000research.com/articles/6-2074/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,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2777327527","display_name":null,"funder_award_id":"676559","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6574697119","display_name":"ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.","funder_award_id":"676559","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320309680","display_name":"Cleveland Clinic","ror":"https://ror.org/03xjacd83"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2773303631.pdf","grobid_xml":"https://content.openalex.org/works/W2773303631.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W967886317","https://openalex.org/W1583240815","https://openalex.org/W2013434113","https://openalex.org/W2038777423","https://openalex.org/W2135253885","https://openalex.org/W2141541659","https://openalex.org/W2145374174","https://openalex.org/W2160943260","https://openalex.org/W2161645441","https://openalex.org/W2172194140","https://openalex.org/W2214694321","https://openalex.org/W2342484850","https://openalex.org/W2346143774","https://openalex.org/W2516203774","https://openalex.org/W2576576365","https://openalex.org/W2602795292","https://openalex.org/W2604622795","https://openalex.org/W2605742517","https://openalex.org/W2616083879","https://openalex.org/W2625117623","https://openalex.org/W2724155158","https://openalex.org/W2765745983","https://openalex.org/W2952768760","https://openalex.org/W4394448387","https://openalex.org/W4416523943","https://openalex.org/W6892488589","https://openalex.org/W6930081158"],"related_works":["https://openalex.org/W6949398980","https://openalex.org/W967886317","https://openalex.org/W4321101951","https://openalex.org/W2795491802","https://openalex.org/W2605742517","https://openalex.org/W4319217575","https://openalex.org/W4395467502","https://openalex.org/W2137653635","https://openalex.org/W2967150655","https://openalex.org/W3111817325"],"abstract_inverted_index":{"Workbench":[0],"and":[1,25,41,63,119],"workflow":[2],"systems":[3],"such":[4,34,65],"as":[5,66],"Galaxy,":[6],"Taverna,":[7],"Chipster,":[8],"or":[9,50,68,127,161],"Common":[10],"Workflow":[11],"Language":[12],"(CWL)-based":[13],"frameworks,":[14],"facilitate":[15],"the":[16,29,48,77,87,109,113,137,140],"access":[17],"to":[18,70,136,159],"bioinformatics":[19,114],"tools":[20,32,54,80,89],"in":[21,33,86],"a":[22,37,121,124],"user-friendly,":[23],"scalable":[24],"reproducible":[26],"way.":[27],"Still,":[28],"integration":[30,78],"of":[31,53,79,112,139],"environments":[35,95],"remains":[36],"cumbersome,":[38],"time":[39],"consuming":[40],"error-prone":[42],"process.":[43],"A":[44],"major":[45],"consequence":[46],"is":[47,134],"incomplete":[49],"outdated":[51],"description":[52,99],"that":[55],"are":[56],"often":[57],"missing":[58,167],"important":[59],"information,":[60],"including":[61],"parameters":[62],"metadata":[64,145],"publication":[67],"links":[69],"documentation.":[71],"ToolDog":[72,101],"(Tool":[73],"DescriptiOn":[74],"Generator)":[75],"facilitates":[76],"-":[81,92],"which":[82],"have":[83],"been":[84],"registered":[85],"ELIXIR":[88],"registry":[90],"(https://bio.tools)":[91],"into":[93],"workbench":[94],"by":[96,147],"generating":[97],"tool":[98,129,142,164],"templates.":[100],"includes":[102],"two":[103],"modules.":[104],"The":[105,131],"first":[106],"module":[107,133,151],"analyses":[108],"source":[110],"code":[111],"software":[115],"with":[116,166],"language-specific":[117],"plugins,":[118],"generates":[120],"skeleton":[122],"for":[123],"Galaxy":[125],"XML":[126],"CWL":[128],"description.":[130],"second":[132],"dedicated":[135],"enrichment":[138],"generated":[141],"description,":[143],"using":[144],"provided":[146],"bio.tools.":[148],"This":[149],"last":[150],"can":[152],"also":[153],"be":[154],"used":[155],"on":[156],"its":[157],"own":[158],"complete":[160],"correct":[162],"existing":[163],"descriptions":[165],"metadata.":[168]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":10}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2017-12-22T00:00:00"}