{"id":"https://openalex.org/W3135962891","doi":"https://doi.org/10.1021/acs.jproteome.0c00983","title":"APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry","display_name":"APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry","publication_year":2021,"publication_date":"2021-03-15","ids":{"openalex":"https://openalex.org/W3135962891","doi":"https://doi.org/10.1021/acs.jproteome.0c00983","mag":"3135962891","pmid":"https://pubmed.ncbi.nlm.nih.gov/33720735","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8041394"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jproteome.0c00983","doi":"https://doi.org/10.1021/acs.jproteome.0c00983","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.0c00983","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00983","source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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":"Journal of Proteome Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00983","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028743498","display_name":"Vedran Kasalica","orcid":"https://orcid.org/0000-0002-0097-1056","observed_orcids":["https://orcid.org/0000-0002-0097-1056"]},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Vedran Kasalica","raw_affiliation_strings":["Department of Information and Computing Sciences, Utrecht University, Utrecht 3584 CC, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-0097-1056","affiliations":[{"raw_affiliation_string":"Department of Information and Computing Sciences, Utrecht University, Utrecht 3584 CC, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091329986","display_name":"Veit Schw\u00e4mmle","orcid":"https://orcid.org/0000-0002-9708-6722","observed_orcids":["https://orcid.org/0000-0002-9708-6722"]},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Veit Schw\u00e4mmle","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-9708-6722","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059772295","display_name":"Magnus Palmblad","orcid":"https://orcid.org/0000-0002-5865-8994","observed_orcids":["https://orcid.org/0000-0002-5865-8994"]},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Magnus Palmblad","raw_affiliation_strings":["Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-5865-8994","affiliations":[{"raw_affiliation_string":"Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]},{"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/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/I4210138994","display_name":"Institut Fran\u00e7ais de Bioinformatique","ror":"https://ror.org/045f7pv37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210088668","https://openalex.org/I4210138994"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jon Ison","raw_affiliation_strings":["Institut Fran\u00e7ais de Bioinformatique, CNRS, Cr\u00e9mieux F-91000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Fran\u00e7ais de Bioinformatique, CNRS, Cr\u00e9mieux F-91000, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210138994"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046061598","display_name":"Anna-Lena Lamprecht","orcid":"https://orcid.org/0000-0003-1953-5606","observed_orcids":["https://orcid.org/0000-0003-1953-5606"]},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Anna-Lena Lamprecht","raw_affiliation_strings":["Department of Information and Computing Sciences, Utrecht University, Utrecht 3584 CC, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-1953-5606","affiliations":[{"raw_affiliation_string":"Department of Information and Computing Sciences, Utrecht University, Utrecht 3584 CC, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028743498","https://openalex.org/A5046061598"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":{"value":5000,"currency":"USD","value_usd":5000},"fwci":1.9191,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.88088946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"20","issue":"4","first_page":"2157","last_page":"2165"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9824000000953674,"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":0.9824000000953674,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.009399999864399433,"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":0.0015999999595806003,"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/proteomics-workflow","display_name":"proteomics workflow","score":0.8109999895095825},{"id":"https://openalex.org/keywords/edam-ontology","display_name":"EDAM ontology","score":0.8309999704360962},{"id":"https://openalex.org/keywords/tool-discovery","display_name":"tool discovery","score":0.33899998664855957}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7393090724945068},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.7049192786216736},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5002503395080566},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4051715135574341},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3682892322540283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3475611209869385},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.100623220205307},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08716091513633728},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012042","descriptor_name":"Registries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012042","descriptor_name":"Registries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012042","descriptor_name":"Registries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012042","descriptor_name":"Registries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1021/acs.jproteome.0c00983","doi":"https://doi.org/10.1021/acs.jproteome.0c00983","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.0c00983","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00983","source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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":"Journal of Proteome Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8041394","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8041394","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Proteome Res","raw_type":"Text"},{"id":"pmid:33720735","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33720735","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":"Journal of proteome research","raw_type":"Journal Article"},{"id":"pmh:oai:sdu.dk:openaire/bcf6b648-c61d-4459-9a46-9fc5873de4c8","doi":null,"is_oa":true,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/bcf6b648-c61d-4459-9a46-9fc5873de4c8","pdf_url":null,"source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"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":"Kasalica, V, Schw\u00e4mmle, V, Palmblad, M, Ison, J & Lamprecht, A L 2021, 'APE in the Wild : Automated Exploration of Proteomics Workflows in the bio.tools Registry', Journal of Proteome Research, vol. 20, no. 4, pp. 2157\u20132165. https://doi.org/10.1021/acs.jproteome.0c00983","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_3221392","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1887/3221392","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Proteome Research, 20(4), 2157 - 2165. AMER CHEMICAL SOC","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:hal-05130620v1","doi":null,"is_oa":true,"landing_page_url":"https://cnrs.hal.science/hal-05130620","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Proteome Research, 2021, 20 (4), pp.2157--2165. &#x27E8;10.1021/acs.jproteome.0c00983&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:alma.31UKB_LEU:9940741244602711","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/1887/3221392","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Proteome Research, Vol. 20, no. 4, p. 2157-2165","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:dspace.library.uu.nl:1874/411632","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/411632","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3221392","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/1887/3221392","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Proteome Research","raw_type":"Article / Letter to editor"},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/411632","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/411632","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Proteome Research, 20(4), 2157. American Chemical Society","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1021/acs.jproteome.0c00983","doi":"https://doi.org/10.1021/acs.jproteome.0c00983","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.0c00983","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00983","source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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":"Journal of Proteome Research","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3135962891.pdf","grobid_xml":"https://content.openalex.org/works/W3135962891.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W179723585","https://openalex.org/W1480875294","https://openalex.org/W1592797580","https://openalex.org/W1965518084","https://openalex.org/W1979900513","https://openalex.org/W2001653627","https://openalex.org/W2002438471","https://openalex.org/W2009577334","https://openalex.org/W2048619144","https://openalex.org/W2054353156","https://openalex.org/W2114888488","https://openalex.org/W2141541659","https://openalex.org/W2145374174","https://openalex.org/W2167840796","https://openalex.org/W2484917209","https://openalex.org/W2618602062","https://openalex.org/W2752308847","https://openalex.org/W2883524422","https://openalex.org/W2917207851","https://openalex.org/W2969930717","https://openalex.org/W2981131276","https://openalex.org/W3036158206","https://openalex.org/W3084188058","https://openalex.org/W3138912200","https://openalex.org/W4235097469","https://openalex.org/W6904651889"],"related_works":["https://openalex.org/W2883524422","https://openalex.org/W3036158206","https://openalex.org/W6911997657","https://openalex.org/W3138912200","https://openalex.org/W2967150655","https://openalex.org/W7166329801","https://openalex.org/W43631546","https://openalex.org/W2907425742","https://openalex.org/W2761721412","https://openalex.org/W4395467502"],"abstract_inverted_index":{"The":[0,27],"bio.tools":[1,28,168],"registry":[2],"is":[3],"a":[4,74,96,118,141],"main":[5],"catalogue":[6],"of":[7,34,41,61,82,94,99,122,138,144,157,164,200],"computational":[8],"tools":[9,18,62,100,139,149],"in":[10,167],"the":[11,23,51,58,79,87,113,123,131,161,195],"life":[12],"sciences.":[13],"More":[14],"than":[15],"17":[16],"000":[17],"have":[19],"been":[20],"registered":[21],"by":[22],"international":[24],"bioinformatics":[25,53],"community.":[26],"metadata":[29],"schema":[30],"includes":[31],"semantic":[32,165],"annotations":[33,56,166],"tool":[35,174],"functions,":[36],"that":[37,181],"is,":[38],"formal":[39],"descriptions":[40],"tools'":[42],"data":[43],"types,":[44],"formats,":[45],"and":[46,120,140,189],"operations":[47],"with":[48,101],"terms":[49],"from":[50],"EDAM":[52],"ontology.":[54],"Such":[55],"enable":[57],"automated":[59,80],"composition":[60,81,125,148],"into":[63],"multistep":[64],"pipelines":[65],"or":[66,172],"workflows.":[67,84,146,203],"In":[68],"this":[69,155],"Technical":[70],"Note,":[71],"we":[72,105],"revisit":[73],"previous":[75],"case":[76],"study":[77],"on":[78,109],"proteomics":[83],"We":[85,111],"use":[86,112],"same":[88],"four":[89],"workflow":[90,124,190],"scenarios":[91],"but":[92],"instead":[93],"using":[95],"small":[97],"set":[98],"carefully":[102],"handcrafted":[103],"annotations,":[104],"explore":[106,154],"workflows":[107],"directly":[108],"bio.tools.":[110],"Automated":[114,147],"Pipeline":[115],"Explorer":[116],"(APE),":[117],"reimplementation":[119],"extension":[121],"method":[126],"previously":[127],"used.":[128],"Moving":[129],"\"into":[130],"wild\"":[132],"opens":[133],"up":[134],"an":[135],"unprecedented":[136],"wealth":[137],"huge":[142],"number":[143],"alternative":[145],"can":[150,192],"be":[151],"used":[152],"to":[153,170],"space":[156],"possibilities":[158],"systematically.":[159],"Inevitably,":[160],"mixed":[162],"quality":[163],"leads":[169],"unintended":[171],"erroneous":[173],"combinations.":[175],"However,":[176],"our":[177],"results":[178],"also":[179],"show":[180],"additional":[182],"control":[183],"mechanisms":[184],"(tool":[185],"filters,":[186],"configuration":[187],"options,":[188],"constraints)":[191],"effectively":[193],"guide":[194],"exploration":[196],"toward":[197],"smaller":[198],"sets":[199],"more":[201],"meaningful":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2021-03-29T00:00:00"}
