{"id":"https://openalex.org/W3140038043","doi":"https://doi.org/10.1093/bioinformatics/btab233","title":"A decoupled, modular and scriptable architecture for tools to curate data platforms","display_name":"A decoupled, modular and scriptable architecture for tools to curate data platforms","publication_year":2021,"publication_date":"2021-04-07","ids":{"openalex":"https://openalex.org/W3140038043","doi":"https://doi.org/10.1093/bioinformatics/btab233","mag":"3140038043","pmid":"https://pubmed.ncbi.nlm.nih.gov/33830216"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/20/3693/40853799/btab233.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/20/3693/40853799/btab233.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112621161","display_name":"Momo Langenstein","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Momo Langenstein","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK"],"raw_orcid":"https://orcid.org/0000-0002-7923-9609","affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066783652","display_name":"Henning Hermjakob","orcid":"https://orcid.org/0000-0001-8479-0262"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Henning Hermjakob","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028799399","display_name":"Manuel Bernal Llinares","orcid":"https://orcid.org/0000-0002-7368-180X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Manuel Bernal Llinares","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028799399","https://openalex.org/A5066783652"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02978517,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"37","issue":"20","first_page":"3693","last_page":"3694"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4311000108718872,"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":0.4311000108718872,"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/T11937","display_name":"Research Data Management Practices","score":0.3555000126361847,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.08780000358819962,"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/modular-design","display_name":"Modular design","score":0.7737785577774048},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.678177535533905},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6574262976646423},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4863644242286682},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41056448221206665},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4063819944858551},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3374757766723633},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09005039930343628},{"id":"https://openalex.org/keywords/archaeology","display_name":"Archaeology","score":0.06985893845558167}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7737785577774048},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.678177535533905},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6574262976646423},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4863644242286682},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41056448221206665},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4063819944858551},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3374757766723633},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09005039930343628},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.06985893845558167}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/20/3693/40853799/btab233.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33830216","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33830216","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},{"id":"pmh:oai:europepmc.org:7434662","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8545344","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,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8545344","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8545344","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/20/3693/40853799/btab233.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6499999761581421,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G515160390","display_name":"Connected Open Identifiers for Discovery, Access and Use of Research Resources","funder_award_id":"777523","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3140038043.pdf","grobid_xml":"https://content.openalex.org/works/W3140038043.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2153531925","https://openalex.org/W2942967593","https://openalex.org/W2952944698"],"related_works":["https://openalex.org/W2378076731","https://openalex.org/W4286888643","https://openalex.org/W3210795196","https://openalex.org/W2088988140","https://openalex.org/W2803103875","https://openalex.org/W2103019253","https://openalex.org/W2951529875","https://openalex.org/W2391453316","https://openalex.org/W2297768894","https://openalex.org/W2038503502"],"abstract_inverted_index":{"MOTIVATION:":[0],"Curation":[1],"is":[2,186,208],"essential":[3],"for":[4,62,150],"any":[5,130],"data":[6,14,220],"platform":[7,109],"to":[8,25,45,56,71,80,94,132,167],"maintain":[9],"the":[10,13,29,37,107,133,151,160,171,175],"quality":[11],"of":[12,32,39,74,101,128],"it":[15],"provides.":[16],"Today,":[17],"more":[18],"effective":[19],"curation":[20,49,65,97,148,184],"tools":[21,98],"are":[22,51,202,221],"often":[23,52],"vital":[24],"keep":[26],"up":[27],"with":[28,64,174],"rapid":[30],"growth":[31],"existing,":[33],"maintenance-requiring":[34],"databases":[35],"and":[36,54,91,124,169,191,195,200],"amount":[38],"newly":[40],"published":[41,210],"information":[42],"that":[43,159],"needs":[44],"be":[46,57,68,165],"surveyed.":[47],"However,":[48],"interfaces":[50,123],"complex":[53],"challenging":[55],"further":[58],"developed.":[59],"Therefore,":[60],"opportunities":[61],"experimentation":[63],"workflows":[66],"may":[67],"lost":[69],"due":[70],"a":[72,78,88,111,137,147,212],"lack":[73],"development":[75],"resources":[76],"or":[77],"reluctance":[79],"change":[81],"sensitive":[82],"production":[83],"systems.":[84],"RESULTS:":[85],"We":[86],"propose":[87],"decoupled,":[89],"modular":[90],"scriptable":[92],"architecture":[93,105,144],"build":[95],"new":[96],"on":[99,118],"top":[100],"existing":[102,108,134,177],"platforms.":[103],"Our":[104],"treats":[106],"as":[110,211],"black":[112],"box.":[113],"It,":[114],"therefore,":[115],"only":[116],"relies":[117],"its":[119],"public":[120],"application":[121,126],"programming":[122],"web":[125,178],"instead":[127],"requiring":[129],"changes":[131],"infrastructure.":[135],"As":[136],"case":[138],"study,":[139],"we":[140,156],"have":[141],"implemented":[142,187],"this":[143],"in":[145,188],"cmd-iaso,":[146,155],"tool":[149,185],"identifiers.org":[152],"registry.":[153],"With":[154],"also":[157,209],"show":[158],"proposed":[161],"design's":[162],"flexibility":[163],"can":[164],"utilized":[166],"streamline":[168],"enhance":[170],"curator's":[172],"workflow":[173],"platform's":[176],"interface.":[179],"AVAILABILITYAND":[180],"IMPLEMENTATION:":[181],"The":[182],"cmd-iaso":[183],"Python":[189],"3.7+":[190],"supports":[192],"Linux,":[193],"macOS":[194],"Windows.":[196],"Its":[197],"source":[198],"code":[199],"documentation":[201],"freely":[203],"available":[204,222],"from":[205],"https://github.com/identifiers-org/cmd-iaso.":[206],"It":[207],"Docker":[213],"container":[214],"at":[215,223],"https://hub.docker.com/r/identifiersorg/cmd-iaso.":[216],"SUPPLEMENTARY":[217],"INFORMATION:":[218],"Supplementary":[219],"Bioinformatics":[224],"online.":[225]},"counts_by_year":[],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}