{"id":"https://openalex.org/W3206868055","doi":"https://doi.org/10.1515/jib-2021-0020","title":"OMEX metadata specification (version 1.2)","display_name":"OMEX metadata specification (version 1.2)","publication_year":2021,"publication_date":"2021-09-01","ids":{"openalex":"https://openalex.org/W3206868055","doi":"https://doi.org/10.1515/jib-2021-0020","mag":"3206868055","pmid":"https://pubmed.ncbi.nlm.nih.gov/34668356"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2021-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0020/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0020/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010618664","display_name":"John H. Gennari","orcid":"https://orcid.org/0000-0001-8254-4957"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John H. Gennari","raw_affiliation_strings":["University of Washington , Seattle , USA"],"affiliations":[{"raw_affiliation_string":"University of Washington , Seattle , USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012727458","display_name":"Matthias K\u00f6nig","orcid":"https://orcid.org/0000-0003-1725-179X"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias K\u00f6nig","raw_affiliation_strings":["Humboldt University , Berlin , Germany"],"affiliations":[{"raw_affiliation_string":"Humboldt University , Berlin , Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028639846","display_name":"G\u00f6ksel M\u0131s\u0131rl\u0131","orcid":"https://orcid.org/0000-0002-2454-7188"},"institutions":[{"id":"https://openalex.org/I56007636","display_name":"Keele University","ror":"https://ror.org/00340yn33","country_code":"GB","type":"education","lineage":["https://openalex.org/I56007636"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Goksel Misirli","raw_affiliation_strings":["Keele University , Newcastle , UK"],"affiliations":[{"raw_affiliation_string":"Keele University , Newcastle , UK","institution_ids":["https://openalex.org/I56007636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031987031","display_name":"Maxwell L. Neal","orcid":"https://orcid.org/0000-0002-2390-6572"},"institutions":[{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maxwell L. Neal","raw_affiliation_strings":["Seattle Children\u2019s Research Institute , Seattle , USA"],"affiliations":[{"raw_affiliation_string":"Seattle Children\u2019s Research Institute , Seattle , USA","institution_ids":["https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David P. Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, The University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, The University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I36522303","display_name":"Universit\u00e4t Greifswald","ror":"https://ror.org/00r1edq15","country_code":"DE","type":"education","lineage":["https://openalex.org/I36522303"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["University of Greifswald , Greifswald , Germany"],"affiliations":[{"raw_affiliation_string":"University of Greifswald , Greifswald , Germany","institution_ids":["https://openalex.org/I36522303"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010618664"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"],"apc_list":null,"apc_paid":null,"fwci":5.0162,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.95642507,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9839000105857849,"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":0.9839000105857849,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8621262311935425},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7335049510002136},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.637883722782135},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5525863766670227},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4506448209285736},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4312354028224945},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.42922982573509216},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.40969377756118774},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3078463077545166},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.30452704429626465},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11367407441139221}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8621262311935425},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7335049510002136},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.637883722782135},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5525863766670227},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4506448209285736},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4312354028224945},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.42922982573509216},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.40969377756118774},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3078463077545166},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30452704429626465},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11367407441139221},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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}],"locations_count":5,"locations":[{"id":"doi:10.1515/jib-2021-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0020/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34668356","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34668356","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:7466687","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8560343","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8560343","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8560343","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:cc6b53848d884b448b71f90b9561df1c","is_oa":true,"landing_page_url":"https://doaj.org/article/cc6b53848d884b448b71f90b9561df1c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 18, Iss 3 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2021-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0020/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2514841155","display_name":null,"funder_award_id":"436883643","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4838704522","display_name":null,"funder_award_id":"in part","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6955755495","display_name":null,"funder_award_id":"Germany","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8302043125","display_name":null,"funder_award_id":"436883643","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8352764473","display_name":null,"funder_award_id":"031L0054","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3206868055.pdf","grobid_xml":"https://content.openalex.org/works/W3206868055.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1969709265","https://openalex.org/W2016462601","https://openalex.org/W2024741923","https://openalex.org/W2096951208","https://openalex.org/W2113142309","https://openalex.org/W2123604001","https://openalex.org/W2123783513","https://openalex.org/W2127950479","https://openalex.org/W2128501050","https://openalex.org/W2131294353","https://openalex.org/W2150908245","https://openalex.org/W2163670493","https://openalex.org/W2170122529","https://openalex.org/W2342621714","https://openalex.org/W2587434644","https://openalex.org/W2788254992","https://openalex.org/W2971666547","https://openalex.org/W3080133182","https://openalex.org/W4242900685","https://openalex.org/W6743615956"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2095118173","https://openalex.org/W2382021449","https://openalex.org/W2104269053","https://openalex.org/W2106424170","https://openalex.org/W2501188010","https://openalex.org/W4299935056","https://openalex.org/W2768810474","https://openalex.org/W4206575749"],"abstract_inverted_index":{"A":[0],"standardized":[1,157],"approach":[2,151],"to":[3],"annotating":[4,153],"computational":[5],"biomedical":[6],"models":[7,26],"and":[8,16,23,27,29,40,64,116,140,176,185],"their":[9],"associated":[10],"files":[11],"can":[12,172],"facilitate":[13],"model":[14,158,182],"reuse":[15],"reproducibility":[17],"among":[18],"research":[19],"groups,":[20],"enhance":[21],"search":[22],"retrieval":[24],"of":[25,73,94,156],"data,":[28],"enable":[30],"semantic":[31,186],"comparisons":[32],"between":[33],"models.":[34],"Motivated":[35],"by":[36,42,138],"these":[37],"potential":[38],"benefits":[39],"guided":[41],"consensus":[43],"across":[44],"the":[45,74,141],"COmputational":[46],"Modeling":[47,63],"in":[48,61,84,181],"BIology":[49],"NEtwork":[50],"(COMBINE)":[51],"community,":[52],"we":[53],"have":[54],"developed":[55],"a":[56,92,105,120,134,148,154,164],"specification":[57,144,161],"for":[58,114,123,152,167],"encoding":[59],"annotations":[60,97,103],"Open":[62],"EXchange":[65],"(OMEX)-formatted":[66],"archives.":[67],"This":[68,160],"document":[69],"details":[70],"version":[71,79,90,110],"1.2":[72],"specification,":[75],"which":[76],"builds":[77],"on":[78],"1.0":[80,100],"published":[81],"last":[82],"year":[83],"this":[85,89,109,174],"journal.":[86],"In":[87],"particular,":[88],"includes":[91],"set":[93],"initial":[95],"model-level":[96],"(whereas":[98],"v":[99],"described":[101],"exclusively":[102],"at":[104],"smaller":[106],"scale).":[107],"Additionally,":[108],"uses":[111],"best":[112,135],"practices":[113],"namespaces,":[115],"introduces":[117],"omex-library.org":[118],"as":[119,163],"common":[121],"root":[122],"all":[124],"annotations.":[125],"Distributing":[126],"modeling":[127],"projects":[128],"within":[129],"an":[130],"OMEX":[131,142],"archive":[132],"is":[133],"practice":[136],"established":[137],"COMBINE,":[139],"metadata":[143],"presented":[145],"here":[146],"provides":[147],"harmonized,":[149],"community-driven":[150],"variety":[155],"representations.":[159],"acts":[162],"technical":[165],"guideline":[166],"developing":[168],"software":[169],"tools":[170],"that":[171],"support":[173],"standard,":[175],"thereby":[177],"encourages":[178],"broad":[179],"advances":[180],"reuse,":[183],"discovery,":[184],"analyses.":[187]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
