{"id":"https://openalex.org/W3037297315","doi":"https://doi.org/10.1515/jib-2020-0020","title":"Open modeling and exchange (OMEX) metadata specification version 1.0","display_name":"Open modeling and exchange (OMEX) metadata specification version 1.0","publication_year":2020,"publication_date":"2020-06-01","ids":{"openalex":"https://openalex.org/W3037297315","doi":"https://doi.org/10.1515/jib-2020-0020","mag":"3037297315","pmid":"https://pubmed.ncbi.nlm.nih.gov/32589606"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2020-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0020/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-2020-0020/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"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/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":false,"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/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I2799318839","display_name":"Universit\u00e4tsmedizin Greifswald","ror":"https://ror.org/025vngs54","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2799318839"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["University Medicine Greifswald , Greifswald , Germany"],"affiliations":[{"raw_affiliation_string":"University Medicine Greifswald , Greifswald , Germany","institution_ids":["https://openalex.org/I2799318839"]}]},{"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":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","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 , Berlin , Germany"],"affiliations":[{"raw_affiliation_string":"Humboldt University Berlin , Berlin , Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031987031"],"corresponding_institution_ids":["https://openalex.org/I58610484"],"apc_list":null,"apc_paid":null,"fwci":3.2064,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.93983777,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"17","issue":"2-3","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":0.9882000088691711,"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":0.9882000088691711,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9614999890327454,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9462000131607056,"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/computer-science","display_name":"Computer science","score":0.8602871894836426},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8437507152557373},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.6747869253158569},{"id":"https://openalex.org/keywords/metadata-modeling","display_name":"Metadata modeling","score":0.48192930221557617},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.45212462544441223},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43790239095687866},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4111021161079407},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3713380694389343},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35036909580230713},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.2524702548980713},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2419930100440979}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8602871894836426},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8437507152557373},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.6747869253158569},{"id":"https://openalex.org/C110326360","wikidata":"https://www.wikidata.org/wiki/Q17149476","display_name":"Metadata modeling","level":4,"score":0.48192930221557617},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.45212462544441223},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43790239095687866},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4111021161079407},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3713380694389343},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35036909580230713},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.2524702548980713},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2419930100440979},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","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":4,"locations":[{"id":"doi:10.1515/jib-2020-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0020/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:32589606","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32589606","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:pubmedcentral.nih.gov:7756623","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7756623","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:98a2d569742c46f18b958a70e5794c49","is_oa":true,"landing_page_url":"https://doaj.org/article/98a2d569742c46f18b958a70e5794c49","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 17, Iss 2-3 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2020-0020","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0020","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0020/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":0.4399999976158142,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G3565210466","display_name":null,"funder_award_id":"P41-EB023912","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3037297315.pdf"},"referenced_works_count":19,"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/W4242900685","https://openalex.org/W6743615956"],"related_works":["https://openalex.org/W2003742646","https://openalex.org/W2366936177","https://openalex.org/W3122624872","https://openalex.org/W1773645839","https://openalex.org/W2380261968","https://openalex.org/W3084772717","https://openalex.org/W2796209520","https://openalex.org/W2136226335","https://openalex.org/W2050262794","https://openalex.org/W2907247951"],"abstract_inverted_index":{"A":[0],"standardized":[1,98],"approach":[2,92],"to":[3],"annotating":[4,94],"computational":[5],"biomedical":[6],"models":[7,26],"and":[8,16,23,27,29,40,64,81,100,125,136],"their":[9],"associated":[10],"files":[11],"can":[12,121],"facilitate":[13],"model":[14,99,133],"reuse":[15],"reproducibility":[17],"among":[18],"research":[19],"groups,":[20],"enhance":[21],"search":[22],"retrieval":[24],"of":[25,97],"data,":[28],"enable":[30],"semantic":[31,137],"comparisons":[32],"between":[33],"models.":[34],"Motivated":[35],"by":[36,42,79],"these":[37,72],"potential":[38],"benefits":[39],"guided":[41],"consensus":[43],"across":[44],"the":[45,82],"COmputational":[46],"Modeling":[47,63],"in":[48,61,132],"BIology":[49],"NEtwork":[50],"(COMBINE)":[51],"community,":[52],"we":[53],"have":[54],"developed":[55],"a":[56,75,89,95],"specification":[57,85,108],"for":[58,93,113],"encoding":[59,114],"annotations":[60],"Open":[62],"EXchange":[65],"(OMEX)-formatted":[66],"archives.":[67],"Distributing":[68],"modeling":[69],"projects":[70],"within":[71,104],"archives":[73],"is":[74],"best":[76],"practice":[77],"established":[78],"COMBINE,":[80],"OMEX":[83],"metadata":[84],"presented":[86],"here":[87],"provides":[88],"harmonized,":[90],"community-driven":[91],"variety":[96],"data":[101],"representation":[102],"formats":[103],"an":[105],"archive.":[106],"The":[107],"primarily":[109],"includes":[110],"technical":[111],"guidelines":[112],"archive":[115],"metadata,":[116],"so":[117],"that":[118],"software":[119],"tools":[120],"more":[122],"easily":[123],"utilize":[124],"exchange":[126],"it,":[127],"thereby":[128],"spurring":[129],"broad":[130],"advancements":[131],"reuse,":[134],"discovery,":[135],"analyses.":[138]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
