{"id":"https://openalex.org/W2907344965","doi":"https://doi.org/10.1186/s12859-018-2580-9","title":"OMeta: an ontology-based, data-driven metadata tracking system","display_name":"OMeta: an ontology-based, data-driven metadata tracking system","publication_year":2019,"publication_date":"2019-01-07","ids":{"openalex":"https://openalex.org/W2907344965","doi":"https://doi.org/10.1186/s12859-018-2580-9","mag":"2907344965","pmid":"https://pubmed.ncbi.nlm.nih.gov/30612540"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2580-9","doi":"https://doi.org/10.1186/s12859-018-2580-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2580-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2580-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2580-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089982542","display_name":"Indresh Singh","orcid":"https://orcid.org/0000-0002-5522-0903","observed_orcids":["https://orcid.org/0000-0002-5522-0903"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Indresh Singh","raw_affiliation_strings":["J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA. isingh@jcvi.org","J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA"],"raw_orcid":"https://orcid.org/0000-0002-5522-0903","affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA. isingh@jcvi.org","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069023914","display_name":"Mehmet Kuscuoglu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Kuscuoglu","raw_affiliation_strings":["J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA, 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071328878","display_name":"Derek M. Harkins","orcid":"https://orcid.org/0000-0002-4704-0275","observed_orcids":["https://orcid.org/0000-0002-4704-0275"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek M. Harkins","raw_affiliation_strings":["J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028284504","display_name":"Granger G. Sutton","orcid":"https://orcid.org/0000-0001-7498-8048","observed_orcids":["https://orcid.org/0000-0001-7498-8048"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Granger Sutton","raw_affiliation_strings":["J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064828949","display_name":"Derrick E. Fouts","orcid":"https://orcid.org/0000-0003-4323-7668","observed_orcids":["https://orcid.org/0000-0003-4323-7668"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derrick E. Fouts","raw_affiliation_strings":["J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"last","author":{"id":null,"display_name":"Karen E. Nelson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen E. Nelson","raw_affiliation_strings":["J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I1301553790"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089982542"],"corresponding_institution_ids":["https://openalex.org/I1301553790"],"apc_list":{"value":2170,"currency":"USD","value_usd":2170},"apc_paid":{"value":2170,"currency":"USD","value_usd":2170},"fwci":3.123,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.92676155,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9175000190734863,"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"}},"topics":[{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9175000190734863,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.05420000106096268,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.01759999990463257,"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/metadata-tracking","display_name":"metadata tracking","score":0.8360000252723694},{"id":"https://openalex.org/keywords/metadata-standards","display_name":"metadata standards","score":0.7070000171661377},{"id":"https://openalex.org/keywords/ontology-based-metadata","display_name":"ontology-based metadata","score":0.5040000081062317},{"id":"https://openalex.org/keywords/data-driven-web-applications","display_name":"data-driven web applications","score":0.6869999766349792},{"id":"https://openalex.org/keywords/genomic-standards-consortium","display_name":"Genomic Standards Consortium","score":0.6000000238418579},{"id":"https://openalex.org/keywords/mix","display_name":"MIxS","score":0.8980000019073486},{"id":"https://openalex.org/keywords/sample-metadata","display_name":"sample metadata","score":0.5180000066757202},{"id":"https://openalex.org/keywords/metadata-validation","display_name":"metadata validation","score":0.8399999737739563},{"id":"https://openalex.org/keywords/audit-trail","display_name":"audit trail","score":0.7289999723434448},{"id":"https://openalex.org/keywords/metadata-export","display_name":"metadata export","score":0.7020000219345093},{"id":"https://openalex.org/keywords/multi-omics-data","display_name":"multi-omics data","score":0.5450000166893005},{"id":"https://openalex.org/keywords/microbial-genomics","display_name":"microbial genomics","score":0.5770000219345093},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.7279999852180481},{"id":"https://openalex.org/keywords/biomedical-ontologies","display_name":"biomedical ontologies","score":0.492000013589859}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7972750067710876},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6832064986228943},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.61607426404953},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5020406246185303},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.44130992889404297},{"id":"https://openalex.org/C30872290","wikidata":"https://www.wikidata.org/wiki/Q1172389","display_name":"Data element","level":3,"score":0.4306787848472595},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.4200168251991272},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.41448935866355896},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4044948220252991},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3468365967273712},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3209688663482666},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.24155807495117188},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.23974579572677612},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1978045105934143},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.12170052528381348},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09686529636383057},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06506037712097168},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2580-9","doi":"https://doi.org/10.1186/s12859-018-2580-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2580-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2580-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30612540","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30612540","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5301431","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6322262","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":"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:6322262","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6322262","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:70c42d0795dd441aa3768fac8d6e7bbe","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/70c42d0795dd441aa3768fac8d6e7bbe","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":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-15 (2019)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2580-9","doi":"https://doi.org/10.1186/s12859-018-2580-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2580-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2580-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5099999904632568}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1177099277","display_name":null,"funder_award_id":"U19AI110819","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G2394953455","display_name":null,"funder_award_id":"HHSN272200900007C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6027522591","display_name":"The J. Craig Venter Institute Genome Center for Infectious Diseases","funder_award_id":"1u19ai110819-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7703029926","display_name":null,"funder_award_id":"HHSN272200900007C,U19AI110819","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8100668736","display_name":null,"funder_award_id":"HHSN272200900007C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G813750413","display_name":null,"funder_award_id":"U19-AI110819","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000097943","display_name":null,"funder_award_id":"U19-AI-110819","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2907344965.pdf","grobid_xml":"https://content.openalex.org/works/W2907344965.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1977032720","https://openalex.org/W1985283768","https://openalex.org/W2054542377","https://openalex.org/W2060993546","https://openalex.org/W2096503372","https://openalex.org/W2129687578","https://openalex.org/W2130430745","https://openalex.org/W2156995961","https://openalex.org/W2232679723","https://openalex.org/W2474227261","https://openalex.org/W2559133556","https://openalex.org/W2565191020","https://openalex.org/W2756388071","https://openalex.org/W2949119845","https://openalex.org/W2954023597","https://openalex.org/W4232494644"],"related_works":["https://openalex.org/W2379265733","https://openalex.org/W2170906434","https://openalex.org/W3084772717","https://openalex.org/W3199469221","https://openalex.org/W2374379029","https://openalex.org/W1503116306","https://openalex.org/W2183628870","https://openalex.org/W2189603309","https://openalex.org/W2383201407","https://openalex.org/W2545809202"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"development":[2],"of":[3,12,14,33,51,76,193,300,319],"high-throughput":[4],"sequencing":[5,259],"and":[6,18,36,49,59,70,98,126,148,176,201,213,217,242,261,275,306,340,346],"analysis":[7,262],"has":[8,185],"accelerated":[9],"multi-omics":[10],"studies":[11,23,28,43,56],"thousands":[13],"microbial":[15],"species,":[16],"metagenomes,":[17],"infectious":[19],"disease":[20,52],"pathogens.":[21],"Omics":[22],"are":[24,57],"enabling":[25],"genotype-phenotype":[26],"association":[27],"which":[29],"identify":[30],"genetic":[31],"determinants":[32],"pathogen":[34],"virulence":[35],"drug":[37],"resistance,":[38],"as":[39,41],"well":[40],"phylogenetic":[42],"designed":[44],"to":[45,144,170,280],"track":[46],"the":[47,74,102,115,123,156,237,282],"origin":[48],"spread":[50],"outbreaks.":[53],"These":[54],"omics":[55,77],"complex":[58],"often":[60],"employ":[61],"multiple":[62],"assay":[63],"technologies":[64],"including":[65,254],"genomics,":[66],"metagenomics,":[67],"transcriptomics,":[68],"proteomics,":[69],"metabolomics.":[71],"To":[72,151],"maximize":[73],"impact":[75],"studies,":[78],"it":[79],"is":[80,333],"essential":[81],"that":[82,167,204,332],"data":[83,320,342],"be":[84,221,249,278],"accompanied":[85],"by":[86,108,190,304],"detailed":[87],"contextual":[88],"metadata":[89,105,110,219,308],"(e.g.,":[90],"specimen,":[91],"spatial-temporal,":[92],"phenotypic":[93],"characteristics)":[94],"in":[95,155,267,310],"clear,":[96],"organized,":[97],"consistent":[99],"formats.":[100],"Over":[101],"years,":[103],"many":[104],"standards":[106,111,121,226],"developed":[107,187],"various":[109,268],"initiatives":[112],"have":[113],"arisen;":[114],"Genomic":[116],"Standards":[117],"Consortium's":[118],"minimal":[119],"information":[120,233,247],"(MIxS),":[122],"GSCID/BRC":[124],"Project":[125,216],"Sample":[127],"Application":[128],"Standard.":[129],"Some":[130],"tools":[131],"exist":[132],"for":[133,188,209,285,316,338],"tracking":[134],"metadata,":[135],"but":[136],"they":[137],"do":[138],"not":[139],"provide":[140,205],"event":[141,160],"based":[142,161,223,228,251],"capabilities":[143],"configure,":[145,172],"collect,":[146,173],"validate,":[147,174],"distribute":[149],"metadata.":[150,178,215,348],"address":[152],"this":[153],"gap":[154],"scientific":[157],"community,":[158],"an":[159,206],"data-driven":[162,181,336],"application,":[163,183],"OMeta,":[164,184,327],"was":[165],"created":[166],"allows":[168,307],"users":[169,305],"quickly":[171],"distribute,":[175],"integrate":[177],"RESULTS:":[179],"A":[180],"web":[182],"been":[186],"use":[189,281],"researchers":[191],"consisting":[192],"a":[194,197,289,296,328],"browser-based":[195],"interface,":[196],"command-line":[198],"interface":[199],"(CLI),":[200],"server-side":[202],"components":[203],"intuitive":[207],"platform":[208],"configuring,":[210],"capturing,":[211,344],"viewing,":[212],"sharing":[214,347],"sample":[218,255,257],"can":[220,248,277],"set":[222],"on":[224,229,236,252,335],"existing":[225],"or":[227],"projects":[230],"goals.":[231],"Recorded":[232],"includes":[234],"details":[235],"biological":[238],"samples,":[239],"procedures,":[240],"protocols,":[241],"experimental":[243],"technologies,":[244],"etc.":[245],"This":[246],"organized":[250],"events,":[253],"collection,":[256],"quantification,":[258],"assay,":[260],"results.":[263],"OMeta":[264,294],"enables":[265],"configuration":[266],"presentation":[269],"types:":[270],"checkbox,":[271],"file,":[272],"drop-box,":[273],"ontology,":[274],"fields":[276],"configured":[279],"National":[283],"Center":[284],"Biomedical":[286],"Ontology":[287],"(NCBO),":[288],"biomedical":[290],"ontology":[291],"server.":[292],"Furthermore,":[293],"maintains":[295],"complete":[297],"audit":[298],"trail":[299],"all":[301],"changes":[302],"made":[303],"export":[309],"comma":[311],"separated":[312],"value":[313],"(CSV)":[314],"format":[315],"convenient":[317],"deposition":[318],"into":[321],"public":[322],"databases.":[323],"CONCLUSIONS:":[324],"We":[325],"present,":[326],"web-based":[329],"software":[330],"application":[331],"built":[334],"principles":[337],"configuring":[339],"customizing":[341],"standards,":[343],"curating,":[345]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2026-10-12T09:40:04.860316","created_date":"2025-10-10T00:00:00"}
