{"id":"https://openalex.org/W2202347610","doi":"https://doi.org/10.1093/nar/gkv1049","title":"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models","display_name":"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models","publication_year":2015,"publication_date":"2015-10-17","ids":{"openalex":"https://openalex.org/W2202347610","doi":"https://doi.org/10.1093/nar/gkv1049","mag":"2202347610","pmid":"https://pubmed.ncbi.nlm.nih.gov/26476456"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkv1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1049","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D515/16661243/gkv1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/44/D1/D515/16661243/gkv1049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075454403","display_name":"Zachary A. King","orcid":"https://orcid.org/0000-0003-1238-1499"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary A. King","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073661107","display_name":"Justin S. Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin Lu","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0002-1240-5553","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016224466","display_name":"Philip Miller","orcid":"https://orcid.org/0000-0003-4908-2716"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip Miller","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079197003","display_name":"Stephen Federowicz","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Federowicz","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057750162","display_name":"Joshua A. Lerman","orcid":"https://orcid.org/0000-0003-0377-2674"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua A. Lerman","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0003-0377-2674","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101406018","display_name":"Ali Ebrahim","orcid":"https://orcid.org/0000-0002-4009-2128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali Ebrahim","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210106615","display_name":"Novo Nordisk (United States)","ror":"https://ror.org/011y67d23","country_code":"US","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210106615","https://openalex.org/I4210159963"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA","Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I2802640032","https://openalex.org/I4210106615"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074538839","display_name":"Nathan E. Lewis","orcid":"https://orcid.org/0000-0001-7700-3654"},"institutions":[{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210106615","display_name":"Novo Nordisk (United States)","ror":"https://ror.org/011y67d23","country_code":"US","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210106615","https://openalex.org/I4210159963"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nathan E. Lewis","raw_affiliation_strings":["Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA nlewisres@ucsd.edu","Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA nlewisres@ucsd.edu","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I2802640032","https://openalex.org/I4210106615"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5074538839"],"corresponding_institution_ids":["https://openalex.org/I2802640032","https://openalex.org/I36258959","https://openalex.org/I4210106615"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":25.7551,"has_fulltext":true,"cited_by_count":1020,"citation_normalized_percentile":{"value":0.99764853,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"44","issue":"D1","first_page":"D515","last_page":"D522"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9957000017166138,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9947999715805054,"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/identifier","display_name":"Identifier","score":0.6117731928825378},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6057368516921997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6019989848136902},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49513307213783264},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.45741814374923706},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4567069709300995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44687420129776},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.44158411026000977},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43229392170906067},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.42802631855010986},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.41518086194992065},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26297253370285034},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.17990928888320923},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14621198177337646},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10373646020889282}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6117731928825378},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6057368516921997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6019989848136902},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49513307213783264},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.45741814374923706},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4567069709300995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44687420129776},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.44158411026000977},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43229392170906067},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.42802631855010986},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.41518086194992065},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26297253370285034},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.17990928888320923},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14621198177337646},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10373646020889282},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1093/nar/gkv1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1049","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D515/16661243/gkv1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:26476456","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26476456","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:osti.gov:1253623","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1253623","pdf_url":"https://www.osti.gov/servlets/purl/1253623","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:ark:/13030/qt1gt8p4zc","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt1gt8p4zc","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1gt8p4zc","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic acids research, vol 44, iss D1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3680700","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4702785","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/D1/D515","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/D1/D515","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pure.atira.dk:publications/71799399-3bf7-430d-88a8-ff1a1c3d4c94","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/71799399-3bf7-430d-88a8-ff1a1c3d4c94","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"King , Z A , Lu , J , Dr\u00e4ger , A , Miller , P , Federowicz , S , Lerman , J A , Ebrahim , A , Palsson , B &amp; Lewis , N 2016 , ' BiGG Models: A platform for integrating, standardizing and sharing genome-scale models ' , Nucleic Acids Research , vol. 44 , gkv1049 , pp. D515-D522 . https://doi.org/10.1093/nar/gkv1049","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkv1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1049","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D515/16661243/gkv1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"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/W2202347610.pdf","grobid_xml":"https://content.openalex.org/works/W2202347610.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1665355332","https://openalex.org/W1730769032","https://openalex.org/W1952553890","https://openalex.org/W1989277387","https://openalex.org/W1999938932","https://openalex.org/W2009940763","https://openalex.org/W2012896813","https://openalex.org/W2014482592","https://openalex.org/W2044935306","https://openalex.org/W2048465561","https://openalex.org/W2052250375","https://openalex.org/W2062581381","https://openalex.org/W2063028213","https://openalex.org/W2075283200","https://openalex.org/W2081213475","https://openalex.org/W2082382448","https://openalex.org/W2084769889","https://openalex.org/W2085993965","https://openalex.org/W2090120515","https://openalex.org/W2091507117","https://openalex.org/W2100084634","https://openalex.org/W2113365252","https://openalex.org/W2120167281","https://openalex.org/W2124737787","https://openalex.org/W2126175129","https://openalex.org/W2128601422","https://openalex.org/W2128763542","https://openalex.org/W2131848047","https://openalex.org/W2136101247","https://openalex.org/W2145435867","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2157122545","https://openalex.org/W2159739447","https://openalex.org/W2163732522","https://openalex.org/W2165373392","https://openalex.org/W2167539386","https://openalex.org/W2311016706","https://openalex.org/W4230770774","https://openalex.org/W4235121031","https://openalex.org/W4237335579"],"related_works":["https://openalex.org/W2013728941","https://openalex.org/W4225274103","https://openalex.org/W2154046714","https://openalex.org/W2189613078","https://openalex.org/W2579659702","https://openalex.org/W2923661510","https://openalex.org/W1574055964","https://openalex.org/W1965329638","https://openalex.org/W2542318691","https://openalex.org/W3160708108"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,13,96],"models":[2,42,46,112,127,166],"are":[3],"mathematically-structured":[4],"knowledge":[5,85],"bases":[6],"that":[7],"can":[8,21,102],"be":[9,44,56],"used":[10],"to":[11,49,58,113,128,130],"predict":[12],"pathway":[14],"usage":[15],"and":[16,23,52,83,105,116,120,133,154,164,177],"growth":[17],"phenotypes.":[18],"Furthermore,":[19,139],"they":[20],"generate":[22],"test":[24],"hypotheses":[25],"when":[26],"integrated":[27],"with":[28,152],"experimental":[29,183],"data.":[30,184],"To":[31,69],"maximize":[32],"the":[33,99],"value":[34],"of":[35,40,167,181],"these":[36,71],"models,":[37],"centralized":[38],"repositories":[39],"high-quality":[41],"must":[43,47,55],"established,":[45],"adhere":[48],"established":[50],"standards":[51,132],"model":[53,63],"components":[54],"linked":[57],"relevant":[59],"databases.":[60,118],"Tools":[61],"for":[62,148,160],"visualization":[64],"further":[65],"enhance":[66],"their":[67],"utility.":[68],"meet":[70],"needs,":[72],"we":[73],"present":[74],"BiGG":[75,87,108,140,150,169],"Models":[76,88,109,141,151,170],"(http://bigg.ucsd.edu),":[77],"a":[78,143,158],"completely":[79],"redesigned":[80],"Biochemical,":[81],"Genetic":[82],"Genomic":[84],"base.":[86],"contains":[89],"more":[90],"than":[91],"75":[92],"high-quality,":[93],"manually-curated":[94],"genome-scale":[95,111],"models.":[97,107,138],"On":[98],"website,":[100],"users":[101],"browse,":[103],"search":[104],"visualize":[106],"connects":[110],"genome":[114],"annotations":[115],"external":[117],"Reaction":[119],"metabolite":[121],"identifiers":[122],"have":[123],"been":[124],"standardized":[125,163],"across":[126,137],"conform":[129],"community":[131],"enable":[134],"rapid":[135],"comparison":[136],"provides":[142],"comprehensive":[144],"application":[145],"programming":[146],"interface":[147],"accessing":[149],"modeling":[153],"analysis":[155,180],"tools.":[156],"As":[157],"resource":[159],"highly":[161],"curated,":[162],"accessible":[165],"metabolism,":[168],"will":[171],"facilitate":[172],"diverse":[173,182],"systems":[174],"biology":[175],"studies":[176],"support":[178],"knowledge-based":[179]},"counts_by_year":[{"year":2026,"cited_by_count":45},{"year":2025,"cited_by_count":92},{"year":2024,"cited_by_count":130},{"year":2023,"cited_by_count":132},{"year":2022,"cited_by_count":112},{"year":2021,"cited_by_count":91},{"year":2020,"cited_by_count":129},{"year":2019,"cited_by_count":116},{"year":2018,"cited_by_count":85},{"year":2017,"cited_by_count":56},{"year":2016,"cited_by_count":29}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
