{"id":"https://openalex.org/W4387948540","doi":"https://doi.org/10.1093/bioinformatics/btad658","title":"An automated model annotation system (AMAS) for SBML models","display_name":"An automated model annotation system (AMAS) for SBML models","publication_year":2023,"publication_date":"2023-10-24","ids":{"openalex":"https://openalex.org/W4387948540","doi":"https://doi.org/10.1093/bioinformatics/btad658","pmid":"https://pubmed.ncbi.nlm.nih.gov/37882737"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad658","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/11/btad658/52771878/btad658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/article-pdf/39/11/btad658/52771878/btad658.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026812944","display_name":"Woosub Shin","orcid":"https://orcid.org/0000-0002-2319-2960"},"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":true,"raw_author_name":"Woosub Shin","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland , 1010 Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland , 1010 Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John H Gennari","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038863305","display_name":"Joseph L. Hellerstein","orcid":"https://orcid.org/0000-0003-0802-4069"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph L Hellerstein","raw_affiliation_strings":["Paul G. Allen School of Computer Science, University of Washington , Seattle, WA 98195, United States","eScience Institute, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"eScience Institute, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Herbert M Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026812944"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3045,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.64361842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9994000196456909,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.994700014591217,"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/sbml","display_name":"SBML","score":0.9168884754180908},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8287790417671204},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.785059928894043},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7625566720962524},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6604123711585999},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4983031749725342},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48389682173728943},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4345470666885376},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.39500564336776733},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37221771478652954},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20240607857704163},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1744224727153778},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11670094728469849},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11532804369926453},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.10313406586647034}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9168884754180908},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8287790417671204},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.785059928894043},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7625566720962524},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6604123711585999},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4983031749725342},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48389682173728943},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4345470666885376},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.39500564336776733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37221771478652954},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20240607857704163},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1744224727153778},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11670094728469849},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11532804369926453},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.10313406586647034},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad658","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/11/btad658/52771878/btad658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37882737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37882737","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10628433","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10628433","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10628433/pdf/btad658.pdf","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad658","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/11/btad658/52771878/btad658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2954150100","display_name":null,"funder_award_id":"2013-10-29","funder_id":"https://openalex.org/F4320306202","funder_display_name":"Gordon and Betty Moore Foundation"},{"id":"https://openalex.org/G5708185203","display_name":null,"funder_award_id":"2013-10-29","funder_id":"https://openalex.org/F4320306151","funder_display_name":"Alfred P. Sloan Foundation"},{"id":"https://openalex.org/G6732895847","display_name":null,"funder_award_id":"EB023912","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7792449127","display_name":null,"funder_award_id":"P41 E","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8877730500","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/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320306854","display_name":"Washington Research Foundation","ror":"https://ror.org/00hasdx88"},{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387948540.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W2004548026","https://openalex.org/W2033377040","https://openalex.org/W2074231493","https://openalex.org/W2098769288","https://openalex.org/W2100084634","https://openalex.org/W2103017472","https://openalex.org/W2103148772","https://openalex.org/W2107903949","https://openalex.org/W2108723491","https://openalex.org/W2128501050","https://openalex.org/W2128852521","https://openalex.org/W2135621733","https://openalex.org/W2140470365","https://openalex.org/W2145435867","https://openalex.org/W2155049977","https://openalex.org/W2739999456","https://openalex.org/W2749464300","https://openalex.org/W2766958291","https://openalex.org/W2788254992","https://openalex.org/W2966440819","https://openalex.org/W2972248834","https://openalex.org/W2980260871","https://openalex.org/W2981865785","https://openalex.org/W3095583226","https://openalex.org/W3211402536","https://openalex.org/W4213009331","https://openalex.org/W4294990920","https://openalex.org/W4384338858"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"Our":[0,15],"project":[1],"is":[2,18],"hosted":[3],"at":[4],"https://github.com/sys-bio/AMAS,":[5],"where":[6],"we":[7],"provide":[8],"examples,":[9],"documentation,":[10],"and":[11],"source":[12,16],"code":[13,17],"files.":[14],"licensed":[19],"under":[20],"the":[21],"MIT":[22],"open-source":[23],"license.":[24]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
