{"id":"https://openalex.org/W4384338858","doi":"https://doi.org/10.1093/bioinformatics/btad437","title":"SBOannotator: a Python tool for the automated assignment of systems biology ontology terms","display_name":"SBOannotator: a Python tool for the automated assignment of systems biology ontology terms","publication_year":2023,"publication_date":"2023-07-01","ids":{"openalex":"https://openalex.org/W4384338858","doi":"https://doi.org/10.1093/bioinformatics/btad437","pmid":"https://pubmed.ncbi.nlm.nih.gov/37449910"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad437","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad437/50883185/btad437.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/advance-article-pdf/doi/10.1093/bioinformatics/btad437/50883185/btad437.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054063665","display_name":"Nantia Leonidou","orcid":"https://orcid.org/0000-0002-0248-6679"},"institutions":[{"id":"https://openalex.org/I4210115305","display_name":"German Center for Infection Research","ror":"https://ror.org/028s4q594","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210115305","https://openalex.org/I4405256427"]},{"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"],"is_corresponding":false,"raw_author_name":"Nantia Leonidou","raw_affiliation_strings":["Controlling Microbes to Fight Infections,\u2019 Eberhard Karl University of T\u00fcbingen Cluster of Excellence \u2018 , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","German Center for Infection Research (DZIF), partner site T\u00fcbingen , Germany"],"raw_orcid":"https://orcid.org/0000-0002-0248-6679","affiliations":[{"raw_affiliation_string":"Controlling Microbes to Fight Infections,\u2019 Eberhard Karl University of T\u00fcbingen Cluster of Excellence \u2018 , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"German Center for Infection Research (DZIF), partner site T\u00fcbingen , Germany","institution_ids":["https://openalex.org/I4210115305"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054261485","display_name":"Elisabeth Fritze","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Elisabeth Fritze","raw_affiliation_strings":["Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015301033","display_name":"Alina Renz","orcid":"https://orcid.org/0000-0003-3851-9978"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Alina Renz","raw_affiliation_strings":["Cluster of Excellence \u2018Controlling Microbes to Fight Infections,\u2019 Eberhard Karl University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3851-9978","affiliations":[{"raw_affiliation_string":"Cluster of Excellence \u2018Controlling Microbes to Fight Infections,\u2019 Eberhard Karl University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I4210115305","display_name":"German Center for Infection Research","ror":"https://ror.org/028s4q594","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210115305","https://openalex.org/I4405256427"]},{"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"],"is_corresponding":true,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Eberhard Karl University of T\u00fcbingen Cluster of Excellence \u2018Controlling Microbes to Fight Infections,\u2019 , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","German Center for Infection Research (DZIF) , partner site T\u00fcbingen, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1240-5553","affiliations":[{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Cluster of Excellence \u2018Controlling Microbes to Fight Infections,\u2019 , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Eberhard Karl University of T\u00fcbingen Department of Computer Science, , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"German Center for Infection Research (DZIF) , partner site T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210115305"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065854572"],"corresponding_institution_ids":["https://openalex.org/I4210115305","https://openalex.org/I8087733"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6985,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.90345183,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.39899998903274536,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.39899998903274536,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.23680000007152557,"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":0.1867000013589859,"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":0.8381046056747437},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8021019697189331},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.790268063545227},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6744771599769592},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5449227094650269},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5289259552955627},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5040280222892761},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.45596712827682495},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.45383620262145996},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.44188469648361206},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3775225281715393},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2917298972606659},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2667357325553894},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13518959283828735},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10321122407913208}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8381046056747437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8021019697189331},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.790268063545227},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6744771599769592},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5449227094650269},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5289259552955627},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5040280222892761},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.45596712827682495},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.45383620262145996},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.44188469648361206},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3775225281715393},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2917298972606659},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2667357325553894},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13518959283828735},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10321122407913208},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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},{"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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad437","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad437/50883185/btad437.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:37449910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37449910","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:10371491","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10371491","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10371491/pdf/btad437.pdf","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,"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/btad437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad437","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad437/50883185/btad437.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/G160184881","display_name":null,"funder_award_id":"390838134","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2036822895","display_name":null,"funder_award_id":"EXC 2124","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4771072336","display_name":null,"funder_award_id":"390838134","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G530113113","display_name":null,"funder_award_id":"8020708703","funder_id":"https://openalex.org/F4320311052","funder_display_name":"Deutsches Zentrum f\u00fcr Infektionsforschung"}],"funders":[{"id":"https://openalex.org/F4320311052","display_name":"Deutsches Zentrum f\u00fcr Infektionsforschung","ror":"https://ror.org/028s4q594"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4384338858.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1981021538","https://openalex.org/W2128852521","https://openalex.org/W2145435867","https://openalex.org/W2276489244","https://openalex.org/W2916475656","https://openalex.org/W2987028578","https://openalex.org/W3080133182","https://openalex.org/W6770172025"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2043776573","https://openalex.org/W3091139413","https://openalex.org/W2152827261","https://openalex.org/W2211443823","https://openalex.org/W2367709763","https://openalex.org/W2026725606","https://openalex.org/W2735157934","https://openalex.org/W3080133182","https://openalex.org/W2041228025"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,80,121],"number":[2],"and":[3,17,27,36,51,88,95,159,172,196,210,228],"size":[4],"of":[5,48,54,70,113,132,152,179,201,230],"computational":[6,59],"models":[7,222],"in":[8,33,220],"biology":[9],"have":[10],"drastically":[11],"increased":[12],"over":[13],"the":[14,31,46,52,61,68,101,119,126,129,150,153,177,197,221,225],"past":[15],"years":[16],"continue":[18],"to":[19,85,110,156,164,191],"grow.":[20],"Modeled":[21],"networks":[22],"are":[23,169,173,187,212],"becoming":[24],"more":[25],"complex,":[26],"reconstructing":[28],"them":[29],"from":[30,240],"beginning":[32],"an":[34],"exchangeable":[35],"reproducible":[37],"manner":[38],"is":[39,67,237],"challenging.":[40],"Using":[41],"precisely":[42],"defined":[43],"ontologies":[44],"enables":[45],"encoding":[47],"field-specific":[49],"knowledge":[50,66],"association":[53],"disparate":[55],"data":[56],"types.":[57],"In":[58],"modeling,":[60],"medium":[62],"for":[63],"representing":[64],"domain":[65],"set":[69],"orthogonal":[71],"structured":[72],"controlled":[73],"vocabularies":[74],"named":[75,118],"Systems":[76],"Biology":[77],"Ontology":[78],"(SBO).":[79],"SBO":[81,108,134,218],"terms":[82,109,147,163,190],"enable":[83],"modelers":[84],"explicitly":[86],"define":[87],"describe":[89],"model":[90,205],"entities,":[91,206],"including":[92],"their":[93,137],"roles":[94],"characteristics.":[96],"RESULTS:":[97],"Here,":[98],"we":[99],"present":[100],"first":[102],"standalone":[103],"tool":[104],"that":[105,183],"automatically":[106],"assigns":[107],"multiple":[111],"entities":[112],"a":[114],"given":[115,188],"SBML":[116],"model,":[117],"SBOannotator.":[120],"main":[122],"focus":[123],"lies":[124],"on":[125,176],"reactions,":[127],"as":[128,208],"correct":[130],"assignment":[131],"precise":[133,158],"annotations":[135,219],"requires":[136],"extensive":[138],"classification.":[139],"Our":[140],"implementation":[141],"does":[142],"not":[143],"consider":[144],"only":[145],"top-level":[146],"but":[148],"examines":[149],"functionality":[151],"underlying":[154],"enzymes":[155],"allocate":[157],"highly":[160],"specific":[161],"ontology":[162],"biochemical":[165,231],"reactions.":[166],"Transport":[167],"reactions":[168],"examined":[170],"separately":[171],"classified":[174],"based":[175],"mechanism":[178],"molecule":[180],"transport.":[181],"Pseudo-reactions":[182],"serve":[184],"modeling":[185],"purposes":[186],"reasonable":[189],"distinguish":[192],"between":[193],"biomass":[194],"production":[195],"import":[198],"or":[199],"export":[200],"metabolites.":[202],"Finally,":[203],"other":[204],"such":[207],"metabolites":[209],"genes,":[211],"annotated":[213],"with":[214],"appropriate":[215],"terms.":[216],"Including":[217],"will":[223],"enhance":[224],"reproducibility,":[226],"usability,":[227],"analysis":[229],"networks.":[232],"AVAILABILITY":[233],"AND":[234],"IMPLEMENTATION:":[235],"SBOannotator":[236],"freely":[238],"available":[239],"https://github.com/draeger-lab/SBOannotator/.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
