{"id":"https://openalex.org/W2947660247","doi":"https://doi.org/10.1093/nar/gkz440","title":"BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data","display_name":"BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data","publication_year":2019,"publication_date":"2019-05-11","ids":{"openalex":"https://openalex.org/W2947660247","doi":"https://doi.org/10.1093/nar/gkz440","mag":"2947660247","pmid":"https://pubmed.ncbi.nlm.nih.gov/31131402"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz440","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W225/28879921/gkz440.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/47/W1/W225/28879921/gkz440.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081391218","display_name":"Fedor Kolpakov","orcid":"https://orcid.org/0000-0002-0396-0256"},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Fedor Kolpakov","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041561056","display_name":"Ilya R. Akberdin","orcid":"https://orcid.org/0000-0003-0010-8620"},"institutions":[{"id":"https://openalex.org/I188973947","display_name":"Novosibirsk State University","ror":"https://ror.org/04t2ss102","country_code":"RU","type":"education","lineage":["https://openalex.org/I188973947"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ilya Akberdin","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Novosibirsk State University, Novosibirsk 630090, Russian Federation"],"raw_orcid":"https://orcid.org/0000-0003-0010-8620","affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Novosibirsk State University, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I188973947"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002256789","display_name":"Timur A. Kashapov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Timur Kashapov","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023433489","display_name":"llya Kiselev","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"llya Kiselev","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008033532","display_name":"Semyon Kolmykov","orcid":"https://orcid.org/0000-0002-9259-0495"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210127387","display_name":"Siberian Branch of the Russian Academy of Sciences","ror":"https://ror.org/02frkq021","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210127387"]},{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Semyon Kolmykov","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]},{"raw_affiliation_string":"Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210116466","https://openalex.org/I4210127387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047929867","display_name":"Yury V. Kondrakhin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Yury Kondrakhin","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066125570","display_name":"Elena Kutumova","orcid":"https://orcid.org/0000-0001-7746-5760"},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Elena Kutumova","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023995949","display_name":"Nikita Mandrik","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Nikita Mandrik","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076464196","display_name":"Sergey Pintus","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Sergey Pintus","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055277352","display_name":"Anna S. Ryabova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anna Ryabova","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040778329","display_name":"Ruslan Sharipov","orcid":"https://orcid.org/0000-0003-2182-5493"},"institutions":[{"id":"https://openalex.org/I188973947","display_name":"Novosibirsk State University","ror":"https://ror.org/04t2ss102","country_code":"RU","type":"education","lineage":["https://openalex.org/I188973947"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ruslan Sharipov","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Novosibirsk State University, Novosibirsk 630090, Russian Federation"],"raw_orcid":"https://orcid.org/0000-0003-2182-5493","affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Novosibirsk State University, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I188973947"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072702454","display_name":"Ivan Yevshin","orcid":"https://orcid.org/0000-0001-7687-8002"},"institutions":[{"id":"https://openalex.org/I4210137651","display_name":"Federal Research Center for Information and Computational Technologies","ror":"https://ror.org/02x3mf211","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210137651"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ivan Yevshin","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210137651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016954113","display_name":"Alexander Kel","orcid":"https://orcid.org/0000-0001-6775-2467"},"institutions":[{"id":"https://openalex.org/I4210091979","display_name":"Institute of Chemical Biology and Fundamental Medicine","ror":"https://ror.org/00gmz2d02","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210091979","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210123556","display_name":"GeneXplain (Germany)","ror":"https://ror.org/02qeyb550","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210123556"]},{"id":"https://openalex.org/I4210127387","display_name":"Siberian Branch of the Russian Academy of Sciences","ror":"https://ror.org/02frkq021","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210127387"]}],"countries":["DE","RU"],"is_corresponding":false,"raw_author_name":"Alexander Kel","raw_affiliation_strings":["BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russian Federation","geneXplain GmbH, 38302 Wolfenb\u00fcttel, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation","institution_ids":[]},{"raw_affiliation_string":"Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russian Federation","institution_ids":["https://openalex.org/I4210091979","https://openalex.org/I4210127387"]},{"raw_affiliation_string":"geneXplain GmbH, 38302 Wolfenb\u00fcttel, Germany","institution_ids":["https://openalex.org/I4210123556"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5081391218"],"corresponding_institution_ids":["https://openalex.org/I4210137651"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.7341,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.91192771,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"47","issue":"W1","first_page":"W225","last_page":"W233"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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":0.9977999925613403,"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":0.9955000281333923,"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/workflow","display_name":"Workflow","score":0.6867271065711975},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6239116191864014},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5819753408432007},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5306341052055359},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4984760284423828},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.48273321986198425},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4688210189342499},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4631587266921997},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.4533710479736328},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.45308247208595276},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.45206862688064575},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.41547706723213196},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23939362168312073},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.12579691410064697},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11283522844314575}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6867271065711975},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6239116191864014},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5819753408432007},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5306341052055359},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4984760284423828},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.48273321986198425},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4688210189342499},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4631587266921997},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.4533710479736328},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.45308247208595276},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.45206862688064575},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.41547706723213196},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23939362168312073},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.12579691410064697},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11283522844314575},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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/nar/gkz440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz440","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W225/28879921/gkz440.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31131402","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31131402","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:europepmc.org:5577231","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602424","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz440","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W225/28879921/gkz440.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5899999737739563}],"awards":[{"id":"https://openalex.org/G7199292446","display_name":null,"funder_award_id":"19-14-00295","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947660247.pdf","grobid_xml":"https://content.openalex.org/works/W2947660247.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W122404453","https://openalex.org/W295766806","https://openalex.org/W1966450819","https://openalex.org/W1969709265","https://openalex.org/W1973094248","https://openalex.org/W1975508939","https://openalex.org/W1980832751","https://openalex.org/W1984234901","https://openalex.org/W1994606774","https://openalex.org/W2000479281","https://openalex.org/W2013434113","https://openalex.org/W2023503314","https://openalex.org/W2028133290","https://openalex.org/W2038264484","https://openalex.org/W2039488050","https://openalex.org/W2042443829","https://openalex.org/W2056090982","https://openalex.org/W2059246518","https://openalex.org/W2061364094","https://openalex.org/W2061417134","https://openalex.org/W2061674320","https://openalex.org/W2069157810","https://openalex.org/W2078734278","https://openalex.org/W2081781433","https://openalex.org/W2094036688","https://openalex.org/W2102653059","https://openalex.org/W2103925486","https://openalex.org/W2109745408","https://openalex.org/W2117453669","https://openalex.org/W2123783513","https://openalex.org/W2125615370","https://openalex.org/W2132788187","https://openalex.org/W2139321392","https://openalex.org/W2140305379","https://openalex.org/W2142414392","https://openalex.org/W2144144709","https://openalex.org/W2145620209","https://openalex.org/W2150908245","https://openalex.org/W2151339633","https://openalex.org/W2158734140","https://openalex.org/W2159675211","https://openalex.org/W2163500926","https://openalex.org/W2166751342","https://openalex.org/W2167154952","https://openalex.org/W2168648059","https://openalex.org/W2171617577","https://openalex.org/W2183784918","https://openalex.org/W2319515949","https://openalex.org/W2411390783","https://openalex.org/W2441893520","https://openalex.org/W2520812741","https://openalex.org/W2534008312","https://openalex.org/W2791048175","https://openalex.org/W2810755205","https://openalex.org/W2884300959","https://openalex.org/W2898671507","https://openalex.org/W2901144895","https://openalex.org/W2917207851","https://openalex.org/W2952076809","https://openalex.org/W3102018295","https://openalex.org/W3209128066","https://openalex.org/W4233961094","https://openalex.org/W4241685680","https://openalex.org/W4249302577","https://openalex.org/W6610552418","https://openalex.org/W6635164943","https://openalex.org/W6649026457","https://openalex.org/W6686295506"],"related_works":["https://openalex.org/W2093416473","https://openalex.org/W4247806713","https://openalex.org/W4378700020","https://openalex.org/W4238519267","https://openalex.org/W2390396596","https://openalex.org/W2170060741","https://openalex.org/W3180179400","https://openalex.org/W2118366689","https://openalex.org/W2477652530","https://openalex.org/W2116888309"],"abstract_inverted_index":{"BioUML":[0,27,45,88],"(homepage:":[1],"http://www.biouml.org,":[2],"main":[3],"public":[4],"server:":[5],"https://ict.biouml.org)":[6],"is":[7,29,149],"a":[8,32,47,69,76,112,116,138,150],"web-based":[9],"integrated":[10],"environment":[11],"(platform)":[12],"for":[13,59,92,137],"systems":[14,60],"biology":[15,61],"and":[16,42,67,75,86,153],"the":[17,83,93,102],"analysis":[18],"of":[19,50,95],"biomedical":[20],"data":[21],"generated":[22],"by":[23],"omics":[24,96],"technologies.":[25],"The":[26,98,157],"vision":[28],"to":[30,35,54,80,104,164],"provide":[31],"computational":[33],"platform":[34,85],"build":[36],"virtual":[37,39,43],"cell,":[38],"physiological":[40],"human":[41],"patient.":[44],"spans":[46],"comprehensive":[48],"range":[49],"capabilities,":[51],"including":[52],"access":[53],"biological":[55],"databases,":[56],"powerful":[57,90],"tools":[58],"(visual":[62],"modelling,":[63],"simulation,":[64],"parameters":[65],"fitting":[66],"analyses),":[68],"genome":[70],"browser,":[71],"scripting":[72],"(R,":[73],"JavaScript)":[74],"workflow":[77],"engine.":[78],"Due":[79],"integration":[81],"with":[82],"Galaxy":[84],"R/Bioconductor,":[87],"provides":[89],"possibilities":[91],"analyses":[94],"data.":[97],"plug-in-based":[99],"architecture":[100],"allows":[101],"user":[103,113],"add":[105],"new":[106],"functionalities":[107],"using":[108],"plug-ins.":[109],"To":[110,141],"facilitate":[111],"focus":[114],"on":[115,145],"particular":[117],"task":[118],"or":[119],"database,":[120],"we":[121],"have":[122],"developed":[123],"several":[124,161],"predefined":[125],"perspectives":[126],"that":[127,134],"display":[128],"only":[129],"those":[130],"web":[131],"interface":[132],"elements":[133],"are":[135],"needed":[136],"specific":[139],"task.":[140],"support":[142],"collaborative":[143],"work":[144],"scientific":[146],"projects,":[147],"there":[148],"central":[151],"authentication":[152],"authorization":[154],"system":[155],"(https://bio-store.org).":[156],"diagram":[158],"editor":[159],"enables":[160],"remote":[162],"users":[163],"simultaneously":[165],"edit":[166],"diagrams.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
