{"id":"https://openalex.org/W2795410052","doi":"https://doi.org/10.1515/jib-2017-0078","title":"SBML Level 3 package: Render, Version 1, Release 1","display_name":"SBML Level 3 package: Render, Version 1, Release 1","publication_year":2018,"publication_date":"2018-04-02","ids":{"openalex":"https://openalex.org/W2795410052","doi":"https://doi.org/10.1515/jib-2017-0078","mag":"2795410052","pmid":"https://pubmed.ncbi.nlm.nih.gov/29605822"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2017-0078","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0078","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-1/jib-2017-0078/jib-2017-0078.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"http://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-1/jib-2017-0078/jib-2017-0078.xml","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Frank T. Bergmann","raw_affiliation_strings":["BioQuant/COS, Heidelberg University, Heidelberg, Germany","Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioQuant/COS, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]},{"raw_affiliation_string":"Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049649026","display_name":"Sarah Keating","orcid":"https://orcid.org/0000-0002-3356-3542"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sarah M. Keating","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambrigeshire, United Kingdom of Great Britain and Northern Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambrigeshire, United Kingdom of Great Britain and Northern Ireland","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041448665","display_name":"Ralph Gauges","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124927","display_name":"Albstadt-Sigmaringen University","ror":"https://ror.org/03crxcn36","country_code":"DE","type":"education","lineage":["https://openalex.org/I4210124927"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ralph Gauges","raw_affiliation_strings":["Hochschule Albstadt-Sigmaringen, Sigmaringen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hochschule Albstadt-Sigmaringen, Sigmaringen, Germany","institution_ids":["https://openalex.org/I4210124927"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964760","display_name":"Sven Sahle","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sven Sahle","raw_affiliation_strings":["BioQuant/COS, Heidelberg University, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioQuant/COS, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036842800","display_name":"Katja Wengler","orcid":null},"institutions":[{"id":"https://openalex.org/I141584323","display_name":"University of Hertfordshire","ror":"https://ror.org/0267vjk41","country_code":"GB","type":"education","lineage":["https://openalex.org/I141584323"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Katja Wengler","raw_affiliation_strings":["University of Hertfordshire, Hertfordshire, United Kingdom of Great Britain and Northern Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Hertfordshire, Hertfordshire, United Kingdom of Great Britain and Northern Ireland","institution_ids":["https://openalex.org/I141584323"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049649026"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":null,"apc_paid":null,"fwci":1.8025,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.89168838,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"15","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9681000113487244,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9681000113487244,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9460180997848511},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8460547924041748},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.6678156852722168},{"id":"https://openalex.org/keywords/scalable-vector-graphics","display_name":"Scalable Vector Graphics","score":0.6586390137672424},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5933027863502502},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4530961811542511},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40257444977760315},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3458792567253113},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.20489272475242615},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15869581699371338},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.1570919156074524}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9460180997848511},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8460547924041748},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.6678156852722168},{"id":"https://openalex.org/C202629362","wikidata":"https://www.wikidata.org/wiki/Q2078","display_name":"Scalable Vector Graphics","level":2,"score":0.6586390137672424},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5933027863502502},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4530961811542511},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40257444977760315},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3458792567253113},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.20489272475242615},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15869581699371338},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.1570919156074524}],"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","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":"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1515/jib-2017-0078","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0078","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-1/jib-2017-0078/jib-2017-0078.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29605822","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29605822","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:5327986","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6167038","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:authors.library.caltech.edu:86114","is_oa":true,"landing_page_url":"https://authors.library.caltech.edu/86114/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:2c08b604510a4496a3f6183e10ded41b","is_oa":false,"landing_page_url":"https://doaj.org/article/2c08b604510a4496a3f6183e10ded41b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"Journal of Integrative Bioinformatics, Vol 15, Iss 1 (2018)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2017-0078","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0078","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-1/jib-2017-0078/jib-2017-0078.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2795410052.pdf","grobid_xml":"https://content.openalex.org/works/W2795410052.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1525863646","https://openalex.org/W2102653059","https://openalex.org/W3145460265","https://openalex.org/W6630086920","https://openalex.org/W6675376083","https://openalex.org/W6680025739"],"related_works":["https://openalex.org/W1833372769","https://openalex.org/W2128782793","https://openalex.org/W4226414617","https://openalex.org/W4225469991","https://openalex.org/W4226134703","https://openalex.org/W4206318408","https://openalex.org/W2157092888","https://openalex.org/W3157390305","https://openalex.org/W1546880839","https://openalex.org/W2122529434"],"abstract_inverted_index":{"Many":[0,138],"software":[1],"tools":[2],"provide":[3],"facilities":[4],"for":[5,49,135],"depicting":[6],"reaction":[7],"network":[8],"diagrams":[9],"in":[10,34,90,143],"a":[11,18,80,91,100,163,172],"visual":[12,19],"form.":[13],"Two":[14],"aspects":[15],"of":[16,31,41,53,82,87,108,123,139,165],"such":[17],"diagram":[20],"can":[21,119],"be":[22,120],"distinguished:":[23],"the":[24,27,32,35,38,42,46,51,54,64,72,84,88,110,115,140,144,154],"layout":[25,166],"(i.e.:":[26],"positioning":[28],"and":[29,37,58,78,114,168],"connections)":[30],"elements":[33,43,89,141,152],"diagram,":[36],"graphical":[39],"form":[40],"(for":[44],"example,":[45],"glyphs":[47],"used":[48,142],"symbols,":[50],"properties":[52],"lines":[55],"connecting":[56],"them,":[57],"so":[59],"on).":[60],"This":[61,157],"document":[62],"describes":[63],"SBML":[65,73,94,112],"Level":[66,74,95],"3":[67,75,96],"Render":[68,97],"package":[69,77,98],"that":[70,105,126],"complements":[71],"Layout":[76,116],"provides":[79,99],"means":[81],"capturing":[83],"precise":[85],"rendering":[86,104],"diagram.":[92],"The":[93],"flexible":[101],"approach":[102],"to":[103,128,160],"is":[106],"independent":[107],"both":[109],"underlying":[111],"model":[113],"information.":[117],"There":[118],"one":[121],"block":[122,134],"render":[124,146,169],"information":[125,167,170],"applies":[127],"all":[129],"layouts":[130],"or":[131],"an":[132],"additional":[133],"each":[136],"layout.":[137],"current":[145],"specification":[147],"are":[148],"based":[149],"on":[150],"corresponding":[151],"from":[153],"SVG":[155,173],"specification.":[156],"allows":[158],"us":[159],"easily":[161],"convert":[162],"combination":[164],"into":[171],"drawing.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
