{"id":"https://openalex.org/W2170776520","doi":"https://doi.org/10.1093/bioinformatics/btt159","title":"Biographer: web-based editing and rendering of SBGN compliant biochemical networks","display_name":"Biographer: web-based editing and rendering of SBGN compliant biochemical networks","publication_year":2013,"publication_date":"2013-04-10","ids":{"openalex":"https://openalex.org/W2170776520","doi":"https://doi.org/10.1093/bioinformatics/btt159","mag":"2170776520","pmid":"https://pubmed.ncbi.nlm.nih.gov/23574737"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt159","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1467/587780/btt159.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1467/587780/btt159.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111505379","display_name":"Falko Krause","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Falko Krause","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079222008","display_name":"Marvin Schulz","orcid":"https://orcid.org/0009-0009-7565-9460"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marvin Schulz","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015624339","display_name":"Ben Ripkens","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ben Ripkens","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025830249","display_name":"Max Fl\u00f6ttmann","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Max Fl\u00f6ttmann","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067310765","display_name":"Marcus Krantz","orcid":"https://orcid.org/0000-0001-7843-8342"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marcus Krantz","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003799374","display_name":"Edda Klipp","orcid":"https://orcid.org/0000-0002-0567-7075"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Edda Klipp","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064813825","display_name":"Thomas Handorf","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Thomas Handorf","raw_affiliation_strings":["1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5003799374","https://openalex.org/A5064813825"],"corresponding_institution_ids":["https://openalex.org/I39343248"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1978,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79221577,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"29","issue":"11","first_page":"1467","last_page":"1468"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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":0.9986000061035156,"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/computer-science","display_name":"Computer science","score":0.8359618186950684},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.7122218012809753},{"id":"https://openalex.org/keywords/html5","display_name":"HTML5","score":0.5515859723091125},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.5500963926315308},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5359467267990112},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.48732075095176697},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4586614966392517},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45704561471939087},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.4471311569213867},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4463629722595215},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.361314594745636},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.29930639266967773},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.2476770281791687},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.18135347962379456},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.16612908244132996},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12689277529716492}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8359618186950684},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7122218012809753},{"id":"https://openalex.org/C84063617","wikidata":"https://www.wikidata.org/wiki/Q2053","display_name":"HTML5","level":2,"score":0.5515859723091125},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.5500963926315308},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5359467267990112},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.48732075095176697},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4586614966392517},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45704561471939087},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.4471311569213867},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4463629722595215},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.361314594745636},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.29930639266967773},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2476770281791687},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.18135347962379456},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.16612908244132996},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12689277529716492}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt159","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1467/587780/btt159.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:23574737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23574737","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:3661053","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3661053","pdf_url":null,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt159","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1467/587780/btt159.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320309327","display_name":"Google","ror":"https://ror.org/00njsd438"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170776520.pdf","grobid_xml":"https://content.openalex.org/works/W2170776520.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1970594207","https://openalex.org/W2020561965","https://openalex.org/W2069157810","https://openalex.org/W2098769288","https://openalex.org/W2117364474","https://openalex.org/W2126132608","https://openalex.org/W2134185611","https://openalex.org/W2135290856","https://openalex.org/W2143969914","https://openalex.org/W2147714160","https://openalex.org/W2159482845","https://openalex.org/W2163993275"],"related_works":["https://openalex.org/W4390142841","https://openalex.org/W2484907013","https://openalex.org/W2606134820","https://openalex.org/W562146691","https://openalex.org/W2984839098","https://openalex.org/W2137830470","https://openalex.org/W2342903424","https://openalex.org/W2750121105","https://openalex.org/W602441967","https://openalex.org/W88324370"],"abstract_inverted_index":{"The":[0,14],"biographer":[1],"tool":[2],"can":[3],"be":[4],"used":[5],"at":[6,36],"and":[7,30],"downloaded":[8],"from":[9],"the":[10,39],"web":[11,26],"page":[12],"http://biographer.biologie.hu-berlin.de/.":[13],"different":[15],"software":[16],"packages,":[17],"including":[18],"a":[19,25],"server-independent":[20],"version":[21],"as":[22,24],"well":[23],"server":[27],"for":[28],"Windows":[29],"Linux":[31],"based":[32],"systems,":[33],"are":[34],"available":[35],"http://code.google.com/p/biographer/":[37],"under":[38],"open-source":[40],"license":[41],"LGPL":[42]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
