{"id":"https://openalex.org/W2134999036","doi":"https://doi.org/10.1093/bioinformatics/bth278","title":"PaVESy: Pathway Visualization and Editing System","display_name":"PaVESy: Pathway Visualization and Editing System","publication_year":2004,"publication_date":"2004-04-22","ids":{"openalex":"https://openalex.org/W2134999036","doi":"https://doi.org/10.1093/bioinformatics/bth278","mag":"2134999036","pmid":"https://pubmed.ncbi.nlm.nih.gov/15105280"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2841/48906451/bioinformatics_20_16_2841.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2841/48906451/bioinformatics_20_16_2841.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087871753","display_name":"Alexander L\u00fcdemann","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alexander L\u00fcdemann","raw_affiliation_strings":["Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany","institution_ids":["https://openalex.org/I4210105972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075361200","display_name":"Daniel Weicht","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Weicht","raw_affiliation_strings":["Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany","institution_ids":["https://openalex.org/I4210105972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034181383","display_name":"Joachim Selbig","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Joachim Selbig","raw_affiliation_strings":["Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany","institution_ids":["https://openalex.org/I4210105972"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073438755","display_name":"Joachim Kopka","orcid":"https://orcid.org/0000-0001-9675-4883"},"institutions":[{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Joachim Kopka","raw_affiliation_strings":["Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute of Molecular Plant Physiology, Am M\u00fchlenberg 1, 14476 Golm, Germany","institution_ids":["https://openalex.org/I4210105972"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087871753"],"corresponding_institution_ids":["https://openalex.org/I4210105972"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.1554,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.87031905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"16","first_page":"2841","last_page":"2844"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6036999821662903,"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":0.6036999821662903,"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":0.11230000108480453,"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":0.05310000106692314,"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/visualization","display_name":"Visualization","score":0.7458810806274414},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6949495673179626},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4415932893753052},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22976773977279663}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7458810806274414},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6949495673179626},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4415932893753052},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22976773977279663}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2841/48906451/bioinformatics_20_16_2841.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15105280","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15105280","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:edoc.mpg.de:228840","is_oa":false,"landing_page_url":"http://edoc.mpg.de/228840","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":"Bioinformatics, v.20, 2841-2844 (2004)","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2841/48906451/bioinformatics_20_16_2841.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4399999976158142}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1502432690","https://openalex.org/W1549912426","https://openalex.org/W2018045523","https://openalex.org/W2020541351","https://openalex.org/W2049483248","https://openalex.org/W2074906123","https://openalex.org/W2082844044","https://openalex.org/W2100471807","https://openalex.org/W2113221321","https://openalex.org/W2123280311","https://openalex.org/W2137591509","https://openalex.org/W2138844251","https://openalex.org/W2145889895","https://openalex.org/W2148753315","https://openalex.org/W2150908245","https://openalex.org/W2151225518","https://openalex.org/W2155254562","https://openalex.org/W2159628188","https://openalex.org/W2159675211"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3124914020","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"UNLABELLED:":[0],"A":[1,142],"data":[2,233],"managing":[3],"system":[4],"for":[5,185,204],"editing":[6,95,181],"and":[7,21,43,52,105,114,119,138,177,182,188,200,208],"visualization":[8,183,189,219],"of":[9,17,35,63,73,83,90,96,123,165,190,217,229],"biological":[10,36,54,64],"pathways":[11],"is":[12,24,115,212],"presented.":[13],"The":[14,30,56],"main":[15],"component":[16],"PaVESy":[18],"(Pathway":[19],"Visualization":[20],"Editing":[22],"System)":[23],"a":[25,111,215],"relational":[26],"SQL":[27,169],"database":[28,31,57,98,108,121,136,152,192],"system.":[29],"design":[32],"allows":[33],"storage":[34],"objects,":[37],"such":[38,171,221],"as":[39,150,172,222],"metabolites,":[40],"proteins,":[41],"genes":[42],"respective":[44],"relations,":[45],"which":[46,148,161],"are":[47,75,198],"required":[48],"to":[49,117,155],"assemble":[50],"metabolic":[51],"regulatory":[53],"interactions.":[55],"model":[58],"accommodates":[59],"highly":[60],"flexible":[61],"annotation":[62,207],"objects":[65,74,122],"by":[66],"user-defined":[67,84],"attributes.":[68],"In":[69],"addition,":[70],"specific":[71],"roles":[72],"derived":[76],"from":[77],"these":[78],"attributes":[79],"in":[80,87,168,187],"the":[81,88,97,101,107,135,151,163,191],"context":[82],"interactions,":[85,174],"e.g.":[86],"course":[89],"pathway":[91,196],"generation":[92],"or":[93,224,231],"during":[94],"content.":[99,193],"Furthermore,":[100],"user":[102,140],"may":[103,201],"organize":[104],"arrange":[106],"content":[109,137],"within":[110,125],"folder":[112],"structure":[113],"free":[116],"group":[118],"annotate":[120],"interest":[124],"customizable":[126],"subsets.":[127,178],"Thus,":[128],"we":[129],"allow":[130],"an":[131],"individualized":[132],"view":[133],"on":[134],"facilitate":[139],"customization.":[141],"JAVA-based":[143],"class":[144],"library":[145],"was":[146],"developed,":[147],"serves":[149],"programming":[153],"interface":[154],"PaVESy.":[156],"This":[157],"API":[158],"provides":[159],"classes,":[160],"implement":[162],"concepts":[164],"object":[166],"persistence":[167],"databases,":[170],"entries,":[173],"annotations,":[175],"folders":[176],"We":[179],"created":[180],"tools":[184],"navigation":[186],"User":[194],"approved":[195],"assemblies":[197],"stored":[199],"be":[202],"retrieved":[203],"continued":[205],"modification,":[206],"export.":[209],"Data":[210],"export":[211],"interfaced":[213],"with":[214],"range":[216],"network":[218],"programs,":[220],"Pajek":[223],"other":[225],"software":[226],"allowing":[227],"import":[228],"SBML":[230],"GML":[232],"format.":[234],"AVAILABILITY:":[235],"http://pavsey.mpimp-golm.mpg.de":[236]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}