{"id":"https://openalex.org/W2119298353","doi":"https://doi.org/10.1093/bioinformatics/btq423","title":"PathwayAccess: CellDesigner plugins for pathway databases","display_name":"PathwayAccess: CellDesigner plugins for pathway databases","publication_year":2010,"publication_date":"2010-07-20","ids":{"openalex":"https://openalex.org/W2119298353","doi":"https://doi.org/10.1093/bioinformatics/btq423","mag":"2119298353","pmid":"https://pubmed.ncbi.nlm.nih.gov/20647521"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq423","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq423","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/2345/48858443/bioinformatics_26_18_2345.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/26/18/2345/48858443/bioinformatics_26_18_2345.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020860521","display_name":"John L. Van Hemert","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John L. Van Hemert","raw_affiliation_strings":["1 Bioinformatics and Computational Biology and 2Electrical and Computer Engineering Department, Iowa State University, Ames, IA, 50011, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Computational Biology and 2Electrical and Computer Engineering Department, Iowa State University, Ames, IA, 50011, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077949687","display_name":"Julie Dickerson","orcid":"https://orcid.org/0000-0003-4973-5641"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie A. Dickerson","raw_affiliation_strings":["1 Bioinformatics and Computational Biology and 2Electrical and Computer Engineering Department, Iowa State University, Ames, IA, 50011, USA"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Computational Biology and 2Electrical and Computer Engineering Department, Iowa State University, Ames, IA, 50011, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020860521"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3554,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.80094528,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"26","issue":"18","first_page":"2345","last_page":"2346"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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":0.9988999962806702,"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/plug-in","display_name":"Plug-in","score":0.9374856948852539},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7383642792701721},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.682028591632843},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6271842122077942},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6224974393844604},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5945894122123718},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5765212774276733},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5710017085075378},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.49883079528808594},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4571859538555145},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4452779293060303},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3998098373413086},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3455701470375061},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.3192266821861267}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.9374856948852539},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7383642792701721},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.682028591632843},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6271842122077942},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6224974393844604},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5945894122123718},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5765212774276733},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5710017085075378},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.49883079528808594},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4571859538555145},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4452779293060303},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3998098373413086},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3455701470375061},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.3192266821861267},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"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":"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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq423","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq423","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/2345/48858443/bioinformatics_26_18_2345.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20647521","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20647521","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:2935416","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2935416","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq423","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq423","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/2345/48858443/bioinformatics_26_18_2345.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5199999809265137,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1754317222","display_name":null,"funder_award_id":"EEC 0813570","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6658813440","display_name":null,"funder_award_id":"0813570","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7940261862","display_name":"Functional Genomics of Bud Endodormancy Induction in Grapevines (Vitis)","funder_award_id":"0604755","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119298353.pdf","grobid_xml":"https://content.openalex.org/works/W2119298353.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1999895438","https://openalex.org/W2038264484","https://openalex.org/W2060730816","https://openalex.org/W2091050840","https://openalex.org/W2096144498","https://openalex.org/W2124879678","https://openalex.org/W2146116329","https://openalex.org/W2150908245","https://openalex.org/W2152376294","https://openalex.org/W2155331065","https://openalex.org/W2159675211","https://openalex.org/W2164453232","https://openalex.org/W2482615868","https://openalex.org/W4246402725"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"Implemented":[0],"in":[1],"Java,":[2],"PathwayAccess":[3],"plugins":[4],"run":[5],"with":[6],"CellDesigner":[7],"version":[8],"4.0.1":[9],"and":[10,18,20,26],"were":[11],"tested":[12],"on":[13],"Ubuntu":[14],"Linux,":[15],"Windows":[16],"XP":[17],"7,":[19],"MacOSX.":[21],"Source":[22],"code,":[23],"binaries,":[24],"documentation":[25],"video":[27],"walkthroughs":[28],"are":[29],"freely":[30],"available":[31],"at":[32],"http://vrac.iastate.edu/~jlv.":[33]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
