{"id":"https://openalex.org/W2096883695","doi":"https://doi.org/10.1186/s12859-015-0585-1","title":"PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways","display_name":"PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways","publication_year":2015,"publication_date":"2015-05-18","ids":{"openalex":"https://openalex.org/W2096883695","doi":"https://doi.org/10.1186/s12859-015-0585-1","mag":"2096883695","pmid":"https://pubmed.ncbi.nlm.nih.gov/25982732"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0585-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0585-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0585-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0585-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113171251","display_name":"Yongnan Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]},{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yongnan Zhu","raw_affiliation_strings":["Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. yongnan@umbc.edu","Department of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang Province, P.R. China. yongnan@umbc.edu","Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA","Department of Computer Science, Hangzhou Dianzi University, Hangzhou, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. yongnan@umbc.edu","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang Province, P.R. China. yongnan@umbc.edu","institution_ids":["https://openalex.org/I50760025"]},{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Computer Science, Hangzhou Dianzi University, Hangzhou, P.R. China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101475441","display_name":"Liang Sun","orcid":"https://orcid.org/0000-0003-1634-4716"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Sun","raw_affiliation_strings":["Department of Animal & Food Sciences, University of Delaware, Newark, DE, USA. sunliang@udel.edu","Department of Animal & Food Sciences, University of Delaware, Newark, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal & Food Sciences, University of Delaware, Newark, DE, USA. sunliang@udel.edu","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Animal & Food Sciences, University of Delaware, Newark, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016500905","display_name":"Alexander Garbarino","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Garbarino","raw_affiliation_strings":["Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. garba1@umbc.edu","Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. garba1@umbc.edu","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004246605","display_name":"Carl J. Schmidt","orcid":"https://orcid.org/0000-0002-8386-4781"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carl Schmidt","raw_affiliation_strings":["Department of Animal & Food Sciences, University of Delaware, Newark, DE, USA. schmidtc@udel.edu","Department of Animal & Food Sciences, University of Delaware, Newark, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal & Food Sciences, University of Delaware, Newark, DE, USA. schmidtc@udel.edu","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Animal & Food Sciences, University of Delaware, Newark, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082765502","display_name":"Jinglong Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jinglong Fang","raw_affiliation_strings":["Department of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang Province, P.R. China. fjl@hdu.edu.cn","Department of Computer Science, Hangzhou Dianzi University, Hangzhou, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang Province, P.R. China. fjl@hdu.edu.cn","institution_ids":["https://openalex.org/I50760025"]},{"raw_affiliation_string":"Department of Computer Science, Hangzhou Dianzi University, Hangzhou, P.R. China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100326441","display_name":"Jian Chen","orcid":"https://orcid.org/0000-0002-2542-9669"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jian Chen","raw_affiliation_strings":["Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. jichen@umbc.edu","Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA. jichen@umbc.edu","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, USA","institution_ids":["https://openalex.org/I79272384"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5004246605","https://openalex.org/A5082765502","https://openalex.org/A5100326441"],"corresponding_institution_ids":["https://openalex.org/I50760025","https://openalex.org/I79272384","https://openalex.org/I86501945"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3103,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.86778799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"16","issue":"1","first_page":"165","last_page":"165"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.676800012588501,"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":0.676800012588501,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.17550000548362732,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0421999990940094,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.7050261497497559},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7047119140625},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5641718506813049},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.5116677284240723},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.5022671222686768},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.5009894371032715},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.48227742314338684},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4555157721042633},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4394316077232361},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4336088001728058},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.27018433809280396},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26707351207733154},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19714763760566711},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1312868595123291}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7050261497497559},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7047119140625},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5641718506813049},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.5116677284240723},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.5022671222686768},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.5009894371032715},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.48227742314338684},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4555157721042633},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4394316077232361},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4336088001728058},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27018433809280396},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26707351207733154},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19714763760566711},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1312868595123291},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0585-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0585-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0585-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25982732","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25982732","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:udspace.udel.edu:19716/17287","is_oa":true,"landing_page_url":"http://udspace.udel.edu/handle/19716/17287","pdf_url":null,"source":{"id":"https://openalex.org/S4377196565","display_name":"Library, Museums and Press - UDSpace (University of Delaware)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I86501945","host_organization_name":"University of Delaware","host_organization_lineage":["https://openalex.org/I86501945"],"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":"BMC Bioinformatics","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3398372","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4436019","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:10.1186/s12859-015-0585-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0585-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0585-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1607701488","display_name":null,"funder_award_id":"DBI-1260795","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2180012574","display_name":"GV: Small: Collaborative Research: Supporting Knowledge Discovery through a Scientific Visualization Language","funder_award_id":"1302755","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G218590244","display_name":null,"funder_award_id":"2011-67003-30228","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G2464809234","display_name":null,"funder_award_id":"2011-67003-30228","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G2574429505","display_name":"ABI Development:   PathBubbles for Dynamic Visualization and Integration of Biological Information","funder_award_id":"1260795","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2832184943","display_name":"Collaborative Research:  ABI Development: PathBubbles for Dynamic Visualization and Integration of Biological Information","funder_award_id":"1147029","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7760063100","display_name":null,"funder_award_id":"IIS-1302755","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8638643015","display_name":null,"funder_award_id":"NSF DBI-1260795","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"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096883695.pdf","grobid_xml":"https://content.openalex.org/works/W2096883695.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1668625893","https://openalex.org/W1965264154","https://openalex.org/W2020350008","https://openalex.org/W2028133290","https://openalex.org/W2046649416","https://openalex.org/W2066081314","https://openalex.org/W2090950329","https://openalex.org/W2092043944","https://openalex.org/W2093890259","https://openalex.org/W2106441507","https://openalex.org/W2110751128","https://openalex.org/W2121411279","https://openalex.org/W2122914905","https://openalex.org/W2123247102","https://openalex.org/W2129999614","https://openalex.org/W2130178067","https://openalex.org/W2130410032","https://openalex.org/W2135415614","https://openalex.org/W2143349559","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W3149127250","https://openalex.org/W2158984754","https://openalex.org/W2080934634","https://openalex.org/W2081749267","https://openalex.org/W2112083262","https://openalex.org/W2143428259","https://openalex.org/W4378086562","https://openalex.org/W2056189874","https://openalex.org/W2013467770","https://openalex.org/W4389880955"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"methods":[2],"are":[3,87,146],"generating":[4],"biological":[5,107,117],"data":[6,18,52,80,171,247,283],"on":[7,96,172,297],"a":[8,41,54,102,128,195],"vast":[9],"scale.":[10],"In":[11],"many":[12],"instances,":[13],"genomic,":[14],"transcriptomic,":[15],"and":[16,27,56,74,83,115,122,133,139,151,231,291],"proteomic":[17],"must":[19],"be":[20,60,184],"interpreted":[21],"in":[22,53,127,186,248],"the":[23,91,166,191,249,282,292],"context":[24,250],"of":[25,153,165,168,245,251],"signaling":[26,123],"metabolic":[28,121],"pathways":[29,124,140,174,181,252],"to":[30,77,89,113,136,175,206,240,259],"yield":[31],"testable":[32],"hypotheses.":[33],"Since":[34],"humans":[35,63],"can":[36,183,262],"interpret":[37,50,116],"visual":[38,45,84,177,196,243],"information":[39,182],"rapidly,":[40],"means":[42],"for":[43,111,148],"interactive":[44,104,242],"exploration":[46,197],"that":[47,193,217],"lets":[48],"biologists":[49,112],"such":[51],"comprehensive":[55],"exploratory":[57,85],"manner":[58],"would":[59],"invaluable.":[61],"However,":[62],"have":[64,71],"limited":[65,72],"memory":[66],"capacity.":[67],"Current":[68],"visualization":[69,109,280],"tools":[70,86],"viewing":[73],"manipulation":[75],"capabilities":[76],"address":[78],"complex":[79,226],"analysis":[81,152,244],"problems,":[82],"needed":[88],"reduce":[90],"high":[92],"mental":[93],"workload":[94],"imposed":[95],"biologists.":[97],"RESULTS:":[98],"We":[99],"present":[100],"PathRings,":[101],"new":[103,187,257],"web-based,":[105],"scalable":[106],"pathway":[108],"tool":[110],"explore":[114],"pathways.":[118],"PathRings":[119,161,236,285],"integrates":[120],"from":[125],"Reactome":[126],"single":[129],"compound":[130],"graph":[131],"visualization,":[132],"uses":[134],"color":[135],"highlight":[137],"genes":[138],"affected":[141],"by":[142,211,254],"input":[143,157],"data.":[144],"Pathways":[145],"available":[147,287],"multiple":[149],"species":[150,155],"user-defined":[154],"or":[156],"is":[158,204,286,295],"also":[159],"possible.":[160],"permits":[162],"an":[163],"overview":[164],"impact":[167],"gene":[169],"expression":[170],"all":[173],"facilitate":[176],"pattern":[178],"finding.":[179],"Detailed":[180],"opened":[185],"visualizations":[188],"while":[189],"maintaining":[190],"overview,":[192],"form":[194],"provenance.":[198],"A":[199],"dynamic":[200,275],"multi-view":[201,233,278],"bubbles":[202],"interface":[203,260],"designed":[205,239],"support":[207,264],"biologists'":[208,220],"analytical":[209,221],"tasks":[210,227,266],"letting":[212],"users":[213],"construct":[214],"incremental":[215],"views":[216],"further":[218],"reflect":[219],"process.":[222],"This":[223],"approach":[224,258],"decomposes":[225],"into":[228],"simpler":[229],"ones":[230],"automates":[232],"management.":[234],"CONCLUSIONS:":[235],"has":[237],"been":[238],"accommodate":[241],"experimental":[246],"defined":[253],"Reactome.":[255],"Our":[256],"design":[261],"effectively":[263],"comparative":[265],"over":[267],"substantially":[268],"larger":[269],"collection":[270],"than":[271],"existing":[272],"tools.":[273],"The":[274],"interaction":[276],"among":[277],"dataset":[279],"improves":[281],"exploration.":[284],"free":[288],"at":[289],"http://raven.anr.udel.edu/~sunliang/PathRings":[290],"source":[293],"code":[294],"hosted":[296],"Github:":[298],"https://github.com/ivcl/PathRings":[299],".":[300]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
