{"id":"https://openalex.org/W2888881870","doi":"https://doi.org/10.1093/bioinformatics/bty770","title":"PDV: an integrative proteomics data viewer","display_name":"PDV: an integrative proteomics data viewer","publication_year":2018,"publication_date":"2018-08-30","ids":{"openalex":"https://openalex.org/W2888881870","doi":"https://doi.org/10.1093/bioinformatics/bty770","mag":"2888881870","pmid":"https://pubmed.ncbi.nlm.nih.gov/30169737"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1249/48968393/bioinformatics_35_7_1249.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/35/7/1249/48968393/bioinformatics_35_7_1249.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100399851","display_name":"Kai Li","orcid":"https://orcid.org/0000-0002-0810-2437"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Li","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, China","China National GeneBank, BGI-Shenzhen, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I4210149137"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037607788","display_name":"Marc Vaudel","orcid":"https://orcid.org/0000-0003-1179-9578"},"institutions":[{"id":"https://openalex.org/I2800740805","display_name":"Haukeland University Hospital","ror":"https://ror.org/03np4e098","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I2800740805"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Marc Vaudel","raw_affiliation_strings":["Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway","Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway","institution_ids":["https://openalex.org/I2800740805"]},{"raw_affiliation_string":"Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100389664","display_name":"Bing Zhang","orcid":"https://orcid.org/0000-0001-8676-2425"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bing Zhang","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100644432","display_name":"Yan Ren","orcid":"https://orcid.org/0000-0002-4007-8625"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Ren","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, China","China National GeneBank, BGI-Shenzhen, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I4210149137"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011332528","display_name":"Bo Wen","orcid":"https://orcid.org/0000-0003-2261-3150"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bo Wen","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-2261-3150","affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011332528","https://openalex.org/A5100644432"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I181547552","https://openalex.org/I4210149137"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":5.2918,"has_fulltext":true,"cited_by_count":145,"citation_normalized_percentile":{"value":0.97479108,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"7","first_page":"1249","last_page":"1251"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9682000279426575,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9682000279426575,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.008500000461935997,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.002899999963119626,"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/proteogenomics","display_name":"Proteogenomics","score":0.7851004600524902},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.698942244052887},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.6379855275154114},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6280955672264099},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5268170833587646},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46695810556411743},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.41353753209114075},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.23979097604751587},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.16522592306137085},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13383319973945618},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.06418812274932861}],"concepts":[{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.7851004600524902},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.698942244052887},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6379855275154114},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6280955672264099},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5268170833587646},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46695810556411743},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.41353753209114075},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.23979097604751587},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.16522592306137085},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13383319973945618},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.06418812274932861},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1249/48968393/bioinformatics_35_7_1249.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:30169737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30169737","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:6060967","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821182","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1249/48968393/bioinformatics_35_7_1249.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":[],"awards":[{"id":"https://openalex.org/G2358021521","display_name":null,"funder_award_id":"U24 CA210954","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3566643606","display_name":"Recruitment of Rising Stars","funder_award_id":"RR160027","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G5734628984","display_name":null,"funder_award_id":"2017YFC0908400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7922605845","display_name":null,"funder_award_id":"CPRIT RR160027","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"}],"funders":[{"id":"https://openalex.org/F4320306422","display_name":"Robert and Janice McNair Foundation","ror":"https://ror.org/01pg81m90"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888881870.pdf","grobid_xml":"https://content.openalex.org/works/W2888881870.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W752259472","https://openalex.org/W1986171504","https://openalex.org/W2016916625","https://openalex.org/W2038615001","https://openalex.org/W2046872827","https://openalex.org/W2080752012","https://openalex.org/W2091754843","https://openalex.org/W2111846704","https://openalex.org/W2120202914","https://openalex.org/W2139397135","https://openalex.org/W2147350830","https://openalex.org/W2161811833","https://openalex.org/W2166437654","https://openalex.org/W2437599638","https://openalex.org/W2736859409","https://openalex.org/W2773925504","https://openalex.org/W2951123013"],"related_works":["https://openalex.org/W2968156700","https://openalex.org/W2061992841","https://openalex.org/W2916022525","https://openalex.org/W4386856376","https://openalex.org/W4399671710","https://openalex.org/W2184473026","https://openalex.org/W4317567415","https://openalex.org/W4236949517","https://openalex.org/W3148091054","https://openalex.org/W1516026788"],"abstract_inverted_index":{"SUMMARY:":[0],"Data":[1],"visualization":[2,68],"plays":[3],"critical":[4],"roles":[5],"in":[6,55,85],"proteomics":[7,28,41,62,79],"studies,":[8],"ranging":[9],"from":[10,60],"quality":[11],"control":[12],"of":[13,18,40,76],"MS/MS":[14,53],"data":[15,29,54,59,125],"to":[16,35],"validation":[17],"peptide":[19],"identification":[20],"results.":[21],"Herein,":[22],"we":[23],"present":[24],"PDV,":[25],"an":[26],"integrative":[27],"viewer":[30],"that":[31,70],"can":[32],"be":[33],"used":[34],"visualize":[36],"a":[37,66],"wide":[38],"range":[39],"data,":[42],"including":[43],"database":[44],"search":[45],"results,":[46,50],"de":[47],"novo":[48],"sequencing":[49],"proteogenomics":[51],"files,":[52],"mzML/mzXML":[56],"format":[57],"and":[58,73,90,99,115],"public":[61],"repositories.":[63],"PDV":[64,97],"is":[65,111,116],"lightweight":[67],"tool":[69],"enables":[71],"intuitive":[72],"fast":[74],"exploration":[75],"diverse,":[77],"large-scale":[78],"datasets":[80],"on":[81],"standard":[82],"desktop":[83],"computers":[84],"both":[86],"graphical":[87],"user":[88,101],"interface":[89],"command":[91],"line":[92],"modes.":[93],"AVAILABILITY":[94],"AND":[95],"IMPLEMENTATION:":[96],"software":[98],"the":[100,119],"manual":[102],"are":[103,126],"freely":[104],"available":[105,112,127],"at":[106,113,128],"http://pdv.zhang-lab.org.":[107],"The":[108],"source":[109],"code":[110],"https://github.com/wenbostar/PDV":[114],"released":[117],"under":[118],"GPL-3":[120],"license.":[121],"SUPPLEMENTARY":[122],"INFORMATION:":[123],"Supplementary":[124],"Bioinformatics":[129],"online.":[130]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":24},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
