{"id":"https://openalex.org/W4319293954","doi":"https://doi.org/10.1093/bioinformatics/btad076","title":"Patpat: a public proteomics dataset search framework","display_name":"Patpat: a public proteomics dataset search framework","publication_year":2023,"publication_date":"2023-02-01","ids":{"openalex":"https://openalex.org/W4319293954","doi":"https://doi.org/10.1093/bioinformatics/btad076","pmid":"https://pubmed.ncbi.nlm.nih.gov/36744907"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad076","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad076/49228301/btad076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad076/49228301/btad076.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046980898","display_name":"Weiheng Liao","orcid":"https://orcid.org/0000-0002-1230-4402"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiheng Liao","raw_affiliation_strings":["State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai 200438, China"],"raw_orcid":"https://orcid.org/0000-0002-1230-4402","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100780692","display_name":"Xuelian Zhang","orcid":"https://orcid.org/0000-0002-9006-6104"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xuelian Zhang","raw_affiliation_strings":["State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai 200438, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100780692"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00737783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"39","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9429000020027161,"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":0.9429000020027161,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.013100000098347664,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.005400000140070915,"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":0.7481277585029602},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.6941720843315125},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6506955623626709},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.6370823383331299},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.5344435572624207},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5113036632537842},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.44204816222190857},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.42405444383621216},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4013550579547882},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36591836810112},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32850778102874756},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3181137144565582},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2228439450263977},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08945629000663757},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06899696588516235}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7481277585029602},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6941720843315125},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6506955623626709},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6370823383331299},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.5344435572624207},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5113036632537842},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.44204816222190857},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.42405444383621216},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4013550579547882},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36591836810112},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32850778102874756},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3181137144565582},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2228439450263977},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08945629000663757},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06899696588516235},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","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":"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":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad076","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad076/49228301/btad076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:36744907","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36744907","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:9933831","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9933831","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9933831/pdf/btad076.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad076","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad076/49228301/btad076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G1075509014","display_name":null,"funder_award_id":"82273974","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7435997171","display_name":null,"funder_award_id":"81971898","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319293954.pdf"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2087481305","https://openalex.org/W2102018304","https://openalex.org/W2155443196","https://openalex.org/W2302501749","https://openalex.org/W2613847904","https://openalex.org/W2751436602","https://openalex.org/W2904043768","https://openalex.org/W2905906027","https://openalex.org/W2910730299","https://openalex.org/W2945048248","https://openalex.org/W2986041539","https://openalex.org/W3112376646","https://openalex.org/W3176586111","https://openalex.org/W3195891740","https://openalex.org/W3208691473","https://openalex.org/W6770119468"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2095118173","https://openalex.org/W2382021449","https://openalex.org/W2104269053","https://openalex.org/W2106424170","https://openalex.org/W2093262417","https://openalex.org/W2501188010","https://openalex.org/W2099969795","https://openalex.org/W2098192829"],"abstract_inverted_index":{"SUMMARY:":[0],"As":[1],"the":[2,14,18,73,100,114,121],"FAIR":[3],"(Findable,":[4],"Accessible,":[5],"Interoperable,":[6],"Reusable)":[7],"principles":[8],"have":[9,33],"become":[10],"widely":[11],"accepted":[12],"in":[13,72],"proteomics":[15,30,47,103],"field,":[16],"under":[17,113],"guidance":[19],"of":[20,70,80,102],"ProteomeXchange":[21],"and":[22,120,129],"The":[23,108],"Human":[24],"Proteome":[25],"Organization":[26],"Proteomics":[27],"Standards":[28],"Initiative,":[29],"public":[31,57],"databases":[32,63,85],"been":[34],"providing":[35],"Application":[36],"Programming":[37],"Interfaces":[38],"for":[39,55,96],"programmatic":[40],"access.":[41],"Based":[42],"on":[43,126],"generating":[44],"logic":[45],"from":[46,61,83],"data,":[48],"we":[49],"present":[50],"Patpat,":[51],"an":[52],"extensible":[53],"framework":[54,110],"searching":[56],"datasets,":[58,98],"merging":[59],"results":[60,82],"multiple":[62,84],"to":[64,88,93],"help":[65],"researchers":[66],"find":[67],"their":[68],"proteins":[69],"interest":[71],"vast":[74],"mass":[75],"spectrometry.":[76],"Patpat's":[77],"2D":[78],"strategy":[79],"combining":[81],"allows":[86],"users":[87],"provide":[89],"only":[90],"protein":[91],"identifiers":[92],"obtain":[94],"metadata":[95],"relevant":[97],"improving":[99],"'Findable'":[101],"data.":[104],"AVAILABILITY":[105],"AND":[106],"IMPLEMENTATION:":[107],"Patpat":[109],"is":[111,124,130],"released":[112],"Apache":[115],"2.0":[116],"license":[117],"open":[118],"source,":[119],"source":[122],"code":[123],"stored":[125],"GitHub":[127],"(https://github.com/henry-leo/Patpat)":[128],"freely":[131],"available.":[132],"SUPPLEMENTARY":[133],"INFORMATION:":[134],"Supplementary":[135],"data":[136],"are":[137],"available":[138],"at":[139],"Bioinformatics":[140],"online.":[141]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}