{"id":"https://openalex.org/W2101521159","doi":"https://doi.org/10.1093/bioinformatics/btk015","title":"ProteomeCommons.org JAF: reference information and tools for proteomics","display_name":"ProteomeCommons.org JAF: reference information and tools for proteomics","publication_year":2006,"publication_date":"2006-01-24","ids":{"openalex":"https://openalex.org/W2101521159","doi":"https://doi.org/10.1093/bioinformatics/btk015","mag":"2101521159","pmid":"https://pubmed.ncbi.nlm.nih.gov/16434446"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btk015","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk015","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085599423","display_name":"Jayson Falkner","orcid":"https://orcid.org/0000-0001-7755-0877"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. A. Falkner","raw_affiliation_strings":["Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108411848","display_name":"J. W. Falkner","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. W. Falkner","raw_affiliation_strings":["Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087472859","display_name":"Philip Andrews","orcid":"https://orcid.org/0000-0001-6843-5420"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. C. Andrews","raw_affiliation_strings":["Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan \u00a0 Ann Arbor, MI 48104, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department Biological Chemistry, University of Michigan Ann Arbor, MI 48104, USA#TAB#","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087472859"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.8168,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.69513372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"22","issue":"5","first_page":"632","last_page":"633"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9304999709129333,"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":0.9304999709129333,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.028699999675154686,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00279999990016222,"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/java","display_name":"Java","score":0.8093423843383789},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.7286257147789001},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7123842239379883},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6488310098648071},{"id":"https://openalex.org/keywords/usable","display_name":"USable","score":0.5768818855285645},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4433678984642029},{"id":"https://openalex.org/keywords/web-browser","display_name":"Web browser","score":0.4234333634376526},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3877374529838562},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3596533536911011},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.26094764471054077},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20019888877868652},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.10324046015739441},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07126837968826294}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.8093423843383789},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.7286257147789001},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7123842239379883},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6488310098648071},{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.5768818855285645},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4433678984642029},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.4234333634376526},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3877374529838562},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3596533536911011},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26094764471054077},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20019888877868652},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.10324046015739441},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07126837968826294},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"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":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btk015","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk015","pdf_url":null,"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:16434446","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16434446","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1243817797","display_name":null,"funder_award_id":"P41RR018627","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1981593008","https://openalex.org/W1982362308","https://openalex.org/W2031095666","https://openalex.org/W2072837612","https://openalex.org/W2122877379","https://openalex.org/W2130706354","https://openalex.org/W2152195293","https://openalex.org/W2166041923"],"related_works":["https://openalex.org/W2528467228","https://openalex.org/W270927586","https://openalex.org/W1575927706","https://openalex.org/W2776291041","https://openalex.org/W2461178623","https://openalex.org/W2377966044","https://openalex.org/W2105803236","https://openalex.org/W3089977198","https://openalex.org/W2756936010","https://openalex.org/W2101521159"],"abstract_inverted_index":{"SUMMARY:":[0],"Analysis":[1,47,105],"of":[2,13,25,30,58,64,72,98,102],"proteomics":[3,51,73],"data,":[4,8,67],"specifically":[5],"mass":[6],"spectrometry":[7],"commonly":[9],"relies":[10],"on":[11],"libraries":[12],"known":[14,20,31,41],"information":[15],"such":[16],"as":[17],"atomic":[18,23],"masses,":[19],"stable":[21],"isotopes,":[22],"compositions":[24],"amino":[26,32,42],"acids,":[27],"observed":[28],"modifications":[29],"acids":[33],"and":[34,95],"ion":[35],"masses":[36],"that":[37,61,82],"directly":[38,86],"correspond":[39],"to":[40],"acid":[43],"sequences.":[44],"The":[45,75,92],"Java":[46,59,104],"Framework":[48,106],"(JAF)":[49],"for":[50,107],"provides":[52],"a":[53,88],"freely":[54,110],"usable,":[55],"open-source":[56],"library":[57],"code":[60],"abstracts":[62],"all":[63,99],"the":[65,103],"aforementioned":[66],"enabling":[68],"more":[69],"rapid":[70],"development":[71],"tools.":[74],"JAF":[76],"also":[77],"includes":[78],"several":[79],"user":[80],"tools":[81],"can":[83],"be":[84],"run":[85],"from":[87],"web":[89],"browser.":[90],"AVAILABILITY:":[91],"current":[93],"version":[94],"an":[96],"archive":[97],"older":[100],"versions":[101],"Proteomics":[108],"is":[109],"available,":[111],"including":[112],"complete":[113],"source-code,":[114],"at":[115],"http://www.proteomecommons.org/current/511/.":[116]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
