{"id":"https://openalex.org/W2120229676","doi":"https://doi.org/10.1093/bib/bbr067","title":"Interfaces to PeptideAtlas: a case study of standard data access systems","display_name":"Interfaces to PeptideAtlas: a case study of standard data access systems","publication_year":2011,"publication_date":"2011-11-22","ids":{"openalex":"https://openalex.org/W2120229676","doi":"https://doi.org/10.1093/bib/bbr067","mag":"2120229676","pmid":"https://pubmed.ncbi.nlm.nih.gov/22941959"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr067","pdf_url":"https://academic.oup.com/bib/article-pdf/13/5/615/1146643/bbr067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/13/5/615/1146643/bbr067.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005430904","display_name":"Sarah Killcoyne","orcid":"https://orcid.org/0000-0003-3686-6167"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. Killcoyne","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA 98109, USA","Institute for Systems Biology, Seattle, WA 98109,\u00a0USA"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA 98109,\u00a0USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031419414","display_name":"Jeremy Handcock","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Handcock","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030395140","display_name":"T. W. E. Robinson","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. Robinson","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070102563","display_name":"Eric W. Deutsch","orcid":"https://orcid.org/0000-0001-8732-0928"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. W. Deutsch","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5056677361","display_name":"John Boyle","orcid":"https://orcid.org/0000-0002-5378-5361"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Boyle","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5005430904"],"corresponding_institution_ids":["https://openalex.org/I3148997608"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.1577,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53389442,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"13","issue":"5","first_page":"615","last_page":"626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.996399998664856,"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":0.996399998664856,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9659000039100647,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9606999754905701,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7806941866874695},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6313363909721375},{"id":"https://openalex.org/keywords/data-access","display_name":"Data access","score":0.6178229451179504},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33372604846954346},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.31480419635772705}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7806941866874695},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6313363909721375},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.6178229451179504},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33372604846954346},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.31480419635772705}],"mesh":[{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbr067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr067","pdf_url":"https://academic.oup.com/bib/article-pdf/13/5/615/1146643/bbr067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22941959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22941959","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2750992","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3431717","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/bib/bbr067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr067","pdf_url":"https://academic.oup.com/bib/article-pdf/13/5/615/1146643/bbr067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.550000011920929}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120229676.pdf","grobid_xml":"https://content.openalex.org/works/W2120229676.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1649645444","https://openalex.org/W1963867594","https://openalex.org/W1978359960","https://openalex.org/W1979853788","https://openalex.org/W1981593008","https://openalex.org/W1982411844","https://openalex.org/W2007176869","https://openalex.org/W2025183726","https://openalex.org/W2026465178","https://openalex.org/W2039950901","https://openalex.org/W2084562402","https://openalex.org/W2096721473","https://openalex.org/W2104764521","https://openalex.org/W2106791611","https://openalex.org/W2112078820","https://openalex.org/W2112846847","https://openalex.org/W2130706354","https://openalex.org/W2131374480","https://openalex.org/W2145825942","https://openalex.org/W2146453000","https://openalex.org/W2159675211","https://openalex.org/W2159763003","https://openalex.org/W2160074540","https://openalex.org/W2161811833","https://openalex.org/W2402984354","https://openalex.org/W2559527235","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Access":[0,48,66],"to":[1,7,14,37,43,49,106,111,136,199],"public":[2,38],"data":[3,39,51,150],"sets":[4,52],"is":[5,53,245],"important":[6],"the":[8,25,87,145,149,152,186,217,220,225,249],"scientific":[9],"community":[10,146],"as":[11,24],"a":[12,41,57,62,80,90],"resource":[13],"develop":[15],"new":[16,20],"experiments":[17],"or":[18],"validate":[19],"data.":[21,47,115,138],"Projects":[22],"such":[23],"PeptideAtlas,":[26],"Ensembl":[27],"and":[28,40,61,82,98,113,124,126,154,175,189,205,243],"The":[29,213],"Cancer":[30],"Genome":[31],"Atlas":[32],"(TCGA)":[33],"offer":[34],"both":[35],"access":[36,112,135,141,148,167,250],"repository":[42,188],"share":[44,114],"their":[45,159,192],"own":[46],"these":[50,104],"often":[54],"provided":[55],"through":[56],"web":[58,63,70,119,170],"page":[59],"form":[60],"service":[64,120],"API.":[65],"technologies":[67,105,121],"based":[68,194],"on":[69,195,224],"protocols":[71],"(e.g.":[72,94,122,231],"http)":[73],"have":[74],"been":[75],"in":[76,133,151,216],"use":[77],"for":[78,89,158,169,191,210,230],"over":[79,129,185],"decade":[81],"are":[83,131,180,207,222],"widely":[84],"adopted":[85],"across":[86],"industry":[88],"variety":[91],"of":[92,219,240],"functions":[93],"search,":[95],"commercial":[96],"transactions,":[97],"social":[99],"media).":[100],"Each":[101],"architecture":[102],"adapts":[103],"provide":[107],"users":[108],"with":[109],"tools":[110],"Both":[116],"commonly":[117],"used":[118],"REST":[123],"SOAP),":[125],"custom-built":[127],"solutions":[128],"HTTP":[130],"utilized":[132],"providing":[134],"research":[137],"Providing":[139],"multiple":[140],"points":[142],"ensures":[143],"that":[144,237],"can":[147],"simplest":[153],"most":[155],"effective":[156],"manner":[157],"particular":[160],"needs.":[161],"This":[162,235],"article":[163],"examines":[164],"three":[165],"common":[166,198],"mechanisms":[168],"accessible":[171],"data:":[172],"BioMart,":[173,201],"caBIG,":[174],"Google":[176,202],"Data":[177,203],"Sources.":[178],"These":[179],"illustrated":[181],"by":[182],"implementing":[183],"each":[184,208,227],"PeptideAtlas":[187],"reviewed":[190],"suitability":[193],"specific":[196,241],"usages":[197],"research.":[200],"Sources,":[204],"caBIG":[206],"suitable":[209],"certain":[211],"uses.":[212],"tradeoffs":[214,244],"made":[215],"development":[218],"technology":[221],"dependent":[223],"uses":[226],"was":[228],"designed":[229],"security":[232],"versus":[233],"speed).":[234],"means":[236],"an":[238],"understanding":[239],"requirements":[242],"necessary":[246],"before":[247],"selecting":[248],"technology.":[251]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
