{"id":"https://openalex.org/W4205545771","doi":"https://doi.org/10.1093/bib/bbab510","title":"PhosPiR: an automated phosphoproteomic pipeline in R","display_name":"PhosPiR: an automated phosphoproteomic pipeline in R","publication_year":2021,"publication_date":"2021-11-25","ids":{"openalex":"https://openalex.org/W4205545771","doi":"https://doi.org/10.1093/bib/bbab510","pmid":"https://pubmed.ncbi.nlm.nih.gov/34882763"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab510","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab510","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab510/43308900/bbab510.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab510/43308900/bbab510.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103171219","display_name":"Ye Hong","orcid":"https://orcid.org/0000-0002-5014-5027"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ye Hong","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019095516","display_name":"Dani Flinkman","orcid":"https://orcid.org/0000-0002-3908-2467"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["FI","SE"],"is_corresponding":false,"raw_author_name":"Dani Flinkman","raw_affiliation_strings":["Lund University, Lund, Sweden","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-3908-2467","affiliations":[{"raw_affiliation_string":"Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082176570","display_name":"Tomi Suomi","orcid":"https://orcid.org/0000-0003-3639-979X"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tomi Suomi","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0003-3639-979X","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020796581","display_name":"Sami Pietil\u00e4","orcid":"https://orcid.org/0000-0002-3825-0967"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Sami Pietil\u00e4","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-3825-0967","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103060544","display_name":"Peter James","orcid":"https://orcid.org/0000-0002-7858-9754"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["FI","SE"],"is_corresponding":false,"raw_author_name":"Peter James","raw_affiliation_strings":["Lund University, Lund, Sweden","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063451537","display_name":"Eleanor T. Coffey","orcid":"https://orcid.org/0000-0002-9717-5610"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Eleanor Coffey","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-9717-5610","affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062339398","display_name":"Laura L. Elo","orcid":"https://orcid.org/0000-0001-5648-4532"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Laura L Elo","raw_affiliation_strings":["Institute of Biomedicine, University of Turku, Turku, Finland","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5063451537"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4061,"currency":"EUR","value_usd":4379},"fwci":0.8613,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.70703125,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"23","issue":"1","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":0.9998999834060669,"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":0.9998999834060669,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"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":0.769110381603241},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.7067421674728394},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7032104134559631},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5660295486450195},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.46896401047706604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44958144426345825},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4430678188800812},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4349236786365509},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26762327551841736},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17020565271377563},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1528463065624237}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.769110381603241},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.7067421674728394},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7032104134559631},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5660295486450195},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.46896401047706604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44958144426345825},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4430678188800812},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4349236786365509},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26762327551841736},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17020565271377563},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1528463065624237},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","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},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbab510","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab510","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab510/43308900/bbab510.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34882763","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34882763","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:pure.atira.dk:openaire/3cc01437-65ed-4307-9924-ac9bab641453","is_oa":true,"landing_page_url":"https://research.abo.fi/en/publications/3cc01437-65ed-4307-9924-ac9bab641453","pdf_url":null,"source":{"id":"https://openalex.org/S4406923060","display_name":"\u00c5bo Akademi University Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Hong, Y, Flinkman, D, Suomi, T, Pietil\u00e4, S, James, P, Coffey, E & Elo, L L 2022, 'PhosPiR: an automated phosphoproteomic pipeline in R', Briefings in Bioinformatics, vol. 23, no. 1. https://doi.org/10.1093/bib/bbab510","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:lup.lub.lu.se:d8ef8ce9-89e8-4dac-8c8d-18b3187b322b","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/d8ef8ce9-89e8-4dac-8c8d-18b3187b322b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1467-5463","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8787428","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8787428","pdf_url":null,"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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:www.utupub.fi:10024/162014","is_oa":true,"landing_page_url":"https://www.utupub.fi/handle/10024/162014","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"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":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbab510","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab510","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab510/43308900/bbab510.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1114563396","display_name":null,"funder_award_id":"1817/31/2015","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G263359668","display_name":null,"funder_award_id":"335611","funder_id":"https://openalex.org/F4320323313","funder_display_name":"Turun Yliopisto"},{"id":"https://openalex.org/G3848519979","display_name":null,"funder_award_id":"26080953","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4039138905","display_name":null,"funder_award_id":"310561","funder_id":"https://openalex.org/F4320323313","funder_display_name":"Turun Yliopisto"},{"id":"https://openalex.org/G4093835166","display_name":null,"funder_award_id":"1545/31/2019","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6810510297","display_name":null,"funder_award_id":"008489","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8705713743","display_name":null,"funder_award_id":"1817/31/2015","funder_id":"https://openalex.org/F4320328501","funder_display_name":"Business Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"},{"id":"https://openalex.org/F4320328139","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48"},{"id":"https://openalex.org/F4320328501","display_name":"Business Finland","ror":"https://ror.org/05bgf9v38"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4205545771.pdf"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W2013686278","https://openalex.org/W2015113576","https://openalex.org/W2017121383","https://openalex.org/W2018258930","https://openalex.org/W2020459598","https://openalex.org/W2035618305","https://openalex.org/W2045949302","https://openalex.org/W2055738212","https://openalex.org/W2080752012","https://openalex.org/W2091505779","https://openalex.org/W2107940314","https://openalex.org/W2128599926","https://openalex.org/W2131478115","https://openalex.org/W2140628770","https://openalex.org/W2153947402","https://openalex.org/W2157658519","https://openalex.org/W2171464043","https://openalex.org/W2254509181","https://openalex.org/W2346627954","https://openalex.org/W2549026759","https://openalex.org/W2611826771","https://openalex.org/W2617446144","https://openalex.org/W2738274199","https://openalex.org/W2785201697","https://openalex.org/W2900569176","https://openalex.org/W2903761629","https://openalex.org/W2904372598","https://openalex.org/W2951203650","https://openalex.org/W2970881020","https://openalex.org/W2979295684","https://openalex.org/W2995791842","https://openalex.org/W3005045932","https://openalex.org/W3006105182","https://openalex.org/W3006607037","https://openalex.org/W3101045033","https://openalex.org/W3174993126","https://openalex.org/W4254687493","https://openalex.org/W4386975223","https://openalex.org/W4399538195","https://openalex.org/W4399546757","https://openalex.org/W4399550252","https://openalex.org/W4399551981","https://openalex.org/W4399568367","https://openalex.org/W4399568835","https://openalex.org/W4399583953","https://openalex.org/W4399611870","https://openalex.org/W4399612221","https://openalex.org/W4399638189","https://openalex.org/W4399649329","https://openalex.org/W4399649500","https://openalex.org/W4399649898","https://openalex.org/W6773613593"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"Large-scale":[0],"phosphoproteome":[1],"profiling":[2],"using":[3],"mass":[4],"spectrometry":[5],"(MS)":[6],"provides":[7,77],"functional":[8],"insight":[9],"that":[10,34,49],"is":[11,26,122],"crucial":[12],"for":[13,38,135],"disease":[14],"biology":[15],"and":[16,69,91,101,104,118],"drug":[17],"discovery.":[18],"However,":[19],"extracting":[20],"biological":[21,57],"understanding":[22,58],"from":[23,59],"these":[24],"data":[25,41,62,78,81,127],"an":[27,46],"arduous":[28],"task":[29],"requiring":[30],"multiple":[31,83],"analysis":[32],"platforms":[33],"are":[35],"not":[36],"adapted":[37],"automated":[39],"high-dimensional":[40],"analysis.":[42,107],"Here,":[43],"we":[44],"introduce":[45],"integrated":[47],"pipeline":[48],"combines":[50],"several":[51],"R":[52],"packages":[53],"to":[54,124],"extract":[55],"high-level":[56],"large-scale":[60],"phosphoproteomic":[61],"by":[63],"seamless":[64],"integration":[65],"with":[66],"existing":[67],"databases":[68],"knowledge":[70],"resources.":[71],"In":[72],"a":[73,133],"single":[74],"run,":[75],"PhosPiR":[76],"clean-up,":[79],"fast":[80],"overview,":[82],"statistical":[84],"testing,":[85],"differential":[86],"expression":[87],"analysis,":[88],"phosphosite":[89],"annotation":[90],"translation":[92],"across":[93],"species,":[94],"multilevel":[95],"enrichment":[96],"analyses,":[97],"proteome-wide":[98,126],"kinase":[99],"activity":[100],"substrate":[102],"mapping":[103],"network":[105],"hub":[106],"Data":[108],"output":[109],"includes":[110],"graphical":[111],"formats":[112],"such":[113],"as":[114],"heatmap,":[115],"box-,":[116],"volcano-":[117],"circos-plots.":[119],"This":[120],"resource":[121],"designed":[123],"assist":[125],"mining":[128],"of":[129],"pathophysiological":[130],"mechanism":[131],"without":[132],"need":[134],"programming":[136],"knowledge.":[137]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}