{"id":"https://openalex.org/W4385246048","doi":"https://doi.org/10.1093/bioinformatics/btad455","title":"ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0\u2014an improved Bayesian-based method for the annotation of LC\u2013MS/MS untargeted metabolomics data","display_name":"ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0\u2014an improved Bayesian-based method for the annotation of LC\u2013MS/MS untargeted metabolomics data","publication_year":2023,"publication_date":"2023-07-01","ids":{"openalex":"https://openalex.org/W4385246048","doi":"https://doi.org/10.1093/bioinformatics/btad455","pmid":"https://pubmed.ncbi.nlm.nih.gov/37490466"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad455","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btad455","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054836720","display_name":"Francesco Del Carratore","orcid":"https://orcid.org/0000-0003-1647-7818"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Francesco Del Carratore","raw_affiliation_strings":["Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom","Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom","institution_ids":["https://openalex.org/I146655781"]},{"raw_affiliation_string":"Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092539758","display_name":"William Eagles","orcid":"https://orcid.org/0009-0006-9956-0404"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"William Eagles","raw_affiliation_strings":["Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111907412","display_name":"J. Borka","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Juraj Borka","raw_affiliation_strings":["Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070145336","display_name":"Rainer Breitling","orcid":"https://orcid.org/0000-0001-7173-0922"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rainer Breitling","raw_affiliation_strings":["Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester , Manchester M1 7DN, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054836720"],"corresponding_institution_ids":["https://openalex.org/I146655781","https://openalex.org/I28407311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7879,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73242152,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":1.0,"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/T12073","display_name":"Isotope Analysis in Ecology","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11667","display_name":"Advanced Chemical Sensor Technologies","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8760942816734314},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7528257369995117},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6744059324264526},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5805410742759705},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.544738233089447},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.511949896812439},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.47976359724998474},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4792780578136444},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45500844717025757},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.4515012800693512},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.44652724266052246},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4121074974536896},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.39431461691856384},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22594806551933289},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16587671637535095},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12218862771987915},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07878836989402771},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0782579779624939}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8760942816734314},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7528257369995117},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6744059324264526},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5805410742759705},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.544738233089447},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.511949896812439},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47976359724998474},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4792780578136444},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45500844717025757},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.4515012800693512},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.44652724266052246},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4121074974536896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.39431461691856384},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22594806551933289},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16587671637535095},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12218862771987915},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07878836989402771},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0782579779624939},{"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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D053719","descriptor_name":"Tandem Mass Spectrometry","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":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad455","pdf_url":null,"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:37490466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37490466","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:pure.atira.dk:openaire/aef61174-a28b-4bb2-9830-f5b661ac2ae9","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/aef61174-a28b-4bb2-9830-f5b661ac2ae9","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Del Carratore, F, Eagles, W, Borka, J & Breitling, R 2023, 'ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0 \u2013 an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data.', Bioinformatics (Oxford, England), vol. 39, no. 7, btad455. https://doi.org/10.1093/bioinformatics/btad455","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:10382385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10382385","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10382385/pdf/btad455.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btad455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad455","pdf_url":null,"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":[],"awards":[{"id":"https://openalex.org/G1238207083","display_name":null,"funder_award_id":"NE/T010959/1","funder_id":"https://openalex.org/F4320320022","funder_display_name":"Sight Research UK"},{"id":"https://openalex.org/G6059269786","display_name":null,"funder_award_id":"NE/T010959/1","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G6884767947","display_name":null,"funder_award_id":"NE/T010959/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"}],"funders":[{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320320022","display_name":"Sight Research UK","ror":"https://ror.org/03z2py885"},{"id":"https://openalex.org/F4320334631","display_name":"Natural Environment Research Council","ror":"https://ror.org/02b5d8509"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W143096088","https://openalex.org/W1964010911","https://openalex.org/W2082706597","https://openalex.org/W2559588208","https://openalex.org/W2902454325","https://openalex.org/W2972554015","https://openalex.org/W3013979697","https://openalex.org/W3181660183","https://openalex.org/W3210489033","https://openalex.org/W3210957482","https://openalex.org/W4220718053","https://openalex.org/W4308449887"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4386463918","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W2789551765","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4226320247"],"abstract_inverted_index":{"The":[0],"source":[1],"code,":[2],"extensive":[3],"documentation,":[4],"and":[5],"tutorials":[6],"are":[7],"freely":[8],"available":[9],"on":[10],"GitHub":[11],"at":[12],"https://github.com/francescodc87/ipaPy2.":[13]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
