{"id":"https://openalex.org/W2801106948","doi":"https://doi.org/10.1093/bioinformatics/bty368","title":"Improved enzyme annotation with EC-specific cutoffs using DETECT v2","display_name":"Improved enzyme annotation with EC-specific cutoffs using DETECT v2","publication_year":2018,"publication_date":"2018-05-01","ids":{"openalex":"https://openalex.org/W2801106948","doi":"https://doi.org/10.1093/bioinformatics/bty368","mag":"2801106948","pmid":"https://pubmed.ncbi.nlm.nih.gov/29722785"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty368","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/19/3393/25839639/bty368.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/19/3393/25839639/bty368.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043745601","display_name":"Nirvana Nursimulu","orcid":"https://orcid.org/0000-0001-5962-5863"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nirvana Nursimulu","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, ON, Canada","Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073701275","display_name":"Leon L. Xu","orcid":"https://orcid.org/0000-0001-5604-0237"},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Leon L Xu","raw_affiliation_strings":["Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064980480","display_name":"James D. Wasmuth","orcid":"https://orcid.org/0000-0002-9516-212X"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"James D Wasmuth","raw_affiliation_strings":["Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058736516","display_name":"Ivan Krukov","orcid":null},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ivan Krukov","raw_affiliation_strings":["Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085182984","display_name":"John Parkinson","orcid":"https://orcid.org/0000-0001-9815-1189"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"John Parkinson","raw_affiliation_strings":["Department of Biochemistry, University of Toronto, Toronto, ON, Canada","Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada","Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Program in Molecular Medicine, The Hospital for Sick Children, 21\u20139709 PGCRL, 686 Bay Street, Toronto, ON, Canada","institution_ids":["https://openalex.org/I2801317318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5085182984"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2801317318"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9279,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.73980661,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"34","issue":"19","first_page":"3393","last_page":"3395"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.30320000648498535,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.30320000648498535,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.125,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.09120000153779984,"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/annotation","display_name":"Annotation","score":0.8088750839233398},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5445282459259033},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4651105999946594},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2969452738761902},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22906166315078735},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.19597983360290527}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8088750839233398},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5445282459259033},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4651105999946594},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2969452738761902},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22906166315078735},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19597983360290527}],"mesh":[{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty368","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/19/3393/25839639/bty368.pdf","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:29722785","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29722785","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:6157075","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6157075","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty368","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/19/3393/25839639/bty368.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2471364152","display_name":null,"funder_award_id":"R21 AI126466","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4282778401","display_name":null,"funder_award_id":"R21AI126466","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5323500438","display_name":null,"funder_award_id":"RGPIN-2014-06664","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320314607","display_name":"Government of Ontario","ror":"https://ror.org/015pzp858"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1973519389","https://openalex.org/W1991716330","https://openalex.org/W2018872784","https://openalex.org/W2044935306","https://openalex.org/W2055043387","https://openalex.org/W2110256992","https://openalex.org/W2111693807","https://openalex.org/W2111973517","https://openalex.org/W2202347610","https://openalex.org/W2606882994","https://openalex.org/W2765384588"],"related_works":["https://openalex.org/W2748952813","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"],"abstract_inverted_index":{"Summary:":[0],"We":[1],"present":[2],"DETECT":[3],"v2-an":[4],"enzyme":[5,34],"annotation":[6],"tool":[7],"which":[8],"considers":[9],"the":[10,37,58],"effect":[11],"of":[12,51,60],"sequence":[13],"diversity":[14],"when":[15],"assigning":[16],"enzymatic":[17],"function":[18],"[as":[19],"an":[20],"Enzyme":[21],"Commission":[22],"(EC)":[23],"number]":[24],"to":[25,31],"a":[26],"protein":[27],"sequence.":[28],"In":[29],"addition":[30],"capturing":[32],"more":[33],"classes":[35],"than":[36],"previous":[38],"version,":[39],"we":[40],"now":[41],"provide":[42],"EC-specific":[43],"cutoffs":[44],"that":[45],"greatly":[46],"increase":[47],"precision":[48],"and":[49,53,63],"recall":[50],"assignments":[52],"show":[54],"its":[55],"performance":[56],"in":[57],"context":[59],"pathways.":[61],"Availability":[62],"implementation:":[64],"https://github.com/ParkinsonLab/DETECT-v2.":[65],"Supplementary":[66,68],"information:":[67],"data":[69],"are":[70],"available":[71],"at":[72],"Bioinformatics":[73],"online.":[74]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
