{"id":"https://openalex.org/W4413381357","doi":"https://doi.org/10.3389/fbinf.2025.1634042","title":"DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics","display_name":"DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics","publication_year":2025,"publication_date":"2025-08-15","ids":{"openalex":"https://openalex.org/W4413381357","doi":"https://doi.org/10.3389/fbinf.2025.1634042","pmid":"https://pubmed.ncbi.nlm.nih.gov/40894377"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1634042","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1634042","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1634042/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1634042/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052016935","display_name":"Christopher D. Golden","orcid":"https://orcid.org/0000-0002-2258-7493"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher Golden","raw_affiliation_strings":["Medical Research Council Centre for Medical Mycology at the University of Exeter, Department of Biosciences, Faculty of Health and Life Sciences, Exeter, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Medical Research Council Centre for Medical Mycology at the University of Exeter, Department of Biosciences, Faculty of Health and Life Sciences, Exeter, United Kingdom","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072609421","display_name":"David J. Studholme","orcid":"https://orcid.org/0000-0002-3010-6637"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David J. Studholme","raw_affiliation_strings":["Biosciences, University of Exeter, Exeter, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Biosciences, University of Exeter, Exeter, United Kingdom","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080533196","display_name":"Rhys A. Farrer","orcid":"https://orcid.org/0000-0001-8456-7458"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Rhys A. Farrer","raw_affiliation_strings":["Medical Research Council Centre for Medical Mycology at the University of Exeter, Department of Biosciences, Faculty of Health and Life Sciences, Exeter, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Medical Research Council Centre for Medical Mycology at the University of Exeter, Department of Biosciences, Faculty of Health and Life Sciences, Exeter, United Kingdom","institution_ids":["https://openalex.org/I23923803"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080533196"],"corresponding_institution_ids":["https://openalex.org/I23923803"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18303265,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1634042","last_page":"1634042"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9984999895095825,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9976000189781189,"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":0.791976809501648},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.716997504234314},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.6395267844200134},{"id":"https://openalex.org/keywords/laptop","display_name":"Laptop","score":0.554783284664154},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.49422791600227356},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4801023304462433},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4704526960849762},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46242135763168335},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35777217149734497},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2959694266319275},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.27828994393348694},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.2630774974822998},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2001103162765503},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1703067123889923},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14565721154212952}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.791976809501648},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.716997504234314},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.6395267844200134},{"id":"https://openalex.org/C2780008327","wikidata":"https://www.wikidata.org/wiki/Q3962","display_name":"Laptop","level":2,"score":0.554783284664154},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.49422791600227356},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4801023304462433},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4704526960849762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46242135763168335},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35777217149734497},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2959694266319275},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.27828994393348694},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.2630774974822998},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2001103162765503},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1703067123889923},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14565721154212952},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1634042","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1634042","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1634042/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40894377","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40894377","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:06d4d86aca6049b284aa43b29b710661","is_oa":true,"landing_page_url":"https://doaj.org/article/06d4d86aca6049b284aa43b29b710661","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12394471","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12394471","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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1634042","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1634042","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1634042/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413381357.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1560020441","https://openalex.org/W1964895626","https://openalex.org/W2012361142","https://openalex.org/W2045204781","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2116423958","https://openalex.org/W2131229759","https://openalex.org/W2141545183","https://openalex.org/W2147526198","https://openalex.org/W2164154943","https://openalex.org/W2168909179","https://openalex.org/W2171815113","https://openalex.org/W2194609845","https://openalex.org/W2612812586","https://openalex.org/W2947780575","https://openalex.org/W2949841808","https://openalex.org/W2951731136","https://openalex.org/W2952218450","https://openalex.org/W2973232653","https://openalex.org/W2989608901","https://openalex.org/W3209545809","https://openalex.org/W4213149192","https://openalex.org/W4225769528","https://openalex.org/W4294216483","https://openalex.org/W4313528741","https://openalex.org/W4323036511","https://openalex.org/W4409448590"],"related_works":["https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W2009940763","https://openalex.org/W4386637333","https://openalex.org/W2946410450","https://openalex.org/W4361192415","https://openalex.org/W2126804125","https://openalex.org/W2162782320","https://openalex.org/W2137318037","https://openalex.org/W1760213857"],"abstract_inverted_index":{"DIAMOND2GO":[0],"(D2GO)":[1],"is":[2,28,153],"a":[3,81],"high-speed":[4],"toolset":[5],"for":[6],"assigning":[7],"Gene":[8],"Ontology":[9],"(GO)":[10],"terms":[11,47,67,102],"to":[12,30,56,68,86,97],"genes":[13],"or":[14],"proteins":[15],"based":[16],"on":[17,80],"sequence":[18],"similarity.":[19],"Leveraging":[20],"the":[21,52,123,159],"ultra-fast":[22],"alignment":[23],"capabilities":[24],"of":[25,41,70,105,127],"DIAMOND,":[26],"which":[27],"100":[29],"20,000":[31],"times":[32],"faster":[33],"than":[34],"BLAST,":[35],"D2GO":[36,44,61,88,109,152],"enables":[37],"rapid":[38],"functional":[39],"annotation":[40,150],"large-scale":[42],"datasets.":[43],"maps":[45],"GO":[46,66,101],"from":[48],"pre-annotated":[49],"sequences":[50],"in":[51,76,122,145],"NCBI":[53],"non-redundant":[54],"database":[55],"query":[57],"sequences.":[58,106],"During":[59],"benchmarking,":[60],"assigned":[62],"over":[63],"2":[64],"million":[65],"98%":[69],"130,184":[71],"predicted":[72],"human":[73],"protein":[74],"isoforms":[75],"under":[77,158],"13":[78],"min":[79],"standard":[82],"laptop.":[83],"In":[84],"addition":[85],"annotation,":[87],"includes":[89],"an":[90],"enrichment":[91],"analysis":[92],"tool":[93],"that":[94,141],"allows":[95],"users":[96],"identify":[98],"significantly":[99],"overrepresented":[100],"between":[103],"subsets":[104],"We":[107],"compared":[108],"against":[110],"two":[111],"widely":[112],"used":[113],"tools,":[114],"Blast2GO":[115],"and":[116,118,125,135,139,155],"eggNOG-mapper,":[117],"observed":[119],"substantial":[120],"differences":[121],"number":[124],"type":[126],"annotations":[128],"produced.":[129],"These":[130],"discrepancies":[131],"reflect":[132],"varying":[133],"sensitivities":[134],"specificities":[136],"across":[137],"tools":[138],"suggest":[140],"using":[142],"multiple":[143],"methods":[144],"tandem":[146],"may":[147],"improve":[148],"overall":[149],"coverage.":[151],"open-source":[154],"freely":[156],"available":[157],"MIT":[160],"license":[161],"at":[162],"https://github.com/rhysf/DIAMOND2GO.":[163]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
