{"id":"https://openalex.org/W2102344709","doi":"https://doi.org/10.1093/nar/gku1152","title":"MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data","display_name":"MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data","publication_year":2014,"publication_date":"2014-11-14","ids":{"openalex":"https://openalex.org/W2102344709","doi":"https://doi.org/10.1093/nar/gku1152","mag":"2102344709","pmid":"https://pubmed.ncbi.nlm.nih.gov/25398900"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku1152","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1152","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D270/7321394/gku1152.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/43/D1/D270/7321394/gku1152.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009003438","display_name":"Ikuo Uchiyama","orcid":"https://orcid.org/0000-0002-9197-5000"},"institutions":[{"id":"https://openalex.org/I138804964","display_name":"National Institute for Basic Biology","ror":"https://ror.org/05q8wtt20","country_code":"JP","type":"education","lineage":["https://openalex.org/I1319490839","https://openalex.org/I138804964","https://openalex.org/I199525922"]},{"id":"https://openalex.org/I199525922","display_name":"National Institutes of Natural Sciences","ror":"https://ror.org/055n47h92","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I199525922"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ikuo Uchiyama","raw_affiliation_strings":["Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan uchiyama@nibb.ac.jp","Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan","Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan uchiyama@nibb.ac.jp","institution_ids":[]},{"raw_affiliation_string":"Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan","institution_ids":["https://openalex.org/I199525922","https://openalex.org/I138804964"]},{"raw_affiliation_string":"Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan","institution_ids":["https://openalex.org/I199525922","https://openalex.org/I138804964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108854416","display_name":"Motohiro Mihara","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Motohiro Mihara","raw_affiliation_strings":["Dynacom Co., Ltd. 5-1-27, Onoedori, Chuo-ku, Kobe, Hyogo 651-0088, Japan"],"affiliations":[{"raw_affiliation_string":"Dynacom Co., Ltd. 5-1-27, Onoedori, Chuo-ku, Kobe, Hyogo 651-0088, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003691395","display_name":"Hiroyo Nishide","orcid":null},"institutions":[{"id":"https://openalex.org/I199525922","display_name":"National Institutes of Natural Sciences","ror":"https://ror.org/055n47h92","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I199525922"]},{"id":"https://openalex.org/I138804964","display_name":"National Institute for Basic Biology","ror":"https://ror.org/05q8wtt20","country_code":"JP","type":"education","lineage":["https://openalex.org/I1319490839","https://openalex.org/I138804964","https://openalex.org/I199525922"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroyo Nishide","raw_affiliation_strings":["Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan"],"affiliations":[{"raw_affiliation_string":"Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan","institution_ids":["https://openalex.org/I199525922","https://openalex.org/I138804964"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059383385","display_name":"Hirokazu Chiba","orcid":"https://orcid.org/0000-0003-4062-8903"},"institutions":[{"id":"https://openalex.org/I199525922","display_name":"National Institutes of Natural Sciences","ror":"https://ror.org/055n47h92","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I199525922"]},{"id":"https://openalex.org/I138804964","display_name":"National Institute for Basic Biology","ror":"https://ror.org/05q8wtt20","country_code":"JP","type":"education","lineage":["https://openalex.org/I1319490839","https://openalex.org/I138804964","https://openalex.org/I199525922"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hirokazu Chiba","raw_affiliation_strings":["Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan","institution_ids":["https://openalex.org/I199525922","https://openalex.org/I138804964"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5009003438"],"corresponding_institution_ids":["https://openalex.org/I138804964","https://openalex.org/I199525922"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.8428,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.94295864,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"43","issue":"D1","first_page":"D270","last_page":"D276"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic 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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic 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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9958000183105469,"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/T10257","display_name":"Oral microbiology and periodontitis research","score":0.9789999723434448,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8407180309295654},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7969365119934082},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5601387023925781},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.5106719136238098},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5092088580131531},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43739351630210876},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.43665629625320435},{"id":"https://openalex.org/keywords/personal-genomics","display_name":"Personal genomics","score":0.41476112604141235},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31705012917518616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.15835347771644592}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8407180309295654},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7969365119934082},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5601387023925781},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5106719136238098},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5092088580131531},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43739351630210876},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.43665629625320435},{"id":"https://openalex.org/C24103923","wikidata":"https://www.wikidata.org/wiki/Q7170583","display_name":"Personal genomics","level":5,"score":0.41476112604141235},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31705012917518616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.15835347771644592},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gku1152","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1152","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D270/7321394/gku1152.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:25398900","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25398900","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:3354899","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4383954","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gku1152","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1152","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D270/7321394/gku1152.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102344709.pdf","grobid_xml":"https://content.openalex.org/works/W2102344709.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1865899696","https://openalex.org/W1976325156","https://openalex.org/W1995281225","https://openalex.org/W1995618926","https://openalex.org/W1997272729","https://openalex.org/W2018345907","https://openalex.org/W2025020367","https://openalex.org/W2030308218","https://openalex.org/W2048448217","https://openalex.org/W2098533519","https://openalex.org/W2106044656","https://openalex.org/W2107644675","https://openalex.org/W2117280851","https://openalex.org/W2120172561","https://openalex.org/W2121270211","https://openalex.org/W2121776973","https://openalex.org/W2133790733","https://openalex.org/W2149023499","https://openalex.org/W2164078810","https://openalex.org/W2165335121","https://openalex.org/W2165627817","https://openalex.org/W4247927165"],"related_works":["https://openalex.org/W2414506155","https://openalex.org/W2099543256","https://openalex.org/W2752117239","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2170130581","https://openalex.org/W2353729507","https://openalex.org/W4318240630","https://openalex.org/W2560359598","https://openalex.org/W1565527690"],"abstract_inverted_index":{"The":[0],"microbial":[1,21,45],"genome":[2,46,87,93,108,130,144],"database":[3,15,121],"for":[4,16,89,194],"comparative":[5,18],"analysis":[6,19],"(MBGD)":[7],"(available":[8],"at":[9],"http://mbgd.genome.ad.jp/)":[10],"is":[11,176,185],"a":[12,118,190],"comprehensive":[13],"ortholog":[14,31,120,137,168],"flexible":[17],"of":[20,37,40,79,95],"genomes,":[22,174],"where":[23],"the":[24,41,50,65,69,80,96,112,123,142,166,172,180],"users":[25,66,113],"are":[26,85,102,132],"allowed":[27],"to":[28,49,58,67,114,150,161],"create":[29],"an":[30,75,135,147],"table":[32,138,169],"among":[33],"any":[34],"specified":[35],"set":[36],"organisms.":[38],"Because":[39,77],"rapid":[42,181],"increase":[43],"in":[44,146],"data":[47,72,84,109,131,145,154],"owing":[48],"next-generation":[51],"sequencing":[52],"technology,":[53],"it":[54],"becomes":[55],"increasingly":[56],"challenging":[57],"maintain":[59],"high-quality":[60,163],"orthology":[61,164],"relationships":[62],"while":[63],"allowing":[64],"incorporate":[68,115],"latest":[70],"genomic":[71,83],"available":[73],"into":[74,117,134],"analysis.":[76],"many":[78],"recently":[81,191],"accumulating":[82],"draft":[86,107,129,153],"sequences":[88,94],"which":[90,175],"some":[91],"complete":[92,143],"same":[97],"or":[98],"closely":[99],"related":[100],"species":[101],"available,":[103],"MBGD":[104],"now":[105,186],"stores":[106],"and":[110],"allows":[111],"them":[116],"user-specific":[119],"using":[122,188,198],"MyMBGD":[124],"functionality.":[125],"In":[126,159],"this":[127],"function,":[128],"incorporated":[133],"existing":[136],"created":[139,178],"only":[140],"from":[141,155],"incremental":[148],"manner":[149],"prevent":[151],"low-quality":[152],"affecting":[156],"clustering":[157,197],"results.":[158],"addition,":[160],"provide":[162],"relationships,":[165],"standard":[167],"containing":[170],"all":[171],"representative":[173],"first":[177],"by":[179],"classification":[182],"program":[183,193],"DomClust,":[184],"refined":[187],"DomRefine,":[189],"developed":[192],"improving":[195],"domain-level":[196],"multiple":[199],"sequence":[200],"alignment":[201],"information.":[202]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":8}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}