{"id":"https://openalex.org/W2099626126","doi":"https://doi.org/10.1093/nar/gkj094","title":"The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information","display_name":"The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2099626126","doi":"https://doi.org/10.1093/nar/gkj094","mag":"2099626126","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381971"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj094","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D741/3925300/gkj094.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","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/34/suppl_1/D741/3925300/gkj094.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111891593","display_name":"Hajime Ohyanagi","orcid":null},"institutions":[{"id":"https://openalex.org/I47232531","display_name":"Bank of Japan","ror":"https://ror.org/04zmdqe71","country_code":"JP","type":"other","lineage":["https://openalex.org/I47232531"]},{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"H. Ohyanagi","raw_affiliation_strings":["Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan"],"affiliations":[{"raw_affiliation_string":"Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan","institution_ids":["https://openalex.org/I4210158934","https://openalex.org/I47232531","https://openalex.org/I113198587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5111891593"],"corresponding_institution_ids":["https://openalex.org/I113198587","https://openalex.org/I4210158934","https://openalex.org/I47232531"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":8.4818,"has_fulltext":true,"cited_by_count":242,"citation_normalized_percentile":{"value":0.98529478,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"34","issue":"90001","first_page":"D741","last_page":"D744"},"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9962000250816345,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.918708086013794},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7929261922836304},{"id":"https://openalex.org/keywords/oryza-sativa","display_name":"Oryza sativa","score":0.7733315825462341},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7320530414581299},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6614106893539429},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.6335358023643494},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.6319142580032349},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.6228079795837402},{"id":"https://openalex.org/keywords/japonica","display_name":"Japonica","score":0.41877979040145874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4041852056980133},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.39421507716178894},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36808866262435913},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3068762421607971},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.18039187788963318},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.1069459617137909}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.918708086013794},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7929261922836304},{"id":"https://openalex.org/C2778543611","wikidata":"https://www.wikidata.org/wiki/Q161426","display_name":"Oryza sativa","level":3,"score":0.7733315825462341},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7320530414581299},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6614106893539429},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.6335358023643494},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.6319142580032349},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.6228079795837402},{"id":"https://openalex.org/C2779409272","wikidata":"https://www.wikidata.org/wiki/Q1757789","display_name":"Japonica","level":2,"score":0.41877979040145874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4041852056980133},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.39421507716178894},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36808866262435913},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3068762421607971},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.18039187788963318},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.1069459617137909}],"mesh":[{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkj094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj094","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D741/3925300/gkj094.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381971","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381971","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:156899","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347456","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347456","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347456","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj094","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D741/3925300/gkj094.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G7693551792","display_name":null,"funder_award_id":"(MEXT)","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099626126.pdf","grobid_xml":"https://content.openalex.org/works/W2099626126.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2070387787","https://openalex.org/W2091545495","https://openalex.org/W2099275700","https://openalex.org/W2118556605","https://openalex.org/W2126764689","https://openalex.org/W2136145671","https://openalex.org/W2145477956","https://openalex.org/W2158304452","https://openalex.org/W2158714788","https://openalex.org/W2167272207","https://openalex.org/W2175948239","https://openalex.org/W4293196852","https://openalex.org/W6799492631"],"related_works":["https://openalex.org/W2984770644","https://openalex.org/W2358634658","https://openalex.org/W4241308152","https://openalex.org/W3034139913","https://openalex.org/W3111061871","https://openalex.org/W2979252419","https://openalex.org/W2099626126","https://openalex.org/W4309908782","https://openalex.org/W2311275990","https://openalex.org/W2034579486"],"abstract_inverted_index":{"With":[0],"the":[1,4,15,18,27,43,51,54,60,74,96,111,122],"completion":[2],"of":[3,29,45,83,121],"rice":[5,30,55,100,118],"genome":[6,19],"sequencing,":[7],"a":[8,115],"standardized":[9],"annotation":[10,36,75,84],"is":[11],"necessary":[12],"so":[13],"that":[14],"information":[16],"from":[17],"sequence":[20],"can":[21,124],"be":[22,125],"fully":[23],"utilized":[24],"in":[25,40,53],"understanding":[26],"biology":[28],"and":[31,47,87,90,107],"other":[32,91,99],"cereal":[33],"crops.":[34],"An":[35],"jamboree":[37],"was":[38],"held":[39],"Japan":[41],"with":[42],"aim":[44],"annotating":[46],"manually":[48],"curating":[49],"all":[50],"genes":[52],"genome.":[56],"Here":[57],"we":[58],"present":[59],"Rice":[61],"Annotation":[62],"Project":[63],"Database":[64],"(RAP-DB),":[65],"which":[66],"has":[67,79],"been":[68],"developed":[69],"to":[70,73,98],"provide":[71],"access":[72],"data.":[76],"The":[77],"RAP-DB":[78,112],"two":[80],"different":[81],"types":[82],"viewers,":[85],"BLAST":[86],"BLAT":[88],"search,":[89],"useful":[92],"features.":[93],"By":[94],"connecting":[95],"annotations":[97],"genomics":[101],"data,":[102],"such":[103],"as":[104,114],"full-length":[105],"cDNAs":[106],"Tos17":[108],"mutant":[109],"lines,":[110],"serves":[113],"hub":[116],"for":[117],"genomics.":[119],"All":[120],"resources":[123],"accessed":[126],"through":[127],"http://rapdb.lab.nig.ac.jp/.":[128]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":12}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
