{"id":"https://openalex.org/W2140450495","doi":"https://doi.org/10.1093/nar/gkj055","title":"ChloroplastDB: the Chloroplast Genome Database","display_name":"ChloroplastDB: the Chloroplast Genome Database","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2140450495","doi":"https://doi.org/10.1093/nar/gkj055","mag":"2140450495","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381961"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj055","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj055","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D692/3924523/gkj055.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/D692/3924523/gkj055.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005484398","display_name":"Liwang Cui","orcid":"https://orcid.org/0000-0002-8338-1974"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"L. Cui","raw_affiliation_strings":["Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5005484398"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.5191,"has_fulltext":true,"cited_by_count":98,"citation_normalized_percentile":{"value":0.81481176,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"90001","first_page":"D692","last_page":"D696"},"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/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9993000030517578,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9958000183105469,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8218733072280884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8157408833503723},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6420878171920776},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.5975418090820312},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5814657807350159},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.4566470980644226},{"id":"https://openalex.org/keywords/gene-density","display_name":"Gene density","score":0.4349173307418823},{"id":"https://openalex.org/keywords/orthologous-gene","display_name":"Orthologous Gene","score":0.4294106960296631},{"id":"https://openalex.org/keywords/chloroplast-dna","display_name":"Chloroplast DNA","score":0.4289635121822357},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.41131591796875},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36374223232269287},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.05943107604980469}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8218733072280884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8157408833503723},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6420878171920776},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.5975418090820312},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5814657807350159},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4566470980644226},{"id":"https://openalex.org/C163096569","wikidata":"https://www.wikidata.org/wiki/Q16966366","display_name":"Gene density","level":5,"score":0.4349173307418823},{"id":"https://openalex.org/C2909108991","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Orthologous Gene","level":4,"score":0.4294106960296631},{"id":"https://openalex.org/C48050816","wikidata":"https://www.wikidata.org/wiki/Q3182853","display_name":"Chloroplast DNA","level":4,"score":0.4289635121822357},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.41131591796875},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36374223232269287},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.05943107604980469}],"mesh":[{"descriptor_ui":"D002736","descriptor_name":"Chloroplasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002736","descriptor_name":"Chloroplasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002736","descriptor_name":"Chloroplasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkj055","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj055","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D692/3924523/gkj055.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381961","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381961","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:156876","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347418","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:1347418","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347418","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/gkj055","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj055","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D692/3924523/gkj055.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"},{"id":"https://openalex.org/F4320337400","display_name":"Division of Environmental Biology","ror":"https://ror.org/03g87he71"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140450495.pdf","grobid_xml":"https://content.openalex.org/works/W2140450495.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W8169164","https://openalex.org/W1250509468","https://openalex.org/W1502417695","https://openalex.org/W1552810186","https://openalex.org/W1579785391","https://openalex.org/W1979514850","https://openalex.org/W1986754151","https://openalex.org/W1992096255","https://openalex.org/W1993591260","https://openalex.org/W1993977643","https://openalex.org/W1998053020","https://openalex.org/W2030467655","https://openalex.org/W2030725911","https://openalex.org/W2059017036","https://openalex.org/W2060478681","https://openalex.org/W2062233253","https://openalex.org/W2083455511","https://openalex.org/W2090083319","https://openalex.org/W2096778187","https://openalex.org/W2097458080","https://openalex.org/W2098902420","https://openalex.org/W2103995327","https://openalex.org/W2110245550","https://openalex.org/W2114671632","https://openalex.org/W2120769212","https://openalex.org/W2141133532","https://openalex.org/W2147096538","https://openalex.org/W2148607481","https://openalex.org/W2150948320","https://openalex.org/W2161192208","https://openalex.org/W2164409449","https://openalex.org/W2169358467","https://openalex.org/W2507014810","https://openalex.org/W4242931187","https://openalex.org/W4252962943"],"related_works":["https://openalex.org/W1969895229","https://openalex.org/W2050040807","https://openalex.org/W2136509799","https://openalex.org/W2079089319","https://openalex.org/W1496946958","https://openalex.org/W2097758894","https://openalex.org/W2108497208","https://openalex.org/W2116252454","https://openalex.org/W2008856488","https://openalex.org/W2794385641"],"abstract_inverted_index":{"The":[0],"Chloroplast":[1],"Genome":[2],"Database":[3],"(ChloroplastDB)":[4],"is":[5,155],"an":[6],"interactive,":[7],"web-based":[8],"database":[9],"for":[10,50,73,96,190],"fully":[11],"sequenced":[12,170],"plastid":[13],"genomes,":[14],"containing":[15],"genomic,":[16],"protein,":[17],"DNA":[18],"and":[19,29,53,93,100,138,152,186,196],"RNA":[20,143],"sequences,":[21],"gene":[22,54,82,89,115,132,136,159],"locations,":[23],"RNA-editing":[24],"sites,":[25],"putative":[26],"protein":[27,146],"families":[28],"alignments":[30],"(http://chloroplast.cbio.psu.edu/).":[31],"With":[32],"recent":[33],"technical":[34],"advances,":[35],"the":[36,47,67,162,167,175],"rate":[37],"of":[38,114,169,193],"generating":[39],"new":[40],"organelle":[41],"genomes":[42,64,172],"has":[43,56],"increased":[44],"dramatically.":[45],"However,":[46],"established":[48],"ontology":[49],"chloroplast":[51,63,97,171,194],"genes":[52,99,195],"features":[55],"not":[57,79],"been":[58],"uniformly":[59],"applied":[60],"to":[61,183],"all":[62,107],"available":[65,177],"in":[66,117,131,178],"sequence":[68,127],"databases.":[69],"For":[70],"example,":[71],"annotations":[72],"some":[74],"published":[75],"genome":[76],"sequences":[77,109],"have":[78],"evolved":[80],"with":[81,110],"naming":[83],"conventions.":[84],"ChloroplastDB":[85,179],"provides":[86],"unified":[87],"annotations,":[88],"name":[90],"search,":[91],"BLAST":[92],"download":[94],"functions":[95],"encoded":[98],"genomic":[101],"sequences.":[102],"A":[103],"user":[104],"can":[105],"retrieve":[106],"orthologous":[108],"one":[111],"search":[112],"regardless":[113],"names":[116],"GenBank.":[118],"This":[119],"feature":[120],"alone":[121],"greatly":[122],"facilitates":[123],"comparative":[124,191],"research":[125],"on":[126],"evolution":[128],"including":[129],"changes":[130],"content,":[133],"codon":[134],"usage,":[135],"structure":[137],"post-transcriptional":[139],"modifications":[140],"such":[141],"as":[142,166],"editing.":[144],"Orthologous":[145],"sets":[147],"are":[148],"classified":[149],"by":[150],"TribeMCL":[151],"each":[153],"set":[154],"assigned":[156],"a":[157],"standard":[158],"name.":[160],"Over":[161],"next":[163],"few":[164],"years,":[165],"number":[168],"increases":[173],"rapidly,":[174],"tools":[176],"will":[180],"allow":[181],"researchers":[182],"easily":[184],"identify":[185],"compile":[187],"target":[188],"data":[189],"analysis":[192],"genomes.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
