{"id":"https://openalex.org/W1748696921","doi":"https://doi.org/10.1093/nar/gki050","title":"The Rat Genome Database (RGD): developments towards a phenome database","display_name":"The Rat Genome Database (RGD): developments towards a phenome database","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W1748696921","doi":"https://doi.org/10.1093/nar/gki050","mag":"1748696921","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608243"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gki050","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540004","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064441294","display_name":"Norberto de la Cruz","orcid":null},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"N. de la Cruz","raw_affiliation_strings":["Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA"],"affiliations":[{"raw_affiliation_string":"Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA","institution_ids":["https://openalex.org/I204308271"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064441294"],"corresponding_institution_ids":["https://openalex.org/I204308271"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":3.8587,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.93997554,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"Database issue","first_page":"D485","last_page":"D491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9970999956130981,"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":0.9970999956130981,"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":0.9934999942779541,"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":0.9927999973297119,"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/biology","display_name":"Biology","score":0.894389271736145},{"id":"https://openalex.org/keywords/phenome","display_name":"Phenome","score":0.8326276540756226},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5729225277900696},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5445826053619385},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44180190563201904},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2632709741592407},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.121697336435318},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.08829152584075928}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.894389271736145},{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.8326276540756226},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5729225277900696},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5445826053619385},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44180190563201904},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2632709741592407},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.121697336435318},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.08829152584075928}],"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gki050","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608243","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608243","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:repository.cshl.edu:22551","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.105.750","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.105.750","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/reprint/33/suppl_1/D485.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:540004","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540004","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:540004","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540004","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.550000011920929}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1509844421","https://openalex.org/W1552651695","https://openalex.org/W1572954579","https://openalex.org/W1578104218","https://openalex.org/W1581558601","https://openalex.org/W1594816032","https://openalex.org/W1981021538","https://openalex.org/W1994458586","https://openalex.org/W2002241222","https://openalex.org/W2014022579","https://openalex.org/W2015267174","https://openalex.org/W2021239799","https://openalex.org/W2041025801","https://openalex.org/W2087352256","https://openalex.org/W2091082435","https://openalex.org/W2093285783","https://openalex.org/W2097040991","https://openalex.org/W2104397421","https://openalex.org/W2104878392","https://openalex.org/W2119229696","https://openalex.org/W2123280311","https://openalex.org/W2131581981","https://openalex.org/W2144975794","https://openalex.org/W2145477956","https://openalex.org/W2148871416","https://openalex.org/W2161062388","https://openalex.org/W2167467514","https://openalex.org/W2168783124","https://openalex.org/W2175779775","https://openalex.org/W2489716800","https://openalex.org/W4255855797"],"related_works":["https://openalex.org/W2086237400","https://openalex.org/W2274048411","https://openalex.org/W2082860237","https://openalex.org/W4282960395","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W3212460220"],"abstract_inverted_index":{"The":[0,82,122,194],"Rat":[1],"Genome":[2],"Database":[3],"(RGD)":[4],"(http://rgd.mcw.edu)":[5],"aims":[6],"to":[7,58,94,112,115,151],"meet":[8],"the":[9,23,72,103,134,143,147,182,206,223],"needs":[10],"of":[11,25,65,74,84,105,109,136,146,178,197,202,208,217,228,232],"its":[12,186],"community":[13],"by":[14,71],"providing":[15],"genetic":[16],"and":[17,31,56,62,78,92,107,118,219,227],"genomic":[18,144,210,220,225],"infrastructure":[19],"while":[20],"also":[21],"annotating":[22],"strengths":[24],"rat":[26,137,183,209],"research:":[27],"biochemistry,":[28],"nutrition,":[29],"pharmacology":[30],"physiology.":[32],"Here,":[33],"we":[34],"report":[35],"on":[36,125,181],"RGD's":[37],"development":[38,196],"towards":[39],"creating":[40],"a":[41,75,152,170,189],"phenome":[42],"database.":[43],"Recent":[44],"developments":[45],"can":[46],"be":[47],"categorized":[48],"into":[49,205],"three":[50],"groups.":[51],"(i)":[52],"Improved":[53],"data":[54,204,221],"collection":[55],"integration":[57,201],"match":[59],"increased":[60,176],"volume":[61],"biological":[63,179,218],"scope":[64],"research.":[66],"(ii)":[67],"Knowledge":[68],"representation":[69],"augmented":[70],"implementation":[73],"new":[76],"ontology":[77],"annotation":[79,177],"system.":[80],"(iii)":[81],"addition":[83],"quantitative":[85],"trait":[86],"loci":[87],"data,":[88],"from":[89],"rat,":[90,148],"mouse":[91],"human":[93,192,224],"our":[95],"advanced":[96],"comparative":[97],"genomics":[98],"tools,":[99],"as":[100,102,188,212,214],"well":[101,213],"creation":[104],"new,":[106],"enhancement":[108],"existing,":[110],"tools":[111],"enable":[113],"users":[114],"efficiently":[116],"browse":[117],"survey":[119],"research":[120],"data.":[121],"emphasis":[123],"is":[124],"helping":[126],"researchers":[127],"find":[128],"genes":[129],"responsible":[130],"for":[131,175,191],"disease":[132],"through":[133,185],"use":[135,187],"models.":[138],"These":[139],"improvements,":[140],"combined":[141],"with":[142,157,222],"sequence":[145,226],"have":[149],"led":[150],"successful":[153],"year":[154],"at":[155],"RGD":[156],"over":[158,166],"two":[159],"million":[160],"page":[161],"accesses":[162],"that":[163],"represent":[164],"an":[165,229],"4-fold":[167],"increase":[168],"in":[169],"year.":[171],"Future":[172],"plans":[173],"call":[174],"information":[180],"elucidated":[184],"model":[190],"pathobiology.":[193],"continued":[195],"toolsets":[198],"will":[199],"facilitate":[200],"these":[203],"context":[207],"sequence,":[211],"allow":[215],"comparisons":[216],"increasing":[230],"number":[231],"organisms.":[233]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}