{"id":"https://openalex.org/W2625668296","doi":"https://doi.org/10.7490/f1000research.1113860.1","title":"Defining standards for the annotation and integration of disease relevant data across the model organism databases of the Alliance of Genome Resources (AGR)","display_name":"Defining standards for the annotation and integration of disease relevant data across the model organism databases of the Alliance of Genome Resources (AGR)","publication_year":2017,"publication_date":"2017-03-31","ids":{"openalex":"https://openalex.org/W2625668296","doi":"https://doi.org/10.7490/f1000research.1113860.1","mag":"2625668296"},"language":"en","primary_location":{"id":"doi:10.7490/f1000research.1113860.1","doi":"https://doi.org/10.7490/f1000research.1113860.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1113860.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7490/f1000research.1113860.1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005252212","display_name":"Steven J Marygold","orcid":"https://orcid.org/0000-0003-2759-266X","observed_orcids":["https://orcid.org/0000-0003-2759-266X"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Steven Marygold","raw_affiliation_strings":["FlyBase, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FlyBase, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111805340","display_name":"Susan M Bello","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Susan Bello","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031573747","display_name":"Yvonne M. Bradford","orcid":"https://orcid.org/0000-0002-9900-7880","observed_orcids":["https://orcid.org/0000-0002-9900-7880"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yvonne Bradford","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110461800","display_name":"Madeline A. Crosby","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Madeline Crosby","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036217383","display_name":"Stacia R. Engel","orcid":"https://orcid.org/0000-0001-5472-917X","observed_orcids":["https://orcid.org/0000-0001-5472-917X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stacia Engel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001134499","display_name":"Ranjana Kishore","orcid":"https://orcid.org/0000-0002-1478-7671","observed_orcids":["https://orcid.org/0000-0002-1478-7671"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ranjana Kishore","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037400577","display_name":"Stanley J. F. Laulederkind","orcid":"https://orcid.org/0000-0001-5356-4174","observed_orcids":["https://orcid.org/0000-0001-5356-4174"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stan Laulederkind","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031193159","display_name":"Mary E. Shimoyama","orcid":"https://orcid.org/0000-0003-1176-0796","observed_orcids":["https://orcid.org/0000-0003-1176-0796"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mary Shimoyama","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5085879565","display_name":"Cynthia L. Smith","orcid":"https://orcid.org/0000-0003-3691-0324","observed_orcids":["https://orcid.org/0000-0003-3691-0324"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cynthia Smith","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5005252212"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9961000084877014,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9961000084877014,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0013000000035390258,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.0007999999797903001,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/model-organism-databases","display_name":"model organism databases","score":0.8299999833106995},{"id":"https://openalex.org/keywords/data-integration","display_name":"data integration","score":0.6389999985694885},{"id":"https://openalex.org/keywords/annotation-standards","display_name":"annotation standards","score":0.7760000228881836},{"id":"https://openalex.org/keywords/disease-ontology","display_name":"disease ontology","score":0.9779999852180481},{"id":"https://openalex.org/keywords/evidence-codes","display_name":"evidence codes","score":0.6309999823570251},{"id":"https://openalex.org/keywords/disease-modifiers","display_name":"disease modifiers","score":0.40700000524520874},{"id":"https://openalex.org/keywords/saccharomyces-genome-database","display_name":"Saccharomyces Genome Database","score":0.8529999852180481},{"id":"https://openalex.org/keywords/wormbase","display_name":"WormBase","score":0.9819999933242798},{"id":"https://openalex.org/keywords/flybase","display_name":"FlyBase","score":0.9990000128746033},{"id":"https://openalex.org/keywords/rat-genome-database","display_name":"Rat Genome Database","score":0.9850000143051147},{"id":"https://openalex.org/keywords/mouse-genome-informatics","display_name":"Mouse Genome Informatics","score":0.9990000128746033}],"concepts":[{"id":"https://openalex.org/C2778431023","wikidata":"https://www.wikidata.org/wiki/Q878249","display_name":"Alliance","level":2,"score":0.772797167301178},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7155900001525879},{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.6174425482749939},{"id":"https://openalex.org/C2778149293","wikidata":"https://www.wikidata.org/wiki/Q309823","display_name":"Open science","level":2,"score":0.5244786143302917},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5209742188453674},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5206307768821716},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.48457181453704834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4792090356349945},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47690725326538086},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.47149723768234253},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4432186484336853},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.44116532802581787},{"id":"https://openalex.org/C2780535194","wikidata":"https://www.wikidata.org/wiki/Q309901","display_name":"Open data","level":2,"score":0.4151607155799866},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4125024378299713},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36270663142204285},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3259139060974121},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.29635030031204224},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.26231443881988525},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.23598334193229675},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1970575451850891},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.1807568073272705},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1464410424232483},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.09539926052093506},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.7490/f1000research.1113860.1","doi":"https://doi.org/10.7490/f1000research.1113860.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1113860.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.7490/f1000research.1113860.1","doi":"https://doi.org/10.7490/f1000research.1113860.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1113860.1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050752","display_name":"Faculty of 1000 Research Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Other"},{"id":"mag:2625668296","doi":null,"is_oa":true,"landing_page_url":"https://f1000research.com/posters/6-408","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":"F1000Research","raw_type":null}],"best_oa_location":{"id":"doi:10.7490/f1000research.1113860.1","doi":"https://doi.org/10.7490/f1000research.1113860.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1113860.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2792132368","https://openalex.org/W762501897","https://openalex.org/W7054508144","https://openalex.org/W4393431031","https://openalex.org/W2890662912","https://openalex.org/W4251298631","https://openalex.org/W2146777736","https://openalex.org/W6944014624","https://openalex.org/W2407168526","https://openalex.org/W2028962241"],"abstract_inverted_index":{"Model":[0],"organisms":[1,31],"are":[2,158,281],"widely":[3],"used":[4],"to":[5,75,83,128,165,199],"augment":[6],"investigation":[7],"into":[8,207,285],"the":[9,34,41,85,102,111,116,143,162,167,172,194,208,215,218,234,243,249,256,275,294,302],"etiopathogenesis":[10],"of":[11,36,43,70,89,151,171,217,253,255,293,298],"human":[12,15,324],"disease.":[13],"Coupling":[14],"sequence,":[16],"phenotypes,":[17],"pathogenicity":[18],"variant":[19],"calls":[20],"and":[21,40,62,65,77,87,121,154,156,169,251,267,280],"other":[22],"biological":[23],"evidence":[24,262],"with":[25,161,312,323],"experimental":[26,230],"data":[27,50,60,80,191,204,272,322],"from":[28,92,274],"tractable":[29],"model":[30,97,133,136,202,307],"can":[32],"accelerate":[33],"identification":[35],"causative":[37],"disease":[38,48,90,135,152,201,245,257,309,316],"variants":[39],"testing":[42],"therapeutic":[44],"candidates.":[45],"At":[46],"present,":[47],"relevant":[49],"reside":[51],"in":[52,81,301],"different":[53],"formats":[54],"within":[55],"multiple":[56],"independent":[57],"databases,":[58],"making":[59],"extraction":[61],"synthesis":[63],"difficult":[64],"time":[66],"consuming.":[67],"The":[68],"Alliance":[69],"Genome":[71,104,118,123],"Resources":[72],"(AGR)":[73],"seeks":[74],"standardize":[76,200],"integrate":[78,320],"these":[79,265],"order":[82],"facilitate":[84],"search":[86],"retrieval":[88],"information":[91],"a":[93,148,189,224,286],"single":[94],"interface.":[95],"Six":[96],"organism":[98,134,308],"databases":[99],"(MODs),":[100],"including":[101],"Saccharomyces":[103],"Database":[105,119],"(SGD),":[106],"WormBase":[107],"(WB),":[108],"FlyBase":[109],"(FB),":[110],"Zebrafish":[112],"Information":[113],"Network":[114],"(ZFIN),":[115],"Rat":[117],"(RGD)":[120],"Mouse":[122],"Informatics":[124],"(MGI),":[125],"have":[126,139,185,277],"collaborated":[127],"create":[129],"annotation":[130,203],"standards":[131],"for":[132,188,205,233,264,315],"data.":[137],"We":[138,184,289],"converged":[140],"upon":[141],"using":[142],"Disease":[144,195],"Ontology":[145],"(DO)":[146],"as":[147,223,237,260],"common":[149,190,287],"source":[150],"terms":[153],"definitions,":[155],"we":[157],"actively":[159],"working":[160],"DO":[163],"group":[164],"enhance":[166],"content":[168],"structure":[170],"ontology":[173],"so":[174],"that":[175,318],"it":[176],"may":[177],"be":[178],"fully":[179],"adopted":[180],"by":[181],"all":[182],"MODs.":[183],"created":[186,279],"specifications":[187],"exchange":[192],"file,":[193],"Association":[196],"File":[197],"(DAF),":[198],"integration":[206],"AGR":[209,304],"unified":[210,303],"resource.":[211,288],"This":[212],"specification":[213],"includes:":[214],"ID":[216],"object":[219],"being":[220,283],"annotated,":[221],"such":[222,236,259],"genotype,":[225],"strain,":[226],"allele":[227],"or":[228,240],"gene;":[229],"conditions":[231],"required":[232],"model,":[235,258],"chemical":[238],"exposure":[239],"dietary":[241],"modification;":[242],"associated":[244],"identifier":[246],"(DO":[247],"ID);":[248],"identity":[250],"effects":[252],"modifiers":[254],"treatments;":[261],"codes":[263],"assertions;":[266],"an":[268],"attributed":[269],"reference.":[270],"DAF":[271],"sets":[273],"MODs":[276],"been":[278],"currently":[282],"pulled":[284],"will":[290,319],"show":[291],"examples":[292],"first":[295],"beta":[296],"version":[297],"gene":[299],"pages":[300],"interface":[305],"showing":[306],"data,":[310],"together":[311],"our":[313],"plans":[314],"reports":[317],"MOD":[321],"gene-to-disease":[325],"associations.":[326]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2017-06-23T00:00:00"}