{"id":"https://openalex.org/W2786765000","doi":"https://doi.org/10.1093/database/bax092","title":"Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases","display_name":"Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2786765000","doi":"https://doi.org/10.1093/database/bax092","mag":"2786765000","pmid":"https://pubmed.ncbi.nlm.nih.gov/31725859"},"language":"en","primary_location":{"id":"doi:10.1093/database/bax092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax092/22473454/bax092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","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/database/article-pdf/doi/10.1093/database/bax092/22473454/bax092.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000749878","display_name":"Sook Jung","orcid":"https://orcid.org/0000-0003-3968-2769"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sook Jung","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056282743","display_name":"Taein Lee","orcid":"https://orcid.org/0000-0002-2000-2586"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taein Lee","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113727607","display_name":"Chun-Huai Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chun-Huai Cheng","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015114586","display_name":"Stephen Ficklin","orcid":"https://orcid.org/0000-0001-9138-6292"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Ficklin","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062668535","display_name":"Jing Yu","orcid":"https://orcid.org/0000-0001-8008-5216"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Yu","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058156769","display_name":"Jodi L. Humann","orcid":"https://orcid.org/0000-0002-9575-6710"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jodi Humann","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045435393","display_name":"Dorrie Main","orcid":"https://orcid.org/0000-0002-1162-2724"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dorrie Main","raw_affiliation_strings":["Department of Horticulture, Washington State University, Pullman, WA, 99164, USA"],"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Washington State University, Pullman, WA, 99164, USA","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5000749878"],"corresponding_institution_ids":["https://openalex.org/I72951846"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.1024,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.81911134,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"2017","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9854000210762024,"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"}},"topics":[{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9854000210762024,"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/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.9851999878883362,"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"}},{"id":"https://openalex.org/T12795","display_name":"Banana Cultivation and Research","score":0.9821000099182129,"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/computer-science","display_name":"Computer science","score":0.7055637836456299},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6832281351089478},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.663426399230957},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4550709128379822},{"id":"https://openalex.org/keywords/database-catalog","display_name":"Database catalog","score":0.4321378171443939},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.3910886347293854},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3269776701927185}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7055637836456299},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6832281351089478},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.663426399230957},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4550709128379822},{"id":"https://openalex.org/C65610166","wikidata":"https://www.wikidata.org/wiki/Q5227399","display_name":"Database catalog","level":4,"score":0.4321378171443939},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.3910886347293854},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3269776701927185}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bax092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax092/22473454/bax092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:31725859","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31725859","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:4643668","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5727400","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/database/bax092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax092/22473454/bax092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G18959679","display_name":null,"funder_award_id":"#1444573","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3044630413","display_name":null,"funder_award_id":"2014-51181-22376","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G4606842200","display_name":null,"funder_award_id":"2014-51181-2237","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G527436128","display_name":null,"funder_award_id":"2014-51181-2237","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G7186528139","display_name":null,"funder_award_id":"2014-51181-22376","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G7618748963","display_name":null,"funder_award_id":"1444573","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8060264394","display_name":null,"funder_award_id":"2009-51181","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8834156931","display_name":null,"funder_award_id":"NRSP10","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320309116","display_name":"Cotton Incorporated","ror":"https://ror.org/058bgdt55"},{"id":"https://openalex.org/F4320309913","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17"},{"id":"https://openalex.org/F4320313568","display_name":"Washington Tree Fruit Research Commission","ror":"https://ror.org/04mz0gg46"},{"id":"https://openalex.org/F4320317096","display_name":"USA Dry Pea and Lentil Council","ror":null},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2786765000.pdf","grobid_xml":"https://content.openalex.org/works/W2786765000.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1967204795","https://openalex.org/W2001709424","https://openalex.org/W2004149738","https://openalex.org/W2015968355","https://openalex.org/W2022296304","https://openalex.org/W2085824957","https://openalex.org/W2098229525","https://openalex.org/W2123171788","https://openalex.org/W2151397621","https://openalex.org/W2168670121","https://openalex.org/W2224343643","https://openalex.org/W2299227554","https://openalex.org/W2545753590","https://openalex.org/W2568239413","https://openalex.org/W2589605652","https://openalex.org/W6733136878"],"related_works":["https://openalex.org/W2374379029","https://openalex.org/W2394393789","https://openalex.org/W1503116306","https://openalex.org/W1504835998","https://openalex.org/W2391915033","https://openalex.org/W2360250168","https://openalex.org/W2354596657","https://openalex.org/W57267792","https://openalex.org/W1507025082","https://openalex.org/W2527789274"],"abstract_inverted_index":{"Tripal":[0,40,175,186],"is":[1,121],"an":[2],"open-source":[3],"database":[4],"platform":[5],"primarily":[6],"used":[7,119],"for":[8,49,61,135,195,206],"development":[9],"of":[10,22,37,153,168],"genomic,":[11],"genetic":[12],"and":[13,29,56,77,94,113,132,148,209],"breeding":[14],"databases.":[15],"We":[16],"report":[17],"here":[18],"on":[19],"the":[20,23,35,38,114,136,143,157,183,192,210],"release":[21],"Chado":[24,26,30,82,102,127,158],"Loader,":[25],"Data":[27,103],"Display":[28,104],"Search":[31,128,159],"modules":[32,45,188],"to":[33,108,145,181],"extend":[34],"functionality":[36,134],"core":[39],"modules.":[41],"These":[42,185],"new":[43],"extension":[44],"provide":[46],"additional":[47],"tools":[48,107,144],"(1)":[50],"data":[51,63,86,95,111,138,169],"loading,":[52],"(2)":[53],"customized":[54,123],"visualization":[55],"(3)":[57],"advanced":[58],"search":[59,131],"functions":[60],"supported":[62,137],"types":[64,180],"such":[65],"as":[66,120,124,164,166],"organism,":[67],"marker,":[68],"QTL/Mendelian":[69],"Trait":[70],"Loci,":[71],"germplasm,":[72],"map,":[73],"project,":[74],"phenotype,":[75],"genotype":[76],"their":[78],"respective":[79],"metadata.":[80],"The":[81,101,126,151],"Loader":[83],"module":[84,105,129,160],"provides":[85,130],"collection":[87],"templates":[88],"in":[89,156,171,191],"Excel":[90],"with":[91,97,177],"defined":[92],"metadata":[93,115,179],"loaders":[96],"front":[98],"end":[99],"forms.":[100],"contains":[106],"visualize":[109,146],"each":[110],"type":[112],"which":[116],"can":[117],"be":[118],"or":[122],"desired.":[125],"download":[133],"types.":[139],"Also":[140],"included":[141],"are":[142,189],"map":[147],"species":[149],"summary.":[150],"use":[152],"materialized":[154],"views":[155],"enables":[161],"better":[162],"performance":[163],"well":[165],"flexibility":[167],"modeling":[170],"Chado,":[172],"allowing":[173],"existing":[174],"databases":[176],"different":[178],"utilize":[182],"module.":[184],"Extension":[187],"implemented":[190],"Genome":[193,201,204],"Database":[194,202,205,215,217],"Rosaceae":[196],"(rosaceae.org),":[197],"CottonGen":[198],"(cottongen.org),":[199],"Citrus":[200],"(citrusgenomedb.org),":[203],"Vaccinium":[207],"(vaccinium.org)":[208],"Cool":[211],"Season":[212],"Food":[213],"Legume":[214],"(coolseasonfoodlegume.org).":[216],"URL:":[218],"https://www.citrusgenomedb.org/,":[219],"https://www.coolseasonfoodlegume.org/,":[220],"https://www.cottongen.org/,":[221],"https://www.rosaceae.org/,":[222],"https://www.vaccinium.org/.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}