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dc.contributor.authorKrishnakumar, Vivek
dc.contributor.authorContrino, Sergio
dc.contributor.authorCheng, Chia-Yi
dc.contributor.authorBelyaeva, Irina
dc.contributor.authorFerlanti, Erik S
dc.contributor.authorMiller, Jason R
dc.contributor.authorVaughn, Matthew W
dc.contributor.authorMicklem, Gos
dc.contributor.authorTown, Christopher D
dc.contributor.authorChan, Agnes P
dc.date.accessioned2018-10-18T10:21:10Z
dc.date.available2018-10-18T10:21:10Z
dc.date.issued2017-01-01
dc.identifier.issn0032-0781
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/284117
dc.description.abstractThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and functional annotation from the Araport11 update, the Col-0 genome sequence, RNA-seq and array expression, co-expression, protein interactions, homologs, pathways, publications, alleles, germplasm and phenotypes. The data are collected from a wide variety of public resources. Users can browse gene-specific data through Gene Report pages, identify and create gene lists based on experiments or indexed keywords, and run GO enrichment analysis to investigate the biological significance of selected gene sets. Developed by the Arabidopsis Information Portal project (Araport, https://www.araport.org/), ThaleMine uses the InterMine software framework, which builds well-structured data, and provides powerful data query and analysis functionality. The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services. Here we describe recent developments in ThaleMine including new features and extensions, and discuss future improvements. InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data. ThaleMine is the first InterMine developed for a plant model. As additional new plant InterMines are developed by the legume and other plant research communities, the potential of cross-organism integrative data analysis will be further enabled.
dc.languageeng
dc.publisherOxford University Press (OUP)
dc.subjectArabidopsis thaliana
dc.subjectInterMine
dc.subjectdata integration
dc.subjectdata warehouse
dc.subjectgenomics
dc.subjectweb services
dc.subjectArabidopsis
dc.subjectArabidopsis Proteins
dc.subjectComputational Biology
dc.subjectDatabases, Genetic
dc.subjectGene Expression Profiling
dc.subjectGene Expression Regulation, Plant
dc.subjectGene Ontology
dc.subjectGenomics
dc.subjectInformation Storage and Retrieval
dc.subjectInternet
dc.subjectProtein Interaction Mapping
dc.subjectProtein Interaction Maps
dc.subjectReproducibility of Results
dc.subjectSequence Analysis, RNA
dc.titleThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.
dc.typeArticle
prism.endingPagee4
prism.issueIdentifier1
prism.publicationDate2017
prism.publicationNamePlant and Cell Physiology
prism.startingPagee4
prism.volume58
dc.identifier.doi10.17863/CAM.31488
dcterms.dateAccepted2016-11-11
rioxxterms.versionofrecord10.1093/pcp/pcw200
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2017-01-01
dc.contributor.orcidMicklem, Gos [0000-0002-6883-6168]
dc.identifier.eissn1471-9053
rioxxterms.typeJournal Article/Review
pubs.funder-project-idBiotechnology and Biological Sciences Research Council (BB/L027151/1)
cam.issuedOnline2016-12-24
rioxxterms.freetoread.startdate2018-01-31


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