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PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.

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cam.issuedOnline2018-10-13
dc.contributor.authorLock, Antonia
dc.contributor.authorRutherford, Kim
dc.contributor.authorHarris, Midori A
dc.contributor.authorHayles, Jacqueline
dc.contributor.authorOliver, Stephen G
dc.contributor.authorBähler, Jürg
dc.contributor.authorWood, Valerie
dc.contributor.orcidHarris, Midori [0000-0003-4148-4606]
dc.contributor.orcidOliver, Stephen [0000-0001-6330-7526]
dc.contributor.orcidWood, Valerie [0000-0001-6330-7526]
dc.date.accessioned2018-11-22T00:33:16Z
dc.date.available2018-11-22T00:33:16Z
dc.date.issued2019-01-08
dc.description.abstractPomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.
dc.format.mediumPrint
dc.identifier.doi10.17863/CAM.30612
dc.identifier.eissn1362-4962
dc.identifier.issn0305-1048
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285693
dc.languageeng
dc.language.isoeng
dc.publisherOxford University Press (OUP)
dc.publisher.urlhttp://dx.doi.org/10.1093/nar/gky961
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectDatabases, Genetic
dc.subjectGenome, Fungal
dc.subjectInternet
dc.subjectSchizosaccharomyces
dc.subjectSoftware
dc.subjectUser-Computer Interface
dc.titlePomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.
dc.typeArticle
dcterms.dateAccepted2018-10-11
prism.endingPageD827
prism.issueIdentifierD1
prism.publicationDate2019
prism.publicationNameNucleic Acids Res
prism.startingPageD821
prism.volume47
pubs.funder-project-idWellcome Trust (104967/Z/14/Z)
rioxxterms.licenseref.startdate2019-01
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
rioxxterms.versionAM
rioxxterms.versionofrecord10.1093/nar/gky961

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