Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.
Identifieur interne : 000029 ( OpenAccess/Analysis ); précédent : 000028; suivant : 000030Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.
Auteurs : Owen Lancaster [Royaume-Uni] ; Tim Beck [Royaume-Uni] ; David Atlan [Belgique] ; Morris Swertz [Pays-Bas] ; Dhiwagaran Thangavelu [Royaume-Uni] ; Colin Veal [Royaume-Uni] ; Raymond Dalgleish [Royaume-Uni] ; Anthony J. Brookes [Royaume-Uni]Source :
- Human mutation [ 1098-1004 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- genetics : Rare Diseases.
- methods : Information Dissemination.
- Databases, Bibliographic, Genetic Predisposition to Disease, Genotype, Humans, Phenotype, Software, User-Computer Interface, Web Browser.
Abstract
Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service.
DOI: 10.1002/humu.22841
PubMed: 26224250
Affiliations:
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pubmed:26224250Le document en format XML
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Brookes</name><affiliation wicri:level="1"><nlm:affiliation>Department of Genetics, University of Leicester, Leicester, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Genetics, University of Leicester, Leicester</wicri:regionArea><wicri:noRegion>Leicester</wicri:noRegion></affiliation></author></analytic><series><title level="j">Human mutation</title><idno type="eISSN">1098-1004</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Bibliographic</term><term>Genetic Predisposition to Disease</term><term>Genotype</term><term>Humans</term><term>Information Dissemination (methods)</term><term>Phenotype</term><term>Rare Diseases (genetics)</term><term>Software</term><term>User-Computer Interface</term><term>Web Browser</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Rare Diseases</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Information Dissemination</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Bibliographic</term><term>Genetic Predisposition to Disease</term><term>Genotype</term><term>Humans</term><term>Phenotype</term><term>Software</term><term>User-Computer Interface</term><term>Web Browser</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service.</div></front></TEI><affiliations><list><country><li>Belgique</li><li>Pays-Bas</li><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Lancaster, Owen" sort="Lancaster, Owen" uniqKey="Lancaster O" first="Owen" last="Lancaster">Owen Lancaster</name></noRegion><name sortKey="Beck, Tim" sort="Beck, Tim" uniqKey="Beck T" first="Tim" last="Beck">Tim Beck</name><name sortKey="Brookes, Anthony J" sort="Brookes, Anthony J" uniqKey="Brookes A" first="Anthony J" last="Brookes">Anthony J. Brookes</name><name sortKey="Dalgleish, Raymond" sort="Dalgleish, Raymond" uniqKey="Dalgleish R" first="Raymond" last="Dalgleish">Raymond Dalgleish</name><name sortKey="Thangavelu, Dhiwagaran" sort="Thangavelu, Dhiwagaran" uniqKey="Thangavelu D" first="Dhiwagaran" last="Thangavelu">Dhiwagaran Thangavelu</name><name sortKey="Veal, Colin" sort="Veal, Colin" uniqKey="Veal C" first="Colin" last="Veal">Colin Veal</name></country><country name="Belgique"><noRegion><name sortKey="Atlan, David" sort="Atlan, David" uniqKey="Atlan D" first="David" last="Atlan">David Atlan</name></noRegion></country><country name="Pays-Bas"><noRegion><name sortKey="Swertz, Morris" sort="Swertz, Morris" uniqKey="Swertz M" first="Morris" last="Swertz">Morris Swertz</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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