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Update on the DAS Registry DAS Workshop 2011

Update on the DAS Registry DAS Workshop 2011 . Jonathan Warren. >50,000. -~1300 sources currently -break sources up by genome, work soon? -Increasing: -Next Gen files in DAS -multiple genomes per organism -many different organisms and genomes sequenced. . Content. -General updates

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Update on the DAS Registry DAS Workshop 2011

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  1. Update on the DAS RegistryDAS Workshop 2011 Jonathan Warren

  2. >50,000 • -~1300 sources currently • -break sources up by genome, work soon? • -Increasing: • -Next Gen files in DAS • -multiple genomes per organism • -many different organisms and genomes sequenced.

  3. Content • -General updates • -Interface/web service improvements • -List Sources • -List Servers • -Search • -To Do In the Future

  4. -Moved to new VMs.. and Tomcat6 -sources now become inactive rather than archived -registered servers have their sources document auto updated in the registry -added .xsd for use with JAXB -changed coordinate system urls to xml response for clients rather than html for browsers http://www.dasregistry.org/coordsys/CS_DS6 -The regsitry web service accepts ; and & -UCSC mirroring via a proxy that guesses matching UCSC coordinate systems http://www.dasregistry.org/ucsc/das/sources -sources and coordinatesystem caching -extra command for registry dasregistry/das/knownCapabilities General Updates

  5. General continued: • -rows support for sources, coordinatesystems requests • Web Service examples http://www.dasregistry.org/DASCommandExamples.jsp • -validate command can be used to validate a server using the das registry and get back an xml sources response containing extra properties pertaining to the validity of specific capabilities: • http://www.dasregistry.org/validate?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173

  6. List Sources: -list sources view -updated list sources page uses the registry web service -old page still available for direct access to database.

  7. List Sources web service: • -http://www.dasregistry.org/das/sources?serverUrl=http://www.ensembl.org/das&rows=1-10 • -request support for sources document for 1.6E compliant sources http://www.dasregistry.org/das1.6/sources as apposed to 1.5 sources http://www.dasregistry.org/das1.5/sources • -sources.xml displays days before deletion if source is scheduled for deletion and spec for all sources • -filter sources based on validcapability as well as capability.

  8. Sources Web Service: • -sorting added to sources web service • -id • -nickname or title • -status (ie. uses leasedate) • -registerdate • -leasedate • -url • -adminemail • -description • -capabilities (user/server specified) • -validcapabilities (sorts on valid capabilities determined by the registry not user/server selected) • -coordinatesystem (sorts by the number of coordinate systems a source specifies). • -reverse=true parameter reverses the order of the above sorts. • -sorts on listSources.jsp

  9. List Servers: • -servers listing capability http://www.dasregistry.org/das/servers • - see listSources.jsp

  10. -search interface -registry web service -lucene back end indexing -search interface implemented in javascript so can be used by any other client in their interface -added search help (links to EBEye search examples to show use of boolean and defaults etc) -added types searching to the new search interface Search:

  11. Scripting for Searching: keywords parameter http://www.dasregistry.org/das/sources?keywords=zebrafish typeskeywords http://www.dasregistry.org/das/sources?typeskeywords=gene keywords parameter http://www.dasregistry.org/das/coordinatesystem?keywords=gorilla

  12. Scripting Continued: • - knownCapabilities (responds with the DAS capabilities that the registry is aware of and supports): • http://www.dasregistry.org/das/knownCapabilities • -validate command can be used to validate a server using the das registry and get back an xml sources response containing extra properties pertaining to the validity of specific capabilities: • http://www.dasregistry.org/validate?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173

  13. Archiving: • -Sources are archived/ labelled inactive if non of the specified capabilities are valid. • - If server controlled archived if not in the sources.xml

  14. To do: • -Get rid of Prefixes for mirrored sources completely • -header validation? • -smoother validation interface with helpful tips and more meaningful validation error messages. • -ping sources to see if responding at all separately

  15. Day 3 topic : • Should the DAS registry say list all sources and just give information on their validity rather than archiving sources. Should clients do all they can to accommodate poor data sources or should they link to validation data and encourage correct data source compliance?(JW)

  16. Acknowledgments: • Andy Jenkinson (EBI) • Rafael Jiminez • Bernat Gel • Jose Villaveces • Gustavo Salazar • James Smith • Andreas Prlic • Gregg Helt • Lincoln Stein • Tim Hubbard • The DAS community

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