Update on the DAS RegistryDAS 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-Interface/web service improvements

-List Sources-List Servers-Search

-To Do In the Future

General Updates-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 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

List Sources:

-list sources view-updated list sources page uses the registry web service

-old page still available for direct access to database.

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.

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

List Servers:

-servers listing capability http://www.dasregistry.org/das/servers

- see listSources.jsp

Search:

-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

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

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

Archiving:

-Sources are archived/ labelled inactive if non of the specified capabilities are valid.

- If server controlled archived if not in the sources.xml

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

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)

Day 3 topic :

Acknowledgments:

Andy Jenkinson (EBI)Rafael JiminezBernat GelJose VillavecesGustavo SalazarJames SmithAndreas PrlicGregg HeltLincoln SteinTim HubbardThe DAS community