UCSC Data proxy

I’ve put up a UCSC sources.xml available from here : http://www.dasregistry.org/ucsc/das/sources generated from their dsn response and a table available from the UCSC that has information about their coordinate systems so I could guess what DAS coordinate system should be used with each source e.g. hg18 for the UCSC will equate to NCBI_36,Chromosome,Homo sapiens in DAS.

The DAS Registry uses this xml to generate entries in the registry for the 16 UCSC data sources that have been converted.

This should mean that ensembl and other data sources should be able to connect to the nearly 4000+ UCSC sources. There is one more thing that needs to be done however : that is allow users in ensembl to attach data sources based on type.

&type=bacEndPairs&type=ensGene needs to be added on the end of a normal features request otherwise too many features are returned and ensembl will time out.  Other DAS clients will find the same issue.

Today I spoke to Rachel who works at the UCSC and we hope to get some collaboration going so that the UCSC and ensembl “formatted” data sources are compatible. I’ve set up the registry so we can search types to enable people to find the UCSC source they want. The registry will filter the types returned that match the given keyword.

  1. No trackbacks yet.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: