Based on the links in the DAS registry (http://das.sanger.ac.uk/das/pfam) , the PFAM das servers appear to be down. Part, no doubt, of the general wind-down of DAS registry and DAS services at EBI/Sanger: http://www.ebi.ac.uk/about/news/service-news/das-services-to-retire
However, DAS access to PFAM from Jalview happily appears to continue to work.
I was wondering if Jalview is in fact using the PFAM das servers, or bypasses them and instead performs a direct download via the ws/dbsources code:
src/jalview/ws/dbsources/PfamFull.java
41 return “http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=”;
src/jalview/ws/dbsources/PfamSeed.java
43 return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=“;
I’m interested because we are planning on serving up our gene family data (currently stored in InterMine) via DAS to Jalview, and were hoping to template off the way Jalview accesses PFAM.
Also wondering if you have a recommendation in terms of whether it’s worth bringing up new sources via DAS for integration with Jalview, or do you expect to provide another similar mechanism (e.g., via REST api’s, as UniProt suggests)
···
–
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley
looking a little more closely at this, it’s become clear we should be thinking about providing access to Phytozome families via a Phytozome dbSource that implements DbSourceProxy. A couple of follow-up questions:
-so it looks like it’s necessary to actually add a class for each new data source? For “simple” data sources (like PFAM and I suspect Phytozome), would it be possible to have a generic class that implements DbSourceProxy which gets its data source specific parameters (the access url, source name, whether it serves up CDS, protein, structures, domains, etc.) from properties files? Then data providers would only need to provide a properties file with jalview, or better yet the property file could be accessed from a registry (analogous to the DAS registry, but possibly served by jabaws?)
-for any of the DAS or DbSourceProxy data sources, is it possible to invoke a sequence fetch at Jalview startup? Meaning one would pass in an identifier and data source name at startup. Slightly preferable to handing in a full access URL.
thanks,
-David
···
On Tue, Sep 23, 2014 at 12:04 PM, David Goodstein <dmgoodstein@lbl.gov> wrote:
Based on the links in the DAS registry (http://das.sanger.ac.uk/das/pfam) , the PFAM das servers appear to be down. Part, no doubt, of the general wind-down of DAS registry and DAS services at EBI/Sanger: http://www.ebi.ac.uk/about/news/service-news/das-services-to-retire
However, DAS access to PFAM from Jalview happily appears to continue to work.
I was wondering if Jalview is in fact using the PFAM das servers, or bypasses them and instead performs a direct download via the ws/dbsources code:
src/jalview/ws/dbsources/PfamFull.java
41 return “http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=”;
src/jalview/ws/dbsources/PfamSeed.java
43 return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=“;
I’m interested because we are planning on serving up our gene family data (currently stored in InterMine) via DAS to Jalview, and were hoping to template off the way Jalview accesses PFAM.
Also wondering if you have a recommendation in terms of whether it’s worth bringing up new sources via DAS for integration with Jalview, or do you expect to provide another similar mechanism (e.g., via REST api’s, as UniProt suggests)
–
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley
–
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley