Fix link out for GO, Pfam, and EnsemblBacteria in Systems table

[kdahlquist]

I'm testing the Backpage links for the Vibrio export. The link for GO is going to the wrong page, stay tuned for how to fix it.

[kdahlquist]

Pfam and EnsemblBacteria also have issues, stay tuned for how to fix it.

[kdahlquist]

If I were to push a fix to this directly to GitHub, where would I put it? Which branch? Where is this file anyway in the code? I think for the sake of expediency, I will need to tell @dondi the changes and have you make them.

[kdahlquist]

For GO terms, the new Link out should be:

http://amigo.geneontology.org/amigo/term/GO:~

For example: http://amigo.geneontology.org/amigo/term/GO:0061621

In our gdb, the "GO:" has been stripped out of the ID column, so I'm thinking that the tilde has to go after the ":", right?

[kdahlquist]

For Pfam the new link out should be:

http://pfam.xfam.org/family/~

For example: http://pfam.xfam.org/family/PF00587

[kdahlquist]

For EnsemblBacteria, the new link out should be:

http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=~;site=ensemblunit

For example: http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=AAF96469;site=ensemblunit

We should also change the link out for OrderedLocusNames for Vibrio to this EnsemblBacteria on. The TIGR CMR is no longer actually online that I can tell.

I'm reassigning this to @dondi .

[dondi]

Sounds great, I will add/modify these link-outs tonight, and release a new build-5 after that.

Just to answer the earlier question, the changes can be submitted (though not tested) by editing this file directly:

https://github.com/lmu-bioinformatics/xmlpipedb/blob/access-64-bit/gmbuilder/src/edu/lmu/xmlpipedb/gmbuilder/databasetoolkit/profiles/VibrioCholeraeUniprotSpeciesProfile.java

The branch where all of this work is currently happening is access-64-bit. (as you know it has grown in scope quite a bit from just 64-bit, but the name has stuck so far)

[dondi]

Follow-up question...are these linkout changes universal, or specific to V. cholerae? If they are universal, they would go in the database template file. If they are specific, they would go in the Java species profile.

(upon inspection they look universal, except for OrderedLocusNames)

[kdahlquist]

You answered your own question. They are universal and need to go into the database template file. The link for OrderedLocusNames fro Vibrio needs to be changed in the profile.

[dondi]

OK, this has been changed. I did an export, loaded the result into GenMAPP, then did a quick back page lookup. The links worked.

[dondi]

Merged into master with pull request #17.