Feedback on new annotation table

[cshenry]

1.) In the subsystem column, these should be links to the PlantSEED subsystem page:
http://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=Acetyl-CoA_biosynthesis_in_plants

In these links, replace "_" with " " in the subsystem name that is visible to the user.

2.) In the functional role column, these should like to this page:
http://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&subsystem=Acetyl-CoA_biosynthesis_in_plants&fr=Pyruvate%20dehydrogenase%20E1%20component%20alpha%20subunit%20(EC%201.2.4.1)

Admittedly, that page loads pretty slowly... but for now it's what we have.

3.) The pathways should link to MetaCyc (or AraCyc - but I couldn't find it):
http://metacyc.org/META/NEW-IMAGE?type=NIL&object=PWY-5172&redirect=T

4.) The features should link to our own feature page for that feature

[samseaver]

Pathways can be linked thus:

http://pmn.plantcyc.org/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5172

I'd rather that the roles were not linked. One can see them in the subsystems.

Features are Arabidopsis exemplars and thus link to the corresponding feature in Athaliana-TAIR10 genome.

Can reactions be linked to the reaction page in biochemistry? (is there such a thing yet?)

[cshenry]

There is no "reaction" page yet. We need one. Not before workshop, but before final release of the site.

Also, we should have our own functional role page... and possibly subsystem page as well. The PubSEED pages are brutally painful in their slowness... but again, not before workshop.

[nconrad]

I can at least add the same reaction slide-out as in the model page. And I
can add anything needed there from the SOLR biochem API.

On Sunday, August 9, 2015, cshenry notifications@github.com wrote:

There is no "reaction" page yet. We need one. Not before workshop, but
before final release of the site.

Also, we should have our own functional role page... and possibly
subsystem page as well. The PubSEED pages are brutally painful in their
slowness... but again, not before workshop.

—
Reply to this email directly or view it on GitHub
#7 (comment).

---

t. 815-508-7951
e. nealconrad@gmail.com

[nconrad]

(1), (3), and (4) should be deployed. I didn't do (2) based on Sam's comment.... The loading of the seed functional role pages were the slowest I ever seen.

The reaction linkage is more complicated than I thought and needs a general solution, so I'm coming back to that later.