Polar auxin transport - missing gene products (and reaction) in projections; diagram misdrawn

PlantReactome / production-issues

Tracker for Plant Reactome issues in Production, whether internally or externally reported.

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Polar auxin transport - missing gene products (and reaction) in projections; diagram misdrawn #1

Closed jaiswalp closed 8 years ago

jaiswalp commented 8 years ago

http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=8858053&PATH=2894885,2744345,2744341 Few issues.

diagram got messed up on the right side
The projections does not recognize anything on the right hand size for PIN protein genes e.g. citrus http://plantreactomedev.oicr.on.ca/PathwayBrowser/#SPECIES=8884629&DIAGRAM=8892891&PATH=8892698,8892697,8892710 A. thaliana http://plantreactomedev.oicr.on.ca/PathwayBrowser/#SPECIES=8950633&DIAGRAM=8955775&PATH=8955592,8955591,8955604

A. thaliana should have picked up the homologs of PIN. Can you check in the homology files rice gene Os01g0643300 has 12 paralogs and orthologs to in A. thaliana i.e. AT1G70940, AT2G01420, AT1G23080.

deustp01 commented 8 years ago

Fixed the diagram in gk_central. (I don't know how to patch a diagram instance in the slice db.)

jaiswalp commented 8 years ago

Thanks Peter. I think for the slice we might have to live with it.

Pankaj

On 3/11/2016 12:14 PM, deustp01 wrote:

Fixed the diagram in gk_central. (I don't know how to patch a diagram instance in the slice db.)

— Reply to this email directly or view it on GitHub https://github.com/PlantReactome/temp-issues/issues/1#issuecomment-195528236.

Pankaj Jaiswal, PhD Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA

Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jaiswalp@oregonstate.edu Web: http://jaiswallab.cgrb.oregonstate.edu/

preecej commented 8 years ago

We could experiment with updating the diagram directly from the curator db to our slice, but I suggest we make that a lower priority and try it if there's time before the release date.

Looking into orthology mapping for genes mentioned.

preecej commented 8 years ago

Cannot directly upload the corrected XML (after downloading from gk_central) to local slice. Tried it; XML property not visible, and does not allow merging. We'll have to get it in the next slice.

PIN gene mentioned now present in At projections. Will not appear in citrus projections until inparanoid clusters downloads for OS ids are appended. Will become a moot point when LOC ids are updated before next release.

preecej commented 8 years ago

Projection fixed and deployed to Test. Verified and closed:

http://plantreactomedev.oicr.on.ca/PathwayBrowser/#SPECIES=8951557&DIAGRAM=8957055&ID=8956851&PATH=8956872,8956871,8956884&DTAB=MT

Diagram repaired in central db. Will appear in Release 51.