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PlantReactome / production-issues

Tracker for Plant Reactome issues in Production, whether internally or externally reported.
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Atlas expression data #6

Closed jaiswalp closed 8 years ago

jaiswalp commented 8 years ago

From Sushma:

1: The expression data is being projected from Human/mouse in the following pathways

Plant Pathways (projections from human) http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=2894885&DTAB=EX

Cellular process (projection from human) http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=2894886&PATH=2894885&DTAB=EX

ABA Biosynthesis and mediated signaling (projection is from human) http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=3899368&PATH=2894885,2744345,2744341&DTAB=EX

Abscisic acid mediated signaling http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=3899368&ID=3899351&PATH=2894885,2744345,2744341&DTAB=EX

Ethylene biosynthesis and signaling (projection is from mouse) http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=5225808&PATH=2894885,2744345,2744341&DTAB=EX

Amine and polyamine biosynthesis (projection is from mouse) http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=5096066&PATH=2894885,2744345&DTAB=EX

jaiswalp commented 8 years ago

Confirming, the same occurs for top level bin pathways on live site:

Works for metabolic pathways http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=2744345&PATH=2894885&DTAB=EX

jaiswalp commented 8 years ago

I believe some of the top level expression views are not working especially for cellular pathways. because we do not generate the indexes for ATLAS configuration. (Justin please confirm). But even if we ignore 'cellular processes' all the 'metabolic and regulatory' ones should show up at the top 'plant pathways'

preecej commented 8 years ago

That's a good guess: no indices for container pathways. Thanks for all the detail. I am looking into it.

jaiswalp commented 8 years ago

confirming: on live site that goes to human ABA http://plantreactome.gramene.org/PathwayBrowser/#DIAGRAM=3899368&PATH=2894885,2744345,2744341&DTAB=EX Ethylene http://plantreactome.gramene.org/PathwayBrowser/#DIAGRAM=5225808&PATH=2894885,2744345,2744341&DTAB=EX

jaiswalp commented 8 years ago

Top level Salicylic acid signaling : http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=6788019&PATH=2894885,2744345,2744341 does not show expression, but expression is visible for individual reactions http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=6788019&ID=6788032&PATH=2894885,2744345,2744341&DTAB=EX or complex http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=6788019&ID=6788138&PATH=2894885,2744345,2744341&DTAB=EX

guptapa commented 8 years ago

Citrulline-nitric oxide cycle No expression dat showing up http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=5633340&PATH=2894885,2744345,2744343&DTAB=EX

guptapa commented 8 years ago

amino acid catabolism showing- no baseline experiment for species Rattus http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=5655124&PATH=2894885,2744345,2744343&DTAB=EX but in sub pathways under this category is all visible

guptapa commented 8 years ago

No expression data in Beta-alanine biosynthesis I http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=1119567&PATH=2894885,2744345,2744343,5655122&DTAB=EX

jaiswalp commented 8 years ago

Same issue with citrulline. not for pathway but shows up for reaction http://plantreactomedev.oicr.on.ca/PathwayBrowser/#DIAGRAM=5633340&ID=1120995&PATH=2894885,2744345,2744343&DTAB=EX

preecej commented 8 years ago

Ok, ok. :) I've got enough examples to work with. Thank you.

preecej commented 8 years ago

The pattern is unclear, and the data for all of these examples appears to be present in the previous release (as well as the current). It seems random whether a particular pathway chooses to display a mouse, human, or rice anatogram, although there is a preponderence of container pathways in the mix.

I will ask Robert.

preecej commented 8 years ago

Please, could you specify a species in your REST call? E.g.: http://www.ebi.ac.uk/gxa/widgets/heatmap/referenceExperiment?geneQuery=5225808&species=oryza+sativa

If no species is provided a search is done across all species and returns the one which we consider is the most relevant.

Let us know if this works for you and don’t hesitate to get in touch with us if you run into any other problems.

Kind regards,

Alfonso

preecej commented 8 years ago

working on species specification in Atlas requests....

preecej commented 8 years ago

Even without species specification in widget call, the new ATLAS data load of latest Plant Reactome release has fixed the issue. All links provided above now return rice examples. No human or mouse anatograms appear.