GRMZM2G104843 does not show up as part of jasmonic acid biosynthesis pathway

[mycrobe]

According to Plant Reactome, GRMZM2G104843 is part of jasmonic acid biosynthesis.

However, it's not in this list of jasmonic genes, and does not show pathway information in its result view.

Marcela has reported that @preecej is dealing with a related issue in Reactome Search.

Acceptance Criteria: Pathway details view shows up for GRMZM2G104843, and GRMZM2G104843 is in the result list for jasmonic acid biosynthesis pathway.

[preecej]

Noted. Working on it.

On 03/15/2016 02:34 PM, Joe Mulvaney wrote:

According to (Plant Reactome)[http://plantreactome.gramene.org/PathwayBrowser/#SPECIES=6951903&DIAGRAM=6957159&ID=6952120&PATH=6957147,6957146,6957157&DTAB=MT], GRMZM2G104843 is part of jasmonic acid biosynthesis.

However, it's not in this list of jasmonic genes http://brie/gramene-search/reactome-img/#%7B%22pathways__ancestors:1119332%22:%7B%22category%22:%22Plant%20Reactome%22,%22display_name%22:%22jasmonic%20acid%20biosynthesis%22,%22fq%22:%22pathways__ancestors:1119332%22%7D,%22taxonomy__ancestors:4577%22:%7B%22category%22:%22Taxonomy%22,%22display_name%22:%22Zea%20mays%22,%22fq%22:%22taxonomy__ancestors:4577%22%7D%7D, and does not show pathway information in its result view http://brie/gramene-search/reactome-img/#%7B%22id:GRMZM2G104843%22:%7B%22category%22:%22Gene%22,%22display_name%22:%22GRMZM2G104843%22,%22fq%22:%22id:GRMZM2G104843%22%7D%7D.

Marcela has reported that @preecej https://github.com/preecej is dealing with a related issue in Reactome Search.

Acceptance Criteria: Pathway details view shows up for GRMZM2G104843, and GRMZM2G104843 is in the result list for jasmonic acid biosynthesis pathway.

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[mycrobe]

@preecej is this a plant reactome issue?

Should gramene search simply expect fixed data for Release 51?

[preecej]

It's both Plant Reactome search (maize) and Gramene search (an indexing issue?). Marcela put both sites' issues in one ticket.

I'm working on fixing the search interface in Plant Reactome, then I'll need to give you & Andrew a new index dump. At that point, we should see if there is something in the formatting of Gramene's data load that is also causing issues, b/c tools.gramene.org takes users to the PR search results page, when it should be linking directly to pathway diagrams.

• j

On 03/15/2016 02:36 PM, Joe Mulvaney wrote:

@preecej https://github.com/preecej is this a plant reactome issue?

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[mycrobe]

Could you please add links to the tickets you mentioned in this one?

Thanks!

On Mar 15, 2016, at 5:56 PM, Justin Preece notifications@github.com wrote:

It's both Plant Reactome search (maize) and Gramene search (an indexing issue?). Marcela put both sites' issues in one ticket.

I'm working on fixing the search interface in Plant Reactome, then I'll need to give you & Andrew a new index dump. At that point, we should see if there is something in the formatting of Gramene's data load that is also causing issues, b/c tools.gramene.org takes users to the PR search results page, when it should be linking directly to pathway diagrams.

• j

On 03/15/2016 02:36 PM, Joe Mulvaney wrote:

@preecej https://github.com/preecej is this a plant reactome issue?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/warelab/gramoogle/issues/131#issuecomment-197031565

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[mycrobe]

The resolution here is to wait for updated data with Release 51.