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Tracker for issues discovered during pre-release testing.
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Polymer not showing all xrefs (example: chitin in fungal pathogen/immunity response pathway) #5

Open preecej opened 6 years ago

preecej commented 6 years ago

Problem: Chitin simpleEntity is not showing the full xrefs for the polymer (R-ALL-9611192).

Possible cause: Appear to be missing some external reference data, or the code to display it.

Pathway examples: Neg: Plant Reactome Pos: Reactome Curator Pos: Human Reactome

naithanis commented 6 years ago

How about peptidoglycan? which is from bacteria.

Do we need to add bacteria and fungal species in slicing or somewhere to show these components?

Sushma

On Fri, Aug 31, 2018 at 11:22 AM, Justin Preece notifications@github.com wrote:

Problem: Chitin simpleEntity is not showing the full xrefs for the polymer (R-ALL-9611192).

Possible cause: Appear to be missing some external reference data, or the code to display it.

Pathway examples: Neg: Plant Reactome http://cord3084-pc7.science.oregonstate.edu/PathwayBrowser/#/R-OSA-9611432&SEL=R-ALL-6786438 Pos: Reactome Curator http://reactomecurator.oicr.on.ca/PathwayBrowser/#/R-OSA-9611432&SEL=R-ALL-6786438&PATH=R-OSA-2894885,R-OSA-9612650 Pos: Human Reactome https://reactome.org/PathwayBrowser/#/R-HSA-8935690&SEL=R-ALL-6786438&PATH=R-HSA-8963743

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jaiswalp commented 6 years ago

We checked. It is not a species problem perse because small molecules don't have species associated with them. Pankaj

On 8/31/2018 11:47 AM, Sushma wrote:

How about peptidoglycan? which is from bacteria.

Do we need to add bacteria and fungal species in slicing or somewhere to show these components?

Sushma

On Fri, Aug 31, 2018 at 11:22 AM, Justin Preece notifications@github.com wrote:

Problem: Chitin simpleEntity is not showing the full xrefs for the polymer (R-ALL-9611192).

Possible cause: Appear to be missing some external reference data, or the code to display it.

Pathway examples: Neg: Plant Reactome

http://cord3084-pc7.science.oregonstate.edu/PathwayBrowser/#/R-OSA-9611432&SEL=R-ALL-6786438 Pos: Reactome Curator

http://reactomecurator.oicr.on.ca/PathwayBrowser/#/R-OSA-9611432&SEL=R-ALL-6786438&PATH=R-OSA-2894885,R-OSA-9612650 Pos: Human Reactome

https://reactome.org/PathwayBrowser/#/R-HSA-8935690&SEL=R-ALL-6786438&PATH=R-HSA-8963743

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https://github.com/notifications/unsubscribe-auth/AH0qa-WEQAMdFsr4zly4EXvNYMb4cUS3ks5uWX79gaJpZM4WVqcP .

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-- 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 http://icbo-conference.org