Missing reactome nodes

[jaredroach]

do we intend to have full reactome?
e.g.
R-HSA-112043. PLC beta mediated events.
R-HSA-1855204. Synthesis of IP3 and IP4 in the cytosol.
I cannot find these in the knowledge graph. I think it would be useful to have these for constructing gold standard pathways. Perhaps even more pathways (e.g., radiation-induced DNA damage), but it might be sufficient to have such nodes as this Reactome node:

3' ends of DNA double strand break
Stable Identifier R-ALL-75155
Type OtherEntity Compartment nucleoplasm

[dkoslicki]

This pathway is apparently not being picked up by the seed-and-expand approach. @saramsey correct me if I'm wrong, but the solutions are:

1. Add these nodes as per have BuildMasterKG load a single TSV file of "seed nodes" #48 (TSV file)
2. Expand more than 3X

[saramsey]

Correct, and I favor (1) over (2).

…

----------------------------------------------------- Stephen Ramsey Assistant Professor, Oregon State University * School of Electrical Engineering and Computer Science * Department of Biomedical Sciences 208A Dryden Hall stephen.ramsey@oregonstate.edu<mailto:stephen.ramsey@oregonstate.edu> http://lab.saramsey.org On Apr 16, 2018, at 1:24 PM, David Koslicki <notifications@github.com<mailto:notifications@github.com>> wrote: This pathway is apparently not being picked up by the seed-and-expand approach. @saramsey<https://github.com/saramsey> correct me if I'm wrong, but the solutions are: 1. Add these nodes as per #48<#48> (TSV file) 2. Expand more than 3X — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#68 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AFTe-3gaVEoxRPTpyLLgeN6JW6meycDVks5tpP3jgaJpZM4TXKte>.

[dkoslicki]

@jaredroach if you have a list of missed pathways, we can add them as @saramsey mentioned.

[saramsey]

rebuilding the KG to get these reactome pathways

[dkoslicki]

@saramsey Is this fixed in the most recent KG, or the one that's still running? I guess I'll leave it to you to close this issue when appropriate.

[saramsey]

fixed in #179