PAINT annotation of PGRP (PTHR11022)

hattrill commented 5 years ago

Could you please block and reassess the annotations propgated from PTN001664863 PTN001664864 PTN001336553

I've got a couple of tickets open on some of these nodes #2555 and #2558 which has prompted me to look at the Peptidoglycan Recognition Proteins. I shall roll these up into this ticket and close those.

Note: I can't see the Tree node information so it's hard for me to dig properly (get "Unable to retrieve family information at this time for null" when following the linkout)

So.....PGRP across species can act in a variety of different ways: some are receptors, some have amidase function, some are peptidoglycan receptors, some are secreted, some are transmembrane and some are even intracellular; some are part of immune response signaling pathways, some positively or negatively regulate these pathways.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412580/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779587/

In short, the variety of activities associated with these related proteins makes it hard to PAINT.

For D.mel all of our PGRPs and one that is not a PGRP have annotations propagated from three nodes:

PTN001664863 peptidoglycan binding
extracellular space

PTN001664864 peptidoglycan receptor activity N-acetylmuramoyl-L-alanine amidase activity

PTN001336553 defense response to Gram-positive bacterium negative regulation of natural killer cell differentiation involved in immune response antimicrobial humoral response

but they do not all have these activities/locations and some activities are directly in conflict e.g. N-acetylmuramoyl-L-alanine amidase activity and peptidoglycan receptor activity

negative regulation of natural killer cell differentiation involved in immune response - is a) too specific and b) vertebrate-specific and there are some odd choices given the number of experimental annotations available: "defense response to Gram-positive bacterium" seems odd to choose as gram-neg response must also be heavily annotated? As does "extracellular space" as there are plenty of int. to plasma membranes. (Fixing the NOT issue would also help with the enzyme activity)

Immune processes are very divergent across species - this is a good example of where some background in the subject and some logic checks would help.

I am in the process of cleaning up any spurious annotations that come from non-IBA sources.

pgaudet commented 5 years ago

@hattrill You get an ''Unable to retrieve family information at this time for null" when following the linkout'' -> from where ? AmiGO ?

I was looking at the IBAs for FBgn0035975 and again we dont see the family ID in AmiGO- I thought this was resolved @dustine32 @kltm ?

hattrill commented 5 years ago

I can still see them in http://amigo.geneontology.org/amigo/search/annotation?q=FB:FBgn0035975 but they may have fixed them in PAINT, but I have no indication of that.

Node tree seems to be working today: http://www.pantree.org/node/annotationNode.jsp?id=PTN001664864 went to coorect page with no error.

pgaudet commented 5 years ago

I meant, the PANTHER family column is empty

hattrill commented 5 years ago

So it is - the link is in the IBA "with": Screenshot 2019-07-17 at 11 40 43

pgaudet commented 5 years ago

Right - there is a link to Pantree. However the PTHRID should be in this table. I think @dustine32 and @kltm know what I mean; I reported this before.

Pascale

dustine32 commented 5 years ago

@pgaudet Yeah those Panther family columns should be filled in with something. Thanks for the examples. I'll track down the reason.

dustine32 commented 5 years ago

@pgaudet @kltm I think this problem is limited to FlyBase (and also likely WormBase) identifiers and is tackled here.

To illustrate, tracing this GP to its Panther family's tree file used in populating the amigo column, I see the line entry for PGRP-LA's ID FB:FBgn0035975:

AN204:DROME|FlyBase=FBgn0035975|UniProtKB=Q95T64;

It's this discrepancy between FB: and FlyBase= prefixes causing the mismatch that prevents the family column population. I fixed this problem for FB: and WB: but only in the tree file generation for 14.1 trees. And amigo (through the release pipeline) is still pulling the 13.1 trees and IBAs. I'm actually hoping to test the 14.1 switch on snapshot today.

kltm commented 5 years ago

@dustine32 Don't we have the FlyBase/FB, WormBase/WB being tracked in another ticket as well?

dustine32 commented 5 years ago

@kltm Oh right! I guess in the Panther helpdesk too: https://github.com/pantherdb/Helpdesk/issues/3

kltm commented 5 years ago

For GO, https://github.com/geneontology/go-site/issues/512 https://github.com/geneontology/go-site/issues/685 Others?

pgaudet commented 5 years ago

(continue discussion on appropriate ticket geneontology/go-site#512)

marcfeuermann commented 5 years ago

The family has been completely reviewed. Only small vertebrate nodes where there are no big duplication patches have been annotated.

geneontology / go-annotation

PAINT annotation of PGRP (PTHR11022) #2559