Re: [Gmod-schema] Group module / dbxref

[Cannon, E. K [C. S] <ekc...@ia...>]

Hi Brandon,


I was eager to put the group module to use when developing a method for storing post-composed term, specifically, EQ statements. The table count exploded, so Naama and I settled on a completely different solution<http://gmod.org/wiki/Chado_Post-Composed_Phenotypes>. It's odd that creating a means of generically grouping data objects should be so difficult.

Maybe the problem was thinking that grouping should be provided via a module, when instead each module should have its own set of grouping tables, similar to all modules having Xprop, X_relationship, X_dbxref, X_Y tables. (Xgroup, Xgroupprop, Xgroup_relationship...?)

Ethy

________________________________
From: Bradford Condon <bra...@gm...>
Sent: Tuesday, February 13, 2018 8:48 AM
To: GMOD Schema/Chado List
Subject: [Gmod-schema] Group module / dbxref

Hi all,

I am working on an ortholog module that will read in OrthoFinder output and store it in Chado.

I’ve read the discussion on the Group Module<http://gmod.org/wiki/Chado_Group_Module> but after reaching out to the authors, they chose to implement ortholog groups for features using feature_<https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>dbxref<https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>.

Do people have recommendations they’d like to share for ortholog groups?  I’ve heard three general solutions:

Group module - This solution appealed to me but I’m gathering it has issues and may just be too complicated if feature groups are the only goal.

dbxref - You create a db with your families, and assign each family an accession in the db.  This works well if you’re using established groups hosted on say photozome, but what if i can’t link my groups to established ones and am using an internal db?  I guess extra info is stored in cvtermprop for each accession?

feature   - You create a feature that is the group feature, and associate the members with it.  Unfortunately this seems to contradict the definition of a feature.

featureprop - you have to annotate each feature as part of the group via feature prop.  This seems very problematic.


Any input or solutions would be greatly appreciated.

Thank you!

Bradford

Bradford Condon
Postdoctoral Scholar, University of Tennessee Knoxville
www.bradfordcondon.com<http://www.bradfordcondon.com>