Re: Opening up comments on changes to Chado

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Re: Opening up comments on changes to Chado

Lacey-Anne Sanderson-3
Hi Scott,
Sorry I’m more than a little late in on this discussion -are you still accepting proposed changes?

If so, I just came across an inconsistency in the project_relationship table. Specifically, the fields include subject_project_id and object_project_id when all other chado _relationship tables just have subject_id and object_id. Is there any way we could get this changed to be more consistent before the next version of chado comes out? It breaks Tripal’s new generic relationship handling API...


> On 8/29/2013 4:28 PM, Scott Cain wrote:
> Hello,
> I'm thinking about changes to Chado and creating a new release (which would be numbered 1.3 since it involves schema changes since the 1.23 release).  Before I move too far down this road, I wanted to highlight changes that have been committed to the Chado schema since the 1.23 release and open them up to public comment.
> The main additions to the Chado schema come from FlyBase, particularly an addtional "submodule" for organism for dealing with strains as well as a few additional tables for organism, like organism_pub and organism_cvterm.  There are several tables added called strain, strainprop, and others that as you might predict.  There are relatively few comments included with the DDL, so perhaps someone at FlyBase can give us the run down on how these tables are used.  One potential concern I have with these tables is that it is already possible to represent strains in Chado using the stock module, so how would we handle that conflict if the strain tables were incorporated.
> There are also a few other additions like library_expression, library_featureprop and library_interaction which are similarly uncommented so more background on how they are used would be great as well.
> I've attached a diff of the two schemas as they stand now for everyone's reference.
> Thanks,
> Scott
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (                     216-392-3087<tel:216-392-3087>
> Ontario Institute for Cancer Research

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