Re: [Gmod-schema] updating the phenotype module

[Chris M. <cjm...@lb...>]

Thanks Naama

Do you intend  to make a pull request for the schema changes? I'm not sure
what the current GMOD policy is but this works well on other standards
projects, with stakeholders giving +1s etc, and having the discussion
linked to the commit trail

If I could attempt a brief summary, sorry if this doesn't fully capture it:
you are moving from the old schema where phenotypes have a fixed number of
slots were available to a flexible number of slots.

Standardization of the slot fields (what you have as PE1, PE2, etc) is key
to successful interoperability. There are a few options here. One way is to
use RO relations. Another way is to treat these as a different layer from
the biological object graph, and to treat them as slots that may have
different meanings in different contexts.

This is actually quite well aligned with the Dead Simple OWL Design
patterns approach that a number of ontologies are switching to. See
https://github.com/dosumis/dead_simple_owl_design_patterns

For some example trait patterns, see
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

I think it would be a good idea to align the cvterms you use with the ones
we are using here. Sorry if this sounds a little opaque, I'll try and
provide more details later.



On Thu, May 26, 2016 at 10:44 AM, Naama Menda <nm...@co...> wrote:

> There are some proposed changes for allowing to post-compose cvterms
> linked to one phenotype
>
> http://gmod.org/wiki/Chado_Post-Composed_Phenotypes
>
> The detailed chnages are in the doc for proposed changes in Chado
>
> https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit
>
> This schema has minimal changes (only 1 new table and 2 new columns in
> phenotype_cvterm) and works well for simple EAV and complex EQ
> statements, as well as with post and pre-composed cvterms.
>
> We'd like to use some of these new features in our breeders databases, so
> if you are using the phenotype module please read those pages and send your
> input
>
>
> Thanks!
>
>
> Naama Menda
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca NY 14853
> USA
>
> (607) 254 3569
> Sol Genomics Network
> http://solgenomics.net/
> nm...@co...
>
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