[Gmod-phendiver] Notes from Natdiv schema changes call

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[Gmod-phendiver] Notes from Natdiv schema changes call

Naama Menda
 
ND paper
Sook and Naama will send a note when the working draft is ready for review. All the authors can view the google doc.
Let Naama know if you'd like to make changes now.

Genotype module

* add type_id to genotype (can be null) 
* add genotypeprop


Phenotype module
 * phenotype table
- drop the Unique constraint from phenotype.unique? - problem with calling a column 'uniquename' but have it non-unique
 also tables should have natural key that is not the PK

--Hilmar
phenotypes and their measurements are forced into 1-1 relationship because they are stored in the same table

--Seth
storing a different table for storing the phenotype value would cause more problems (was discussed at the Hackathon - adding a phenotype observation table)

--Lacey
allow to replicate the same phenotype experiment multiple times. Need a phenotype relationship table to show replication of the same experiment.
We can add a name column to phenotype, this would solve the uniquename problem and will be backward compatible.

--Lukas
post-composing terms should be made possible .
Need an additional linking table for post-composed terms, because these are not props of the phenotype

--Yuri
using phenotypeprop for postcomposed terms was decided at the Hackathon, and it works for us, but I can see how other approaches may be better

--Lukas
terms like 'leaf size in an adult plat' - supporting post-composed terms in a normalized database is important

in normalized database design we realize we have a many-many relationship, adding a linking table would allow specifying as many terms as needed for defining the term.

--Sook
value should stay in the phenotype table

--Seth
post-composition is a topic for another discussion because it raises many new issues. Some were discussed at the Hackaton.

--Naama
all this does not affect the ND paper, because the phenotype module is beyond its scope

*decision - leaving uniquename as is. Those of us who are using it non-uniquely would have to concatenate something to this field
                  Add name column to the phenotype table

--Bob
Flybase does not store quantitative terms, and they don't use PATO terms. They also use either observable_id or attr_id
(see more here http://gmod.org/wiki/Chado_Phenotype_Module_at_FlyBase)

--Naama
adding the name column could be the first step in deprecating some of the columns in the phenotype table, if we go ahead and separate the actual phenotype (EQ model, or anything else) from the measurement (the value that would remain in the phenotype table)

-------
phenotypeprop
some are using this table for post-composing terms, which requires adding a cvalue_id , and also raises the question if this is a good place for it.


Suggestion - add a type_id to phenotype_cvterm (solve the post-composed terms issue). Need this to specify the relationship between the phenotype and the cvterm.
                      think over adding phenotypeprop, but as a standard prop table (without cvalue_id)

*Decision - do not change the schema, and test the above suggestion.
Yuri will add use case to the wiki, and possibly others. This is important for the next phase of the phenotype module.
The suggested changes seem small, but they will change completely the way we store phenotype, measurements, re-use phenotypes, etc.

--Scott
I want to have a new release of Chado more or less together with the submission of the paper. Need to do this soon.

--Lacey
-Add a note to the ND paper about the future changes to the phenotype module that would allow  efficiently post-composition of terms
This is important because whoever uses ND would want to know how to use the phenotype moule
(Naama will add this to the paper)

------
Agreed:
-fill the Doodle for a meeting next week, because we need to talk about Yuri's proposed changes first. This is important for the Chado release and the ND paper.
-Commit the schema changes to the genotype and phenotype modules
-Work on the wiki with the proposal for using phenotype_cvterm for post-composed cvterms (with type_id column). If this does not work, need to consider another linking table specific for phenotypes.










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