Chado Natural Diversity Module/natdiv call notes

From GMOD
Jump to: navigation, search

Notes from the Chado_Natural_Diversity_Module/natdiv_schema_changes_call (May 26th 2011)

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

decisions

  • 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.