Difference between revisions of "Chado Natural Diversity Module/natdiv schema changes call"
From GMOD
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* Add environmentprop. This is useful when creating phenstatements. | * Add environmentprop. This is useful when creating phenstatements. | ||
− | ** Example phenstatement: “The mean of the phenotype | + | ** Example phenstatement: “The mean of the phenotype root length in genotype TN7.4 given an environment of NaCl treatment of 100 millimolar is 10.5 mm” |
− | ** environment: uniquename=' | + | ** environment: uniquename='100 NaCl' |
** environmentprop: type_id='NaCl treatment', value=100, cvalue_id='mM' | ** environmentprop: type_id='NaCl treatment', value=100, cvalue_id='mM' | ||
* Add phenstatementprop. This is useful when creating phenstatements. | * Add phenstatementprop. This is useful when creating phenstatements. | ||
** phenstatement: type_id = 'summary statistic', phenotype_id='flower number', genotype_id='TN7.4', pub_id='experimental result' | ** phenstatement: type_id = 'summary statistic', phenotype_id='flower number', genotype_id='TN7.4', pub_id='experimental result' | ||
− | ** phenstatementprop: type_id='mean', value = 10, cvalue_id=' | + | ** phenstatementprop: type_id='mean', value = 10.5, cvalue_id='mm' |
* Add nd_experiment_protocolprop. I use this to store protocol values specific to an nd_experiment. | * Add nd_experiment_protocolprop. I use this to store protocol values specific to an nd_experiment. | ||
** Eg: nd_protocol.type_id='NaCl treatment', nd_experiment_protocolprop:{type_id='treatment amount', value=100, cvalue_id='mM'} | ** Eg: nd_protocol.type_id='NaCl treatment', nd_experiment_protocolprop:{type_id='treatment amount', value=100, cvalue_id='mM'} | ||
** +1, could definitely use this for same reasons (e,g, same insecticide resistance assay protocol, but with different insecticides, exposure times, and/or concentrations; currently using nd_experimentprop) [[User:Maccallr|Maccallr]] 13:24, 30 May 2011 (UTC) | ** +1, could definitely use this for same reasons (e,g, same insecticide resistance assay protocol, but with different insecticides, exposure times, and/or concentrations; currently using nd_experimentprop) [[User:Maccallr|Maccallr]] 13:24, 30 May 2011 (UTC) | ||
* Add nd_experiment_phenotypeprop. I use this to store phenotype observations specific to an nd_experiment. | * Add nd_experiment_phenotypeprop. I use this to store phenotype observations specific to an nd_experiment. | ||
+ | ** Eg: phenotype.observable_id='root length', nd_experiment_phenotypeprop:{type_id='observation', value=10.5, cvalue_id='mm'} | ||
* Add cvalue_id to NatDiv property tables and related property tables like projectprop. This allows for postcomposition of cvterms like units to the property type_id. | * Add cvalue_id to NatDiv property tables and related property tables like projectprop. This allows for postcomposition of cvterms like units to the property type_id. | ||
+ | ** Eg: type_id='my experimental bucket color', cvalue_id='purple' | ||
** Chado has some way to [http://gmod.org/wiki/Chado_CV_Module#Post-coordinating_Terms post-compose cvterms] which [[User:Maccallr|Maccallr]] 11:56, 17 May 2011 (UTC) doesn't understand. | ** Chado has some way to [http://gmod.org/wiki/Chado_CV_Module#Post-coordinating_Terms post-compose cvterms] which [[User:Maccallr|Maccallr]] 11:56, 17 May 2011 (UTC) doesn't understand. | ||
Revision as of 22:13, 31 May 2011
Conference call to resolve the latest proposed changes to natdiv module.
Contents
Date
Thursday, May 26, 6pm BST / 1pm EST / 10am PST
Participants
- Seth
- Bob Made some notes here
- Scott
- Rob
- Naama
- Lukas
- Sook
- Yuri
- Maren
- Lacey
- Hilmar
Agenda
- Triage proposed changes into the following categories:
- implement before paper publishing
- implement after paper publishing
- do not implement
- Bio::Chado::Schema update
- can someone do one after the changes have been made? Maccallr 14:37, 26 May 2011 (UTC)
Proposed changes
Prop table in genotype module
- change: addition of (vanilla) prop table to genotype module [cvterm_id, value, rank]
- proposer: Seth Redmond / Vectorbase
- reason: enables us to store ontology terms for current genotypes, e.g. presence/absence of specific inversions - impossible under current schema
- Did I understand correctly that for a genotypeprop table that cvterm_id would allow NULL? Scott 17:17, 26 May 2011 (UTC)
Hackathon changes
- phenotype
- phenotypeprop (Can somebody add the reason for adding this table?)
- SVN: gmodnatdiv branch:
- GMOD Evo Hackathon changes to phenotype module 1) Removed UNIQUE and NOT NULL constraints on phenotype.uniquename. 2) Added phenotype.units_id. 3) Added phenotypeprop table. 4) Deprecated phenotype_cvterm table.
- Diff: http://gmod.svn.sourceforge.net/viewvc/gmod/schema/branches/gmodnatdiv/modules/phenotype/phenotype.sql?r1=24150&r2=24140&pathrev=24150
Yuri's proposals
- Add environmentprop. This is useful when creating phenstatements.
- Example phenstatement: “The mean of the phenotype root length in genotype TN7.4 given an environment of NaCl treatment of 100 millimolar is 10.5 mm”
- environment: uniquename='100 NaCl'
- environmentprop: type_id='NaCl treatment', value=100, cvalue_id='mM'
- Add phenstatementprop. This is useful when creating phenstatements.
- phenstatement: type_id = 'summary statistic', phenotype_id='flower number', genotype_id='TN7.4', pub_id='experimental result'
- phenstatementprop: type_id='mean', value = 10.5, cvalue_id='mm'
- Add nd_experiment_protocolprop. I use this to store protocol values specific to an nd_experiment.
- Eg: nd_protocol.type_id='NaCl treatment', nd_experiment_protocolprop:{type_id='treatment amount', value=100, cvalue_id='mM'}
- +1, could definitely use this for same reasons (e,g, same insecticide resistance assay protocol, but with different insecticides, exposure times, and/or concentrations; currently using nd_experimentprop) Maccallr 13:24, 30 May 2011 (UTC)
- Add nd_experiment_phenotypeprop. I use this to store phenotype observations specific to an nd_experiment.
- Eg: phenotype.observable_id='root length', nd_experiment_phenotypeprop:{type_id='observation', value=10.5, cvalue_id='mm'}
- Add cvalue_id to NatDiv property tables and related property tables like projectprop. This allows for postcomposition of cvterms like units to the property type_id.
- Eg: type_id='my experimental bucket color', cvalue_id='purple'
- Chado has some way to post-compose cvterms which Maccallr 11:56, 17 May 2011 (UTC) doesn't understand.
Bob's proposals
Just looking at the NatDiv prop tables, saw some inconsistencies:
- nd_geolocationprop.value is varchar(250) while others in NatDiv are 255. Rest of chado is type 'text'. Propose change to text.
this means we need to change the value type in all nd prop tables to text (Naama)
- nd_experimentprop.value is NOT NULL while all others (in NatDiv) allow NULL (rest of chado is mixed). Propose all allow NULL.
This was already fixed. I committed the SQL a couple of weeks ago (Naama)
- I just haven't rolled it into the default_schema.sql yet Scott 17:10, 26 May 2011 (UTC)