Chado
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GMOD
the GMOD database schema
I'm [creating a Tripal module](https://github.com/NAL-i5K/tripal_eutils) that imports NCBI XML and creates chado records, as well as linked records. I think it would be neat to have a recommended, agreed upon...
as part of mapping NCBI data into chado (see #76 ) I am adding NCBI assemblies as Chado analyses. NCBI assemblies are directly associated with biosamples, which map to chado...
**Summary** Recent versions (9.3+) of PostgreSQL that have been patched for [CVE-2018-1058 ](https://nvd.nist.gov/vuln/detail/CVE-2018-1058) will throw the following error when a vacuum / analyze is attempted on the featureloc table. **Error**...
This issue imported from the [Chado v1.4 requested changes](https://docs.google.com/document/d/1t_Jb4XxUPtgGRSKtznsqvjTjmR4vpFHPQROMQ0OZK9A/edit) google doc: http://gmod.827538.n3.nabble.com/proposal-for-changes-to-the-phenotype-module-tc4044535.html#a4044612 - Deprecate fields of the phenotype table: observable_id, attr_id, cvalue_id, assay_id - New tables: - phenotype_cvtermrelationship - Naama...
This issue imported from the [Chado v1.4 requested changes](https://docs.google.com/document/d/1t_Jb4XxUPtgGRSKtznsqvjTjmR4vpFHPQROMQ0OZK9A/edit) google doc: Changes suggested by Bob MacCallum, VectorBase (population biology browser runs off Chado) **cvterm**: Email discussions in March 2012 ("[Anyone...
Updating table descriptions to generalize mage to include next-gen sequencing experiments and other possible analyses instead of microarray only. This is a suggested topic for the 2018 PAG hackathon. A...
There are a lot of suggestions I have regarding modifications to the Chado schema. How do I best make those suggestions? Is there an automated build system? You have a...
Storing coordinates for features on maps with float coordinates is awkward. featurepos+featureposprop to indicate start and stop coordinates can work, but feels unnecessarily convoluted. Some thoughts and discussion: - Change...
Something I was reflecting on with Tripal is we do a lot of weird checks to determine if a chado table is a base table or not-- and even then,...
http://gmod.org/wiki/Chado_Post-Composed_Phenotypes - Changes requested to phenotype_cvterm for managing relationships - add a ‘grp_id’ to link the phenotype_cvterm table to the group module - Add a ‘type_id’ - Stephen Ficklin says...