Re: [Gmod-schema] Query Regarding Selective Use of Chado Modules for Custom Database Design

[Guignon, V. (A. Bioversity-CIAT) <v.g...@cg...>]

Hi Parwa,

To complete Scott answer, if you consider a web user interface in your project, you definitely should use Tripal/Drupal. It will help you instantiate a Chado schema and even if you just use sub-parts of it, it’s fine! The Tripal community is quite active and holds weekly meetings on Gather Town (where you could get live support and even if the weekly meeting might be late for you, we can chat on slack - https://tripal-project.slack.com/archives/C63AQ0FQE - or you could meet earlier with European people like me on demand).

Regarding your plans, you can give a try to Tripal 4 (at least to instantiate a Chado schema) but if you feel like you’re missing pieces, contact us and we could try to find solutions. I’m currently working on a parallel project also based on Drupal (and compatible with Tripal) that could fill the gaps.

   Valentin


From: Scott Cain <sc...@sc...>
Sent: Thursday, 15 August 2024 18:12
To: PARWAMUHSIN ISMAEL <par...@og...>; GMOD Schema/Chado List <gmo...@li...>
Subject: Re: [Gmod-schema] Query Regarding Selective Use of Chado Modules for Custom Database Design


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Hi Parwa,

I'm not sure what you mean by "supported." Obviously, Chado is open source, so if there are pieces you find useful for your own project, you are welcome to use them (though citing Chado would be nice if this is something that might get published). The loading tools that are "packaged" with Chado are quite old and might not work well for a stock Chado installation. Most people who use Chado use it with Tripal (https://tripal.info/) a Drupal-based web frontend for Chado which comes with its own loading tools. Certainly, your use case would not work with Tripal out of the box either. Basically, what I'm saying, you're likely to need to write your own loading tools.

Scott

On Mon, Aug 12, 2024 at 3:17 PM PARWAMUHSIN ISMAEL <par...@og...<mailto:par...@og...>> wrote:
Dear Chado Support Team,
I hope this message finds you well.
I am currently in the process of designing a database for biological data. For this project, I am considering using a subset of the Chado schema and wanted to inquire about the feasibility and potential implications of this approach.

Specifically, I am interested in using only three modules from the Chado schema:

cv: Limited to the cv and cvterm tables, along with cvterm_dbxref.
organism: In its entirety.
publication: Limited to the pub, pubprop, and pub_dbxref tables.
Additionally, I plan to add some custom tables tailored to the specific needs of my project.

Would this selective use of the Chado schema be supported, or could it potentially lead to any issues in terms of database integrity, compatibility with Chado tools, or future data integration?

I appreciate any insights or recommendations you can provide on this matter.

Thank you for your time and support.

Best regards,
Parwa Muhsin Ismael
Istanbul University


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Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)