Chado Documentation Reorganization

This page is under construction.

Please do not use it until this notice goes away.

We are starting the process of reorganizing the Chado related documentation in this web site. Chado is the database schema of GMOD and it actually has quite a bit of documentation in this web site. However, the doc could be better organized and integrated. This page describes the reorganization plan, and will continue to exist until that plan is completed.

Dave Clements
GMOD Help Desk

Introduction

This page first provides an overview of the most important Chado related pages in this web site. This overview is followed by a proposed new structure. Finally, we talk about the mechanics of the reorganization.

What Exists

This summarizes the major Chado related pages that existed when the reorganization began in early April 2008. It is not an exhaustive list of pages related to Chado. See the Chado Category for that.

Page	Description	Comments
Chado - Getting Started	Sections: 1 Documentation; 2 Modules; 3 Installation; 4 Loading Data; 5 Contacts; 6 Pronunciation	Need to reconstruct it.
Chado Best Practices	Description of how various sequence features can be represented in Chado. Has placeholders for genotypes, phenotypes and a few others.	This be a good starting point for a how do you represent X in Chado page - a best practices page.
Chado Doc Project	Brian Osborne's call-to-arms to write "material that is very practical and specific" meaning "Best Practices" and "module pages". Brian broke Chado up into 8 workpackages and sent out a call for volunteers. 3 of the 8 packages have been claimed.	I'll follow up on this once the first pass at the reorganization is done.
Chado FAQ	Currently has 5 widely disparate questions.	Split questions into FAQs and Best Practices. Best Practices cover "How do you represent 'x' in Chado" questions, and FAQs handle everything else.
Chado Manual	A high level, architectural view of Chado. Has 5 sections: 1) Intro (Modularity, Ontologies, Associated Software, Complexity and Detail, Data Integration, Support), 2) Modules, 3) Naming Conventions 4) Design Patterns, 5) DBMS Functions.	Explains chado from a database practitioners point of view.
Chado New Users	This page, and its associated discussion page follow the learning curve for new Chado users learning the system at CSHL.	A collection of user installation/experience logs would be darn useful. Create a template for this that encourages users to list things like versions used. This reduces the need to keep "Installing component X on platfrom Y" pages up to date for every possible combination. Just have a list of user log pages that detail X and Y.
Introduction to Chado	An explanation of the Sequence module.	Change the title. This is almost entirely about the Sequence module. Chris Mungall also indicates that this page is no longer current.
Sample Chado SQL	Shows 8 or 9 queries.	All but one of the queries involves the feature table. Integrated the SQL with the best practices.
A Chado Case Study (pdf)	The official publication about Chado. From ISMB/ECCB 2007.
Chado Manaul (PDF)	A PDF Chado manual.	The TOC is extensive, but many sections are empty. Much of this information has already been transfered to wiki pages. Sections with content: 1) DBMS Functions (see Chado Manual), 2) The General Module (see Chado Manual), 3) The CV Module (see Chado CV Module), 4) The Sequence Module (see Chado Sequence Module, Chado Best Practices), and 5) Chado Naming Conventions (see Chado Manual). Add pointers to the PDF page to the wiki pages that now cover the same material.
Template:ChadoModules	All the module documentation.	There is a page for each module, and each page contains a complete physical description of each table and column. Many modules also have some explanatory text, as do many tables and columns. Keep and expand this.
GMOD Users	A list of GMOD users. Has a column for Chado users.	List users differently. Problem is maximizing usefulness without maximizing redundancy. Want 1) A list of users per component, including how they use it. For Chado this would include OS, OS release, DBMS, DBMS release, and list of modules in use. 2) List of all GMOD users with pointers to what components they use. The overall list is high level; the component lists are detailed. Keeping them in synch, even though they are at different levels of detail, is the hard part.