I am looking for WordPress chart/diagram system design.
I found only the template hierarchy diagram, but it’s only part of the system.

source: http://upload.wikimedia.org/wikipedia/commons/3/3d/Wordpress_Template_Hierarchy.png
Answers:
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Method 1
More than an Answer, this is a research and a compilation. Database Description already in Damien answer.
A Google search reveals this in WordPress forums:
UML documentation of WordPress
As far as I know, that’s all we have. If you want to write one, I’m sure it’d be welcomed 🙂
(Ipstenu, referring to the Database Description)
UML of WordPress MU?
There will likely never be UML diagrams of WordPress because it’s not
an OO system. Some parts are OO-like, but overall it’s whatever that
particular code contributor made work. There’s no map, just code.And IMO, the point of UML is that it’s done in the architecting phase.
A project like WordPress would be hard-pressed to have this since it’s
a fluid integration of independent developers contributing to the
core.
[…]Welcome to open source.
Note: the Template Hierarchy of WikiMedia in the OP Question differs from the one in the Codex

click to enlarge
But, Chip Bennet has an extended one 🙂

I thought this Question was a duplicate of the following (but mods said it’s not):
Where can I find a real architecture document on WordPress?
In it, Mike Schinkel states:
These generally are not some the open-source WordPress community focuses on doing.
One answer points to an old article with this diagram:
And the other to this WordPress 3.0 Program Flow (PDF)

Rarst answer to this Question ( When should you use WP_Query vs query_posts() vs get_posts()? ) has a nice overview of WP_Query:

Another from Rarst on core load:

And finally, a totally unrelated Question about performance ( Refactoring WordPress to improve memory performance ), but with very nice graphs 🙂

Method 2
If you are looking for the database schema, there is a version on the Codex:

click to enlarge
The image you referenced in your post is the template hierarchy most commonly used by theme developers.
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