Difference between revisions of "Chado New Users"
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== Sample Data== | == Sample Data== | ||
| + | To understand [[Chado Best Practices]], where the documentation is sometimes incomplete, we've tried to get some samples of Chado data in use. Things we've looked at so far, and comments on them: | ||
| + | * Sample yeast data from GFF3 bulk loader. The problem with this is that it doesn't reflect a real use case for Chado, since SGD does not use the Chado Schema | ||
| + | * Flybase SQL dump. Zheng got this and loaded it. Two problems | ||
| + | ** It's huge | ||
| + | ** It's a denormalized version (?) | ||
| + | |||
== Understanding how things are represented in Chado == | == Understanding how things are represented in Chado == | ||
===Central Dogma=== | ===Central Dogma=== | ||
Revision as of 14:58, 12 April 2007
This page, and it's associated discussion page follow the learning curve for new Chado users learning the system at CSHL.
Contents
Getting an empty Chado PostgreSQL on our machines
- Zheng - on PC with Fedora. See Zheng's installation notes
- Mike - on Intel Mac running Fedora partition
- Jim -
- on PPC Mac the hard way See Jim's installation notes
- on CentOS server in Texas
Installation Notes
If the easy way fails, the old documentation outside the wiki can be pretty confusing.
Loading the Ontologies
This works via make ontologies. How to do updates?
Getting the Sequence Module Working
We think GFF3 can be thought of as a view into Chado using the Sequence module and the CV module, or we can think of GFF3 as a denormalized view of Chado.
Migration from other databases
Sample Data
To understand Chado Best Practices, where the documentation is sometimes incomplete, we've tried to get some samples of Chado data in use. Things we've looked at so far, and comments on them:
- Sample yeast data from GFF3 bulk loader. The problem with this is that it doesn't reflect a real use case for Chado, since SGD does not use the Chado Schema
- Flybase SQL dump. Zheng got this and loaded it. Two problems
- It's huge
- It's a denormalized version (?)
Understanding how things are represented in Chado
Central Dogma
See also
- Chado - Getting_Started - and documentation links from there.
- Category:Chado - the Category page for all pages about Chado in this wiki
