Difference between revisions of "Public Chado Databases"
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These projects provide [[Chado]] database dumps that you can copy and learn from. | These projects provide [[Chado]] database dumps that you can copy and learn from. | ||
| − | * [[:Category:FlyBase|FlyBase]]: ftp://flybase. | + | * [[:Category:FlyBase|FlyBase]]: ftp://ftp.flybase.org/releases/current/psql/ - Contains 12 Drosophila genomes. |
* [[ParameciumDB]]: http://paramecium.cgm.cnrs-gif.fr/download/sql/ | * [[ParameciumDB]]: http://paramecium.cgm.cnrs-gif.fr/download/sql/ | ||
* [[:Category:SGD|Yeast]]: http://sgdlite.princeton.edu/download/sgdlite/ | * [[:Category:SGD|Yeast]]: http://sgdlite.princeton.edu/download/sgdlite/ | ||
| + | * [[VectorBase]]: ftp://ftp.vectorbase.org/public_data/databases/chado/ | ||
Please add to this list, if you have a Chado database to share, or know of someone who does. If you have a public Chado database, please consider adding an export dump file. | Please add to this list, if you have a Chado database to share, or know of someone who does. If you have a public Chado database, please consider adding an export dump file. | ||
pg_dump -f mychado.dump mychado | pg_dump -f mychado.dump mychado | ||
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== Direct [[Chado]] Access == | == Direct [[Chado]] Access == | ||
=== [http://flybase.org FlyBase] === | === [http://flybase.org FlyBase] === | ||
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| − | + | * [https://flybase.github.io/docs/chado/index#public-database FlyBase public chado database] | |
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=== [http://www.genedb.org GeneDB] === | === [http://www.genedb.org GeneDB] === | ||
The following connection information is for the preliminary GeneDB Chado database. This database currently contains Plasmodium genomes; more organisms will be added during 2008. This is currently a pre-release database, which may change or disappear without warning. | The following connection information is for the preliminary GeneDB Chado database. This database currently contains Plasmodium genomes; more organisms will be added during 2008. This is currently a pre-release database, which may change or disappear without warning. | ||
| − | '''hostname:''' | + | '''hostname:''' db.genedb.org<br /> |
'''port:''' 5432<br /> | '''port:''' 5432<br /> | ||
'''username:''' genedb_ro<br /> | '''username:''' genedb_ro<br /> | ||
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e.g. | e.g. | ||
| − | psql -h | + | psql -h db.genedb.org -U genedb_ro snapshot |
| + | [[Category:ParameciumDB]] | ||
| + | [[Category:FlyBase]] | ||
| + | [[Category:SGD]] | ||
[[Category:Chado]] | [[Category:Chado]] | ||
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Latest revision as of 14:56, 25 June 2019
Contents
Public Chado Genome Database Releases
Chado PostgreSQL Dumps
These projects provide Chado database dumps that you can copy and learn from.
- FlyBase: ftp://ftp.flybase.org/releases/current/psql/ - Contains 12 Drosophila genomes.
- ParameciumDB: http://paramecium.cgm.cnrs-gif.fr/download/sql/
- Yeast: http://sgdlite.princeton.edu/download/sgdlite/
- VectorBase: ftp://ftp.vectorbase.org/public_data/databases/chado/
Please add to this list, if you have a Chado database to share, or know of someone who does. If you have a public Chado database, please consider adding an export dump file.
pg_dump -f mychado.dump mychado
Direct Chado Access
FlyBase
GeneDB
The following connection information is for the preliminary GeneDB Chado database. This database currently contains Plasmodium genomes; more organisms will be added during 2008. This is currently a pre-release database, which may change or disappear without warning.
hostname: db.genedb.org
port: 5432
username: genedb_ro
password: no password
database name: snapshot
e.g.
psql -h db.genedb.org -U genedb_ro snapshot
