Difference between revisions of "Precompiled Chado Databases"
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| − | [https://cpt.tamu.edu | + | [https://cpt.tamu.edu/chado-prebuilt-schema/ Chado database dumps of precompiled ontologies are publicly available] to save Chado users the time and hassle of downloading and compiling the ontologies themselves. |
| − | Go to the [https://cpt.tamu.edu | + | Go to the [https://cpt.tamu.edu/chado-prebuilt-schema/ download site]. |
The ontologies currently available are: | The ontologies currently available are: | ||
| − | *Chado Feature Properties | + | * Chado Feature Properties |
| − | *Gene Ontology | + | * Gene Ontology |
| − | *Plant Ontology | + | * Plant Ontology |
| − | *Relationship Ontology | + | * Relationship Ontology |
| − | *Sequence Ontology | + | * Sequence Ontology |
These are updated weekly; the workflow is as follows: | These are updated weekly; the workflow is as follows: | ||
| Line 21: | Line 21: | ||
Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem. | Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem. | ||
| − | These database dumps are | + | These database dumps are provided by Eric Rasche and the [https://cpt.tamu.edu/ Center for Phage Technology at Texas A&M University]. Please [https://github.com/erasche/chado-schema-builder/issues/new open an issue] if you are interested in having: |
| + | |||
| + | * other ontologies added to the dumps | ||
| + | * other builds with different (sub)sets of ontologies | ||
| + | |||
| + | All of these features can be added on request. | ||
[[Category:Chado]] | [[Category:Chado]] | ||
Latest revision as of 09:51, 11 September 2017
Chado database dumps of precompiled ontologies are publicly available to save Chado users the time and hassle of downloading and compiling the ontologies themselves.
Go to the download site.
The ontologies currently available are:
- Chado Feature Properties
- Gene Ontology
- Plant Ontology
- Relationship Ontology
- Sequence Ontology
These are updated weekly; the workflow is as follows:
- clone Chado from SVN
- build
- load ontologies
- dump database as SQL
- upload to a publicly accessible webserver
Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.
These database dumps are provided by Eric Rasche and the Center for Phage Technology at Texas A&M University. Please open an issue if you are interested in having:
- other ontologies added to the dumps
- other builds with different (sub)sets of ontologies
All of these features can be added on request.
