Difference between revisions of "Precompiled Chado Databases"

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(Added information on CPT's precompiled databases.)
 
(nomail)
 
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I'm not aware of how many of you regularly have to configure and deploy chado databases, however over time I've found that a significant portion of my time was spent waiting on ontologies to load.
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[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.
  
To this end (and in support of some other projects), I set up a jenkins job to
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Go to the [https://cpt.tamu.edu/chado-prebuilt-schema/ download site].
  
* clone chado from SVN
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The ontologies currently available are:
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* Chado Feature Properties
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* Gene Ontology
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* Plant Ontology
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* Relationship Ontology
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* Sequence Ontology
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These are updated weekly; the workflow is as follows:
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* clone Chado from SVN
 
* build
 
* build
 
* load ontologies
 
* load ontologies
* dump database as sql
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* dump database as SQL
 
* upload to a publicly accessible webserver
 
* upload to a publicly accessible webserver
  
This is done on a weekly basis. I'm making the compiled databases with all 5 ontologies loaded available to the community. They're trivial to use if you're just trying to install chado, as all you need to do is change the username in the precompiled schema
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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.
 
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  sed -i "s/schema_builder/user_name/g" csb.sql
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and load it into the database of your choice.
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  psql -U {user_name} -d {desintation_db} -f csb.sql
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This process takes ~10 seconds, compared to the 1.3 hours (according to my jenkins job) for regular ontology loading.
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The databases can be found here: [[https://cpt.tamu.edu/~docs/chado/]]
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The ontologies currently installed are:
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# Relationship Ontology
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# Sequence Ontology
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# Gene Ontology
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# Chado Feature Properties
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# Plant Ontology
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If anyone is interested in this, and would like:
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* other builds with different (sub)sets of
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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:
* archived copies of schemas over time
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please feel free to request them and we'll add them to the jenkins job/make them available.
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* other ontologies added to the dumps
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* other builds with different (sub)sets of ontologies
  
NB: The caveats of this method are, of course, that none of the scripts are installed, and the gmod conf files are not created in GMOD_ROOT. However, for remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this seems to be fine.
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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.