The Ensembl Browser: Difference between revisions

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Confusing, because all versions are on the same server. Some ideas to help you find your way:
Confusing, because all versions are on the same server. Some ideas to help you find your way:
* species_name_version_obscureNumber is the format of the individual species database (see below)
* species_name_version_obscureNumber is the format of the individual species database (see below)
* ensembl_compara_version stores homology information between species
* Homology information: [[ensembl_compara]]
* ensembl_go_version: Not used anymore? Was used to store gene ontology links.
* ensembl_go_version: Not used anymore? Was used to store gene ontology links.
* ensembl_website_version: Ensembl includes some sort of content management system. This databases includes help articles, bugs, news, the list of species on the frontpage etc. (This database looks somewhat similar to hgcentral)
* ensembl_website_version: Ensembl includes some sort of content management system. This databases includes help articles, bugs, news, the list of species on the frontpage etc. (This database looks somewhat similar to hgcentral)

Revision as of 09:40, 29 October 2009

I am trying to learn how Ensembl is structured. As Ensembl itself does not have a wiki nor a forum nor a public mailing list for user discussions, I'll document it here.

Some ideas:

  • Everything is in mysql databases. No flat text files. Database schema documentation
  • Can be accessed via Perl API (slow) or via biomart.org (~table browser, fast and convenient) or via direct sql queries (very complex schema)
  • An update of everything is done every 6 months. The old code, the old API and all databases are archived. Different mysql servers running on different ports are used to separated older archived from current versions.
    • Genes are not re-predicted each time but only when new data is added to the gene build. The month of the last update of a gene build is stored in genome_db.genebuild
  • The current version (oct 09) is 56
  • Usually, each species has its own database, like in the UCSC browser. The current human one is 'homo_sapiens_core_56_37a'
  • The Web interface is called "webcode", written in Perl and makes extensive use of inheritance (uh-oh), tool-support for reading the code might be helpful

The databases:

Confusing, because all versions are on the same server. Some ideas to help you find your way:

  • species_name_version_obscureNumber is the format of the individual species database (see below)
  • Homology information: ensembl_compara
  • ensembl_go_version: Not used anymore? Was used to store gene ontology links.
  • ensembl_website_version: Ensembl includes some sort of content management system. This databases includes help articles, bugs, news, the list of species on the frontpage etc. (This database looks somewhat similar to hgcentral)
  • ensembl_ancestral_version ??


The species database:

  • Sequences can be accessed using different "coordinate systems", e.g. you can type in a chromsome location or alternatively a contig location. Both will be mapped to chromsome sequences. They are set up in the table 'coord_system'
  • The sequences themselved are stored in the table 'dna' and information about them in 'seq_region'. There is a table dnac for compressed sequences but its empty.

The pipeline:

  • Their pipeline systems inserts jobs into a mysql database as well
  • The genebuild step is predicting genes
  • The xref step is connecting predicted genes to external identifiers
  • The compara step is aligning all genomes and predicted genes and then building phylogenetic trees for all proteins
  • The biomart step is de-normalizing all databases for faster access (It seems that biomart is not archived. If this is true, then one cannot rely on it for whole-genome work as one might end up with inconsistent data)