The Ensembl Browser: Difference between revisions
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* Everything is in mysql databases. No flat text files. [http://www.ensembl.org/info/docs/api/core/core_schema.html Database schema documentation] | * Everything is in mysql databases. No flat text files. [http://www.ensembl.org/info/docs/api/core/core_schema.html 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) | * 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 | * 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' | * Usually, each species has its own database, like in the UCSC browser. The current human one is 'homo_sapiens_core_56_37a' | ||
Revision as of 09:26, 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 tables:
- 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)
