The Ensembl Browser

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I am trying to learn how Ensembl is structured. These notes are partially based on a workshop in 2010 at the EBI.

Basic Information:

  • Everything is in mysql databases. No flat text files.
  • Everything is programmed in PERL (except the UCSC programs?)
  • Main documentation start page
  • Bert Overduin's homepage has a list of all slides and exercises - very handy!
  • Organisation of source code:
    • "core": genome database and related tools
    • "pipeline": the job scheduling system + config files
    • "analysis": all genome annotation tools and wrappers

The pipeline / scheduling system:

  • Job description, input data description and commands are written to MySQL, the cluster writes the results back to mysql
  • the paper has a rough general outline
  • Basic schema is in ensembl-pipeline/sql/table.sql with some documentation
  • The most useful documentation is in in CVS pipeline-docs

Genome data:

  • Basic schema is in ensembl/sql/table.sql, with quite a bit of documentation of the tables
  • Can be accessed via Perl API (slow) or via biomart.org (~table browser, fast and convenient) or via direct sql queries
  • Database schema documentation
  • The database schema is very complex, due to self-referencing tables, whole-genome queries are not possible without biomart at reasonable speed
  • 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 starting month of the last update of a gene build is stored in genome_db.genebuild (not the month when the genebuild ended, so I don't see how you know if genes changed)
    • the current version can be found out with:
      select * from meta meta where meta_key in ("schema_version", "patch")
  • 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 database structure is very normalized. Whereas this is nice from a software engineering perspective, you cannot do large-scale requests. E.g. downloading all homologs between two genomes involves queries on self-referencing tables which take ages to resolve and will time out if run on their server. Use biomart for these types of requests.
  • There are still a lot of older functions lingering in the source code. If a function returns null although it shouldn't have a look into the source code. Often they have been replaced by others. The ensembl-dev mailing list is usually the only way to get more information.


The databases:

All versions of the genomes 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)
  • ensembl_compara includes homologies between proteins and genomes
  • 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.
  • genes are linked to synonyms/names via xref-tables.

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 (All older biomart versions are accessible via the archived old ensembl versions)

Documentation:

  • Most documentation is not accessible from the Ensembl homepage. You have to dig into the CVS repositories to find "pipeline_docs": [1] The file overview.txt gives a very good introduction.