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The Ensembl Database
www.ensembl.org
Lecture 3.1
Bioinformatics
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What is Ensembl?
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Public annotation of the Mammalian genomes
Open source software
Relational database system
The future of genomic bioinformatics?
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The Ensembl Project
“Ensembl is a joint project between EMBL
European Bioinformatics Institute and the
Sanger Institute to develop a software
system which produces and maintains
automatic annotation on eukaryotic
genomes. Ensembl is primarily funded by
the Wellcome Trust”
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The Ensembl Genome Annotation
Ensembl:
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•
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Utilises raw DNA sequence data from public sources
Creates a tracking database (The “Ensembl” database”
Joins the sequences - based on a sequence scaffold or “Golden Path”
Automatically finds genes and other features of the Sequence
Provides a publicly accessible web based interface to the database
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Ensembl Software System
• Uses extensively BioPerl (www.bioperl.org)
• The free mySQL database
• Entire Ensembl code base us freely available
under Apache open source license.
• Mainly written in Perl, extensions in C. Some
viewers have been written in Java (e.g.
Appollo).
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Ensembl Software System
• Core design feature is the “virtual contig”
object.
• Allows genome sequence to be accessed as
a single large contiguous sequence, but is
stored in the database as a collection of
fragments.
• VC object handles reading and writing to the
DNA sequence data.
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Ensembl Software System
• If sequences were stored as single large
sequences, this would be impractical e.g.
whole database entry would need to be
changed if a single base changed. By being
able to store constituent DNA as fragments,
can move easily between database versions
and assemblies.
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Ensembl Software System
• Software can be accessed by FTP
• Can also be accessed through CVS
(concurrent versions system)
• Possible to set up a mirror of the entire
Ensembl system.
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Ensembl Now Supports a Number of
Organisms
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The Chromosome Overview
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Entering through Disease Genes via the OMIM database
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The Ensembl Gene Report
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Expanding Annotation Features, e.g. Unigene and Human mRNA similarities
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Ensembl links out to other databases to access individual entries
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Direct Access to Ensembl
We will use the underlying Ensembl data. For reasons of simplicity and space we
will use the lite version of the Ensembl database
{xhost01}/home/pubseq/acedb> mysql -u anonymous -h kaka.sanger.ac.uk
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 11928 to server version: 3.23.32
Type 'help' for help.
mysql> use homo_sapiens_lite_8_30b
Database changed
;
mysql> show tables ;
+-----------------------------------+
| Tables_in_homo_sapiens_lite_8_30b |
+-----------------------------------+
| cpg
|
| eponine
|
| gene
|
| gene_xref
|
| genscan
|
| repeat
|
| repeat_types
|
| snp
|
| transcript
|
| trna
|
+-----------------------------------+
10 rows in set (0.15 sec)
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Explore the Database
mysql> describe gene ;
+---------------+------------------+------+-----+---------+----------------+
| Field
| Type
| Null | Key | Default | Extra
|
+---------------+------------------+------+-----+---------+----------------+
| id
| int(10) unsigned |
| PRI | NULL
| auto_increment |
| db
| varchar(40)
|
| MUL |
|
|
| type
| varchar(40)
|
|
|
|
| gene_id
| int(10) unsigned |
| MUL | 0
|
|
| gene_name
| varchar(40)
|
| MUL | unknown |
|
| chr_name
| varchar(20)
|
| MUL |
|
|
| chr_start
| int(10) unsigned |
|
| 0
|
|
| chr_end
| int(10) unsigned |
|
| 0
|
|
| chr_strand
| tinyint(4)
|
|
| 0
|
|
| description
| varchar(255)
|
|
|
|
|
| external_db
| varchar(40)
|
|
|
|
|
| external_name | varchar(40)
|
|
|
|
|
|
+---------------+------------------+------+-----+---------+----------------+
12 rows in set (0.14 sec)
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mysql> select * from gene limit 10 ;
+----+------+----------+---------+-----------------+----------+-----------+-----------+------------+-------------+-------------+---------------+
| id | db
| type
| gene_id | gene_name
| chr_name | chr_start | chr_end
| chr_strand | description | external_d b | external_name |
+----+------+----------+---------+-----------------+----------+-----------+-----------+------------+-------------+-------------+---------------+
|
1 | embl | standard |
1 | AB001523.1.1.1
| 21
|
41942232 |
42033272 |
1 |
| protein_id
| BAA21099.1
|
|
2 | embl | standard |
2 | AB001523.1.1.2
| 21
|
42037154 |
42038833 |
1 |
| protein_id
| BAA21100.1
|
|
3 | embl | standard |
3 | AB015355.1.1.1
| 12
|
51605465 |
51627823 |
-1 |
| SPTREMBL
| O94801
|
|
4 | embl | pseudo
|
4 | AB019437.1.1.31 | 14
| 104129078 | 104129346 |
-1 |
| EMBL
| AB019437.1.1
|
|
5 | embl | standard |
5 | AB019437.1.1.23 | 14
| 104166399 | 104166849 |
-1 |
| protein_id
| BAA75024.1
|
|
6 | embl | standard |
6 | AB019437.1.1.15 | 14
| 104214187 | 104214630 |
-1 |
| protein_id
| BAA75022.1
|
|
7 | embl | pseudo
|
7 | AB019437.1.1.24 | 14
| 104163156 | 104163428 |
-1 |
|
|
|
|
8 | embl | standard |
8 | AB019437.1.1.16 | 14
| 104205297 | 104205735 |
-1 |
| protein_id
| BAA75023.1
|
|
9 | embl | pseudo
|
9 | AB019437.1.1.1
| 14
| 104323128 | 104323419 |
-1 |
|
|
|
| 10 | embl | pseudo
|
10 | AB019437.1.1.25 | 14
| 104157422 | 104157916 |
-1 |
|
|
|
+----+------+----------+---------+-----------------+----------+-----------+-----------+------------+-------------+-------------+---------------+
10 rows in set (0.16 sec)
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mysql> select gene_name, chr_start, (chr_end-chr_start) AS Length,
description from gene where chr_name = "2" and chr_start > 20000000 and
chr_end < 20500000 limit 10 ;
+--------------------+-----------+--------+-----------------------------------------------------+
| gene_name
| chr_start | Length | description
|
+--------------------+-----------+--------+-----------------------------------------------------+
| ENSG00000118965
|
20001311 |
79861 |
|
| ENSestG00000028348 |
20004285 |
18142 |
|
| ENSestG00000028342 |
20023444 |
14129 |
|
| ENSestG00000028189 |
20024182 |
33984 |
|
| ENSestG00000028339 |
20044953 |
36215 |
|
| ENSestG00000028192 |
20081242 |
14009 |
|
| ENSestG00000028199 |
20083093 |
2338 |
|
| ENSG00000132031
|
20083093 |
| ENSestG00000028338 |
20085340 |
6263 |
|
| ENSestG00000028337 |
20093048 |
10687 |
|
20642 | MATRILIN-3 PRECURSOR. [Source:SWISSPROT;Acc:O15232] |
+--------------------+-----------+--------+-----------------------------------------------------+
10 rows in set (0.15 sec)
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Using the PERL API
• API means “application programming
interface”
• This gives us a seamless way to access
the mysql database from perl code.
• A JAVA API also exists for Ensembl.
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A typical API interface would involve:1) Connecting to the database
use Bio::EnsEMBL::DBSQL::DBAdaptor;
This line has to be in all your ensembl scripts;
my $host = 'kaka.sanger.ac.uk';
my $user = 'anonymous';
my $dbname = 'current';
The all important variables telling perl where and what your database is.
And now we connect
my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
-user => $user,
-dbname => $dbname);
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2) Use Function calls to access the underlying data
my $clone = $db->get_Clone('AC005663');
The function would return an associative array
print "Clone is " . $clone->id . "\n";
What Functions you can use and what data is returned will be
outlined in the documentation
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3) We can get the API to return a large amount of data in an array
my @contigs = $clone->get_all_Contigs;
We now have an array of contig objects which are very useful for
obtaining information.
Say we want to get the sequence for each contig:
foreach my $contig (@contigs) {
my $seqobj = $contig->primary_seq;
my $length = $contig->length;
my $id = $contig->id;
print $seqobj->seq . "\n";
}
Note: These specific examples are taken from the ensembl tutorial
http://www.ensembl.org/Docs/ensembl_tutorial.pdf
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Further Information
• The Ensembl Project www.ensembl.org
• Ensembl Trace Server trace.ensembl.org
• Ensembl Distributed Annotation Server
servlet.sanger.ac.uk/das
• Human Genome Central Resources
www.ensembl.org/genome/central
• Distribributed Annotation System
www.biodas.org
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