Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

uk.ac.roslin.ensembl.config
Class EnsemblComparaDivision

java.lang.Object
  extended by uk.ac.roslin.ensembl.config.EnsemblType
      extended by uk.ac.roslin.ensembl.config.EnsemblComparaDivision
All Implemented Interfaces:
Serializable, Comparable<EnsemblComparaDivision>, DatabaseType, ObjectType

public class EnsemblComparaDivision
extends EnsemblType
implements DatabaseType, Comparable<EnsemblComparaDivision>

In 'ensembl.org' there is a single 'ensembl_compara' database which contains the pairwise comparison data on all the species in 'ensembl.org. However, in 'ensemblgenomes.org', there are separate 'ensembl_compara' databases for the different taxonomic groupings:

In ensembl.org all species are compared in the ensembl_compara database, and belong to the compara group 'multi'. In each core database (species) in ensemblgenomes.org the 'species.division' key in table 'meta' specifies the group: Orthology / paralogy (peptide) predictions are done between all species of a database, but genomic alignments only between certain combinations of species. Bacteria is a slightly special case in that we compare members of each collection to each other, but not between the collections (its actually 10 comparas merged into one).

ensembl_compara_pan_homology is a peptide compara database produced from a set of selected species that are taken from all EnsemblGenomes divisions and from Ensembl (but doesn't include all species from all divisions). See list at http://metazoa.ensembl.org/info/docs/compara/homology_method.html. One thing to note here is that pan also contains protein family data as well: http://metazoa.ensembl.org/info/docs/compara/family.html. This means that the genome_db table ends up with more entries than are used in the peptide homology comparisons alone and cannot be used to determine membership, so you need to use the species_set/method_link tables as well rather than just relying on genome_db.

See Also:
Serialized Form

Field Summary
static EnsemblComparaDivision BACTERIA
           
static EnsemblComparaDivision FUNGI
           
static EnsemblComparaDivision METAZOA
           
static EnsemblComparaDivision MULTI
           
static EnsemblComparaDivision PAN_HOMOLOGY
           
static EnsemblComparaDivision PLANTS
           
static EnsemblComparaDivision PROTISTS
           
 
Fields inherited from class uk.ac.roslin.ensembl.config.EnsemblType
label
 
Method Summary
 int compareTo(EnsemblComparaDivision other)
           
static Collection<EnsemblComparaDivision> getAllTypes()
           
static String getDBName(String label)
           
static EnsemblComparaDivision getEnsemblComparaDivision(String value)
           
static EnsemblComparaDivision getEnsemblComparaDivisionByMetaValue(String value)
           
 
Methods inherited from class uk.ac.roslin.ensembl.config.EnsemblType
toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

MULTI

public static EnsemblComparaDivision MULTI

PLANTS

public static EnsemblComparaDivision PLANTS

PROTISTS

public static EnsemblComparaDivision PROTISTS

BACTERIA

public static EnsemblComparaDivision BACTERIA

FUNGI

public static EnsemblComparaDivision FUNGI

METAZOA

public static EnsemblComparaDivision METAZOA

PAN_HOMOLOGY

public static EnsemblComparaDivision PAN_HOMOLOGY
Method Detail

getDBName

public static String getDBName(String label)

getAllTypes

public static Collection<EnsemblComparaDivision> getAllTypes()

getEnsemblComparaDivision

public static EnsemblComparaDivision getEnsemblComparaDivision(String value)

getEnsemblComparaDivisionByMetaValue

public static EnsemblComparaDivision getEnsemblComparaDivisionByMetaValue(String value)

compareTo

public int compareTo(EnsemblComparaDivision other)
Specified by:
compareTo in interface Comparable<EnsemblComparaDivision>

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3