EnsEMBL Compara DB Schema Documentation

This document refers to the schema of the EnsEMBL Compara version 26.1. This is the revision 0.3 of this document.

Introduction

EnsEMBL Compara DB is divided into two parts:

Genomic alignments
This part is dedicated to DNA-DNA alignment. It includes alignment made with different alignment tools. It also includes a list of syntenic regions.
Othologues and Protein clusters (or families)
This part contains several types of data.

The first one corresponds to a list of protein orthologues. By now, for each gene, only the longest peptide is considered for homology search. Only pairwise comparisons are taken into account. In principle, only Best Reciprocal Hits (BRH) are considered. Nevertheless extra orthologous relationships are found taking into account the gene order conservation of neighbour genes (RHS, Reciprocal Hit based on Synteny around BRH). Additionally, in Human vs. Chimp relationships may be found Derived from Whole Genome Alignment (DWGA).

Another part is dedicated to protein clusters (or families). In this case, Metazoan entries of the SwissProt/SPTrEMBL database are also taken into account in order to annotate the clusters.

A third part is planed for domain alignments but is not used by now.

List of tables

General Tables
Genomic Alignments Tables
Orthologues and Protein Clusters

General Tables

meta table description
Field	Type	Key	Default	Description
meta_id	int unsigned	PRI	NULL	internal unique ID
meta_key	varchar(40)	MUL
meta_value	varchar(255)	MUL

taxon

Contains all taxa used in this database.

taxon table description
Field	Type	Null	Key	Default	Description
taxon_id	int(10) unsigned		PRI	0	unique ID
genus	varchar(50)	YES	MUL	NULL	e.g. Homo
species	varchar(50)	YES		NULL	e.g. sapiens
sub_species	varchar(50)	YES		NULL
common_name	varchar(100)	YES	MUL	NULL	e.g. Human
classification	mediumtext	YES		NULL	Full taxonomic classification

E.g. the rows

mysql> SELECT * FROM taxon WHERE taxon_id IN (9031, 9606);
+----------+--------+---------+-------------+-------------+-···
| taxon_id | genus  | species | sub_species | common_name | 
+----------+--------+---------+-------------+-------------+-···
|     9031 | Gallus | gallus  | NULL        | Chicken     |
|     9606 | Homo   | sapiens | NULL        | Human       | 
+----------+--------+---------+-------------+-------------+-···

 ···-+-------------------------------------------------------------------···
     | classification                                                           
 ···-+-------------------------------------------------------------------···
     | gallus Gallus Phasianinae Phasianidae Galliformes Neognathae Aves
     | sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia 
 ···-+-------------------------------------------------------------------···

 ···-------------------------------------------------------------------------+
                                                                             |
 ···-------------------------------------------------------------------------+
     Archosauria Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota |
     Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota             |
 ···-------------------------------------------------------------------------+

correspond to the Chicken and the Human species.

genome_db

Contains information about the version of the genome assemblies used in this database.

genome_db table description
Field	Type	Null	Key	Default	Extra	Description
genome_db_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
taxon_id	int(10) unsigned			0		external reference to taxon.taxon_id
name	varchar(40)		MUL			name of the species
assembly	varchar(100)					assembly version of the genome
assembly_default	tinyint(1)	YES		1		boolean value describing if this assembly is the default one or not, so that we can handle more than one assempbly version for a given species.
genebuild	varchar(100)					version of the genebuild
locator	varchar(255)	YES		NULL		used for production purposes or for user configuration in in-house installation.

Eg the rows:

mysql> SELECT * FROM genome_db WHERE genome_db_id IN (1, 11);
+--------------+----------+-------------------------+------------+-···
| genome_db_id | taxon_id | name                    | assembly   |
+--------------+----------+-------------------------+------------+-···
|            1 |     9606 | Homo sapiens            | NCBI34     |
|           11 |     9031 | Gallus gallus           | WASHUC1    |
+--------------+----------+-------------------------+------------+-···

···-+------------------+---------------+---------+
    | assembly_default | genebuild     | locator |
···-+------------------+---------------+---------+
    |                1 | 0405Ensembl   | NULL    |
    |                1 | 0406Ensembl   | NULL    |
···-+------------------+---------------+---------+

correspond to the Human and Chicken genomes

method_link

Contains the list of alignment methods used to find links (homologies) between DNA sequences.

method_link table description
Field	Type	Null	Key	Default	Extra	Description
method_link_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
type	varchar(50)		MUL			the common name of the linking method between species.

Current values are:

mysql> SELECT * FROM method_link;
+----------------+----------------------+
| method_link_id | type                 |
+----------------+----------------------+
|              1 | BLASTZ_NET           |
|              2 | BLASTZ_NET_TIGHT     |
|              3 | BLASTZ_RECIP_NET     |
|              4 | PHUSION_BLASTN       |
|              5 | PHUSION_BLASTN_TIGHT |
|              6 | TRANSLATED_BLAT      |
|              7 | BLASTZ_GROUP         |
|              8 | BLASTZ_GROUP_TIGHT   |
|            101 | SYNTENY              |
|            201 | ENSEMBL_ORTHOLOGUES  |
|            202 | ENSEMBL_PARALOGUES   |
|            301 | FAMILY               |
+----------------+----------------------+

method_link_species_set

This table contains information about the comparisons stored in the database. A given method_link_species_set_id exist for each comparison made and relates a method_link.method_link_id with a set of genome_db.genome_db_id.

method_link_species table description
Field	Type	Null	Key	Default	Extra	Description
method_link_species_set_id	int(10) unsigned		MUL	NULL	auto_increment	internal id.
method_link_id	int(10) unsigned	YES	MUL	NULL		external reference to method_link.method_link_id
genome_db_id	int(10) unsigned	YES		NULL		external reference to genome_db.genome_db_id

E.g. the rows

mysql> SELECT * FROM method_link_species_set WHERE method_link_species_set_id = 71;
+----------------------------+----------------+--------------+
| method_link_species_set_id | method_link_id | genome_db_id |
+----------------------------+----------------+--------------+
|                         71 |              1 |            1 |
|                         71 |              1 |           11 |
+----------------------------+----------------+--------------+

mean that BLASTZ_NET (method_link_id = 1) has been used for linking all the species of this set: Human (genome_db_id = 1) and Chicken (genome_db_id = 11).

Tables For Genomic Alignments

dnafrag

This table defines the genomic sequences used in the comparative genomics analyisis. It is used by the genomic_align_block table to define aligned sequences. It is also used by the dnafrag_region table to define syntenic regions.

dnafrag table description
Field	Type	Null	Key	Default	Extra	Description
dnafrag_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
length	int(11)			0
name	varchar(40)		MUL			name of the DNA sequence (e.g., the name of the chromosome)
genome_db_id	int(10) unsigned			0		external reference to genome_db.genome_db_id
coord_system_name	varchar(40)	YES		NULL		refers to the coord system in which this dnafrag has been defined

E.g. the row

mysql> SELECT * FROM dnafrag WHERE dnafrag_id IN (19, 23227);
+------------+-----------+------+--------------+-------------------+
| dnafrag_id | length    | name | genome_db_id | coord_system_name |
+------------+-----------+------+--------------+-------------------+
|         19 | 105311216 | 14   |            1 | chromosome        |
|      23227 |  56310377 | 5    |           11 | chromosome        |
+------------+-----------+------+--------------+-------------------+

refer to the chromosome 14 of the Human genome (genome_db.genome_db_id = 1 refers to Human genome in this example) which is 105311216 nucleotides length and to the chromosome 5 of the Chicken genome (genome_db.genome_db_id = 11 refers to Chicken genome in this example) which is 56310377 nucleotides length.

genomic_align_block

This table is the key table for the genomic alignments. The software used to align the genomic blocks is refered as an external key to the method_link table. Nevertheless, actual aligned sequences are defined in the genomic_align table.

genomic_align_block table description
Field	Type	Null	Key	Default	Extra	Description
genomic_align_block_id	bigint(20) unsigned		PRI	NULL	auto_increment	internal unique ID
method_link_species_set_id	int(10) unsigned		MUL	0		external reference to method_link_species_set.method_link_species_set_id
score	double	YES		NULL		score returned by the homology search program
perc_id	tinyint(3) unsigned	YES		NULL		Used for pairwise comparison. Defines the percentage of identity between both sequences
length	int(10)	YES		NULL		total length of the alignment

E.g. the row

mysql> SELECT * FROM genomic_align_block WHERE genomic_align_block_id = 5095912;
+------------------------+----------------------------+-------+---------+--------+
| genomic_align_block_id | method_link_species_set_id | score | perc_id | length |
+------------------------+----------------------------+-------+---------+--------+
|                5095912 |                         71 |  1102 |      60 |     53 |
+------------------------+----------------------------+-------+---------+--------+

will refer to a BLASTZ_NET alignment between human and chicken genomes (method_link_species_set.method_link_species_set_id = 71) with a score of 1102, an identity of 60% and a length of 53 nucleotides. The actual sequences corresponding to this aligment are defined in the genomic_align table.

genomic_align

This table contains the coordinates and all the information needed to rebuild genomic alignments. Every entry corresponds to one of the aligned sequences. It also contains an external key to the method_link_species_set which refers to the software and set of species used for getting the corresponding alignment. The aligned sequence is defined by an external reference to the dnafrag table, the starting and ending position within this dnafrag, the strand and a cigar_line.

The original aligned sequence is not stored but it can be retrieved using the cigar_line field and the original sequence. The cigar line defines the sequence of matches/mismatches and deletions (or gaps). For example, this cigar line 2MD3M2D2M will mean that the alignment contains 2 matches/mismatches, 1 deletion (number 1 is omitted in order to save some space), 3 matches/mismatches, 2 deletions and 2 matches/mismatches. If the original sequence is:

Original sequence: AACGCTT

The aligned sequence will be:

cigar line: 2MD3M2D2M
M	M	D	M	M	M	D	D	M	M
A	A	-	C	G	C	-	-	T	T

genomic_align_block table description
Field	Type	Null	Key	Default	Extra	Description
genomic_align_id	bigint(20) unsigned		PRI	NULL	auto_increment	unique internal id
genomic_align_block_id	bigint(10) unsigned		MUL	0		external reference to genomic_align_block.genomic_align_block_id
method_link_species_set_id	int(10) unsigned			0		external reference to method_link_species_set.method_link_species_set_id. This information is redundant because it also appears in the genomic_align_block table but it is used to speed up the queries
dnafrag_id	int(10) unsigned		MUL	0		external reference to dnafrag.dnafrag_id
dnafrag_start	int(10)			0		starting position within the dnafrag defined by dnafrag_id
dnafrag_end	int(10)			0		ending position within the dnafrag defined by dnafrag_id
dnafrag_strand	tinyint(4)			0		strand in the dnafrag defined by dnafrag_id
cigar_line	mediumtext	YES		NULL		internal description of the aligned sequence
level_id	tinyint(2)			0		level of orhologous layer. 1 corresponds to the first layer of orthologous sequences found, 2 and over are addiotional layers. Use for building the syntenies (based on level_id = 1 only)

E.g. the rows

mysql> SELECT * FROM genomic_align WHERE genomic_align_block_id = 5095912;
+------------------+------------------------+----------------------------+------------+-···
| genomic_align_id | genomic_align_block_id | method_link_species_set_id | dnafrag_id |
+------------------+------------------------+----------------------------+------------+-···
|         10191817 |                5095912 |                         71 |      23227 |
|         10191830 |                5095912 |                         71 |         19 |
+------------------+------------------------+----------------------------+------------+-···

 ···-+---------------+-------------+----------------+------------+----------+
     | dnafrag_start | dnafrag_end | dnafrag_strand | cigar_line | level_id |
 ···-+---------------+-------------+----------------+------------+----------+
     |      30021505 |    30021554 |              1 | 37M3D13M   |        2 |
     |      25833506 |    25833558 |             -1 | 53M        |        2 |
 ···-+---------------+-------------+----------------+------------+----------+

correspond to both pieces of sequences included in the alignment described above (see genomic_align_block table description). The first sequence includes the nucleotides from 30021505 to 30021554 in the forwards strand of the chromosome 5 of the Chicken genome (dnafrag.dnafrag_id = 23227). The second sequence includes the nucleotides from 25833506 to 25833558 in the backwards strand of the chromosome 14 of the Human genome (dnafrag.dnafrag_id = 19).

The aligned sequences can be rebuild using the original sequences fetched from the corresponding core databases and the cigar lines as explained before.

genomic_align_group

This table is used to group alignments.

genomic_align_group table description
Field	Type	Key	Default	Extra	Description
group_id	bigint(20) unsigned	MUL	NULL	auto_increment	internal ID
type	varchar(40)				This field allow us to group genomic_aligns in several ways (types)
genomic_align_id	bigint(20) unsigned	MUL	0		external reference to genomic_align.genomic_align_id

E.g. the rows

mysql> SELECT * FROM genomic_align_group WHERE group_id = 64065;
+----------+---------+------------------+
| group_id | type    | genomic_align_id |
+----------+---------+------------------+
|    64065 | default |          1261387 |
|    64065 | default |          1261382 |
|    64065 | default |          1261429 |
|    64065 | default |          1261422 |
|    64065 | default |          8250806 |
|    64065 | default |          8250793 |
|    64065 | default |         10191710 |
|    64065 | default |         10191697 |
|    64065 | default |         10191750 |
|    64065 | default |         10191737 |
|    64065 | default |         10191789 |
|    64065 | default |         10191778 |
|    64065 | default |         10191830 |
|    64065 | default |         10191817 |
|    64065 | default |         10191868 |
|    64065 | default |         10191856 |
|    64065 | default |         10191909 |
|    64065 | default |         10191896 |
|    64065 | default |         11109668 |
|    64065 | default |         11109655 |
|    64065 | default |         14443871 |
|    64065 | default |         14443860 |
|    64065 | default |         19780097 |
|    64065 | default |         19780088 |
|    64065 | default |         22515872 |
|    64065 | default |         22515866 |
|    64065 | default |         23205949 |
|    64065 | default |         23205943 |
|    64065 | default |         31071852 |
|    64065 | default |         31071843 |
|    64065 | default |         54076401 |
|    64065 | default |         54076402 |
+----------+---------+------------------+

correspond to the group of several genomic_align in which the alignment described before is included.

synteny_region

Contains all the syntenic relationships found and the relative orientation of both syntenic regions.

synteny_region table description
Field	Type	Key	Default	Extra	Description
synteny_region_id	int(10) unsigned	PRI	NULL	auto_increment	internal unique ID
method_link_species_set_id	int(10) unsigned		0		external reference to method_link_species_set.method_link_species_set_id.
rel_orientation	tinyint(1)		1		1 when both regions are in the same orientation, 0 otherwise.

E.g. the row

mysql> SELECT * FROM synteny_region WHERE synteny_region_id = 1849;
+-------------------+-----------------+
| synteny_region_id | rel_orientation |
+-------------------+-----------------+
|              1849 |               1 |
+-------------------+-----------------+

means that the syntenic region 1849 corresponds to a syntenic relationship where both genomic regions are in the same orientation. See dnafrag_region table for more details.

dnafrag_region

Contains the genomic regions corresponding to every syntenic relationship found. There are two genomic regions for every syntenic relationship.

dnafrag_region table description
Field	Type	Key	Description
synteny_region_id	int(10) unsigned	PRI	external reference to synteny_region.synteny_region_id
dnafrag_id	int(10) unsigned	PRI	external reference to dnafrag.dnafrag_id
dnafrag_start	int(10) unsigned		first nucleotide from this dnafrag which is in synteny
dnafrag_end	int(10) unsigned		last nucleotide from this dnafrag which is in synteny

E.g. the rows

mysql> SELECT * FROM dnafrag_region WHERE synteny_region_id = 1849;
+-------------------+------------+---------------+--------------+
| synteny_region_id | dnafrag_id | dnafrag_start | dnafrag_end  |
+-------------------+------------+---------------+--------------+
|              1849 |         19 |      23939018 |     37861860 |
|              1849 |      23227 |      29431279 |     34526887 |
+-------------------+------------+---------------+--------------+

correspond to both genomic regions of the syntenic region 1849. In this case, the first genomic region corresponds to the sequence from 23939018 to 37861860 of the chromosome 14 of the Human genome (dnafrag_id = 19 for this chromosome) and the second one corresponds to the sequence from 29431279 to 34526887 of the chromosome 5 of the Chicken genome (dnafrag_id = 23227 for this chromosome). Using the synteny_region table, we know that both syntenic regions are in the same orientation.

Tables For Orthologues and Protein Clusters

member

This table links sequences to the EnsEMBL core DB or to external DBs.

member table description
Field	Type	Null	Key	Default	Extra	Description
member_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
stable_id	varchar(40)					EnsEMBL stable ID or external ID (for Uniprot/SWISSPROT and Uniprot/SPTREMBL)
version	int(10)	YES		0		version of the stable ID (see EnsEMBL core DB)
source_name	varchar(40)					describe the source of the member (Uniprot/SWISSPROT, Uniprot/SPTREMBL, ENSEMBLGENE, ENSEMBLPEP)
taxon_id	int(10) unsigned			0		external reference to taxon.taxon_id
genome_db_id	int(10) unsigned	YES		NULL		external reference to genome_db.genome_db_id
sequence_id	int(10) unsigned		MUL	NULL		external reference to sequence.sequence_id. May be 0 when the sequence is not available in the sequence table, e.g. for a gene instance.
gene_member_id	int(10) unsigned		MUL	NULL		external reference to member.memebr_id to allow linkage from peptides to genes.
description	varchar(255)	YES		NULL		the description of the protein
chr_name	varchar(40)	YES		NULL		chromosome where this sequence is located
chr_start	int(10)	YES		NULL		first nucleotide of this chromosome which corresponds to this member
chr_end	int(10)	YES		NULL		last nucleotide of this chromosome which corresponds to this member
chr_strand	tinyint(1)			0		strand of the chromosome in which the member is

E.g. the row

mysql> SELECT * FROM member WHERE member_id = 1945;
+-----------+--------------------+---------+-------------+----------+--------------+-------------+-···
| member_id | stable_id          | version | source_name | taxon_id | genome_db_id | sequence_id | 
+-----------+--------------------+---------+-------------+----------+--------------+-------------+-···
|      1945 | ENSGALP00000012979 |       1 | ENSEMBLPEP  |     9031 |           11 |        1121 | 
+-----------+--------------------+---------+-------------+----------+--------------+-------------+-···

 ···-+----------------+-···
     | gene_member_id | 
 ···-+----------------+-···
     |           1932 | 
 ···-+----------------+-···
     
 ···-+---------------------------------------------------------------------------------------+-···
     | description                                                                           | 
 ···-+---------------------------------------------------------------------------------------+-···
     | Transcript:ENSGALT00000012994 Gene:ENSGALG00000008004 Chr:1 Start:8903413 End:8906606 | 
 ···-+---------------------------------------------------------------------------------------+-···
     
 ···-+----------+-----------+---------+------------+
     | chr_name | chr_start | chr_end | chr_strand |
 ···-+----------+-----------+---------+------------+
     | 1        |   8903413 | 8906606 |         -1 |
 ···-+----------+-----------+---------+------------+

refers to the chicken (taxon_id = 9031 or genome_db_id = 11) gene ENSGALP00000012979 which is located in the chromosome 1 (from 8903413 to 8906606, in the reverse strand). This gene is described as "Transcript:ENSGALT00000012994 Gene:ENSGALG00000008004 Chr:1 Start:8903413 End:8906606" and the sequence can be found in the sequence table.

sequence

This table contains the protein sequences present in the member table used in the protein alignment part of the EnsEMBL Compara DB.

sequence table description
Field	Type	Null	Key	Default	Extra	Description
sequence_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
sequence	longtext	YES		NULL		the sequence
length	int(10)	YES		NULL		the length of the sequence

E.g. the row

mysql> select * from sequence where sequence_id = 1121;
+-------------+-------------------------------------------+--------+
| sequence_id | sequence                                  | length |
+-------------+-------------------------------------------+--------+
|        1121 | LPNTRGYTQVWECSLAVLIAMVCMTLVGWGLIWLFSVTASV |     41 |
+-------------+-------------------------------------------+--------+

contains a 41 aminoacids long sequence.

analysis

This table is mainly used for production purposes.

analysis table description
Field	Type	Null	Key	Default	Extra	Description
analysis_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
created	datetime			0000-00-00 00:00:00		date to distinguish newer and older versions off the same analysis. Not well maintained so far.
logic_name	varchar(40)		UNI			string to identify the analysis. Used mainly inside pipeline.
db	varchar(120)	YES		NULL		db should be a database name, db version the version of that db
db_version	varchar(40)	YES		NULL
db_file	varchar(120)	YES		NULL		the file system location of that database, probably wiser to generate from just db and configurations
program	varchar(80)	YES		NULL		The binary used to create a feature. Similar semantic to above
program_version	varchar(40)	YES		NULL
program_file	varchar(80)	YES		NULL
parameters	varchar(255)	YES		NULL		a parameter string which is processed by the perl module
module	varchar(80)	YES		NULL		Perl module names (RunnableDBS usually) executing this analysis
module_version	varchar(40)	YES		NULL
gff_source	varchar(40)	YES		NULL		how to make a gff dump from features with this analysis
gff_feature	varchar(40)	YES		NULL		how to make a gff dump from features with this analysis

analysis_description

This table has been added to comply with core Bio::EnsEMBL::DBSQL::AnalysisAdaptor requirements.

analysis_description table description
Field	Type	Null	Key	Default	Description
analysis_id	int(10) unsigned		MUL	0	external reference to analysis.analysis_id
description	text	YES		NULL
display_label	varchar(255)	YES		NULL

peptide_align_feature

This tables stores the raw HSP local alignment results of peptide to peptide alignments returned by a BLAST run it is translated from a FeaturePair object.

peptide_align_feature table description
Field	Type	Null	Key	Default	Extra	Description
peptide_align_feature_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
qmember_id	int(10) unsigned		MUL	0		external reference to member.member_id for the query peptide
hmember_id	int(10) unsigned		MUL	0		external reference to member.member_id for the hit peptide
qgenome_db_id	int(10) unsigned			0		external reference to genome_db.genome_db_id for the query peptide (for query optimization)
hgenome_db_id	int(10) unsigned			0		external reference to genome_db.genome_db_id for the hit peptide (for query optimization)
analysis_id	int(10) unsigned			0		external reference to analysis.analyis_id
qstart	int(10)			0		starting position in the query peptide sequence
qend	int(10)			0		ending position in the query peptide sequence
hstart	int(10)			0		starting position in the hit peptide sequence
hend	int(10)			0		ending position in the hit peptide sequence
score	double(16,4)			0.0000		blast score for this HSP
evalue	varchar(20)	YES		NULL		blast evalue for this HSP
align_length	int(10)	YES		NULL		alignment length of HSP
identical_matches	int(10)	YES		NULL		blast HSP match score
perc_ident	int(10)	YES		NULL		percent identical matches in the HSP length
positive_matches	int(10)	YES		NULL		blast HSP positive score
perc_pos	int(10)	YES		NULL		precent positive matches in the HSP length
hit_rank	int(10)	YES		NULL		rank in blast result
cigar_line	mediumtext	YES		NULL		cigar string coding the actual alignment

E.g. the rows:

mysql> SELECT * FROM peptide_align_feature WHERE qmember_id = 442105;
+--------------------------+------------+------------+---------------+---------------+-···
| peptide_align_feature_id | qmember_id | hmember_id | qgenome_db_id | hgenome_db_id |
+--------------------------+------------+------------+---------------+---------------+-···
|                        1 |     442105 |     248885 |             3 |            12 |
|                        2 |     442105 |      86297 |             3 |            12 |
|                        3 |     442105 |     215369 |             3 |            12 |
|                        4 |     442105 |      67917 |             3 |            12 |
|                        5 |     442105 |     182642 |             3 |            12 |
|                        6 |     442105 |     212528 |             3 |            12 |
|                        7 |     442105 |     215342 |             3 |            12 |
|                        8 |     442105 |     260556 |             3 |             5 |
+--------------------------+------------+------------+---------------+---------------+-···

 ···-+-------------+--------+------+--------+------+----------+---------+--------------+-···
     | analysis_id | qstart | qend | hstart | hend | score    | evalue  | align_length |
 ···-+-------------+--------+------+--------+------+----------+---------+--------------+-···
     |          14 |      3 |  240 |     38 |  276 | 276.0000 | 1.1e-25 |          243 |
     |          14 |     32 |  244 |      8 |  220 | 224.0000 | 3.5e-20 |          219 |
     |          14 |     30 |  213 |      8 |  198 | 212.0000 | 6.6e-19 |          194 |
     |          14 |     32 |  244 |      2 |  219 | 176.0000 | 2.2e-14 |          224 |
     |          14 |     36 |  227 |      1 |  201 | 161.0000 | 5.2e-13 |          205 |
     |          14 |     30 |  219 |      2 |  208 | 158.0000 | 8.5e-12 |          214 |
     |          14 |     29 |  214 |      7 |  201 | 158.0000 | 9.8e-12 |          201 |
     |          15 |     32 |  242 |      8 |  224 | 249.0000 | 1.2e-22 |          220 |
 ···-+-------------+--------+------+--------+------+----------+---------+--------------+-···

 ···-+-------------------+------------+------------------+----------+----------+-···
     | identical_matches | perc_ident | positive_matches | perc_pos | hit_rank |
 ···-+-------------------+------------+------------------+----------+----------+-···
     |                80 |         32 |              124 |       51 |        1 |
     |                66 |         30 |              112 |       51 |        2 |
     |                63 |         32 |              104 |       53 |        3 |
     |                60 |         26 |              107 |       47 |        4 |
     |                61 |         29 |               99 |       48 |        5 |
     |                61 |         28 |               98 |       45 |        6 |
     |                57 |         28 |               97 |       48 |        7 |
     |                73 |         33 |              109 |       49 |        1 |
 ···-+-------------------+------------+------------------+----------+----------+-···

 ···-+---------------------------------------------+
     | cigar_line                                  |
 ···-+---------------------------------------------+
     | 23M2I34MD42MI13MI51MD43M3D28M               |
     | 31M2D9M3I27M2D15MI56MD39MI7MD20MI3M         |
     | 27M2D7MD23M2D20M2I16MI33M2D9MD8M2D38M       |
     | 40M3D8M3D3M2D24M2I8MI33MD21MD43MD16M3I11M   |
     | 33MD5M2D8M5D20MI24MI29M4D17MD42M2I10M       |
     | 25M3D17M2D21M6I57M13D18MD3M4DMI36MD5M       |
     | 30MD7M3D9MI31M2I5M2D17M3I22M3D13M4D29M2D17M |
     | 33M2D7M2D20M4D9MI16MI55MD65MI3M             |
 ···-+---------------------------------------------+

corresponds to all the hits found for the rat peptide defined by the member.member_id 442105.

protein_tree_node

This tables stores the phylogenetic structure of the genetrees.

protein_tree_node description
Field	Type	Null	Key	Default	Extra	Description
node_id	int(10) unsigned	NO	PRI	NULL	auto_increment	node unique ID
parent_id	int(10) unsigned	NO	MUL			parent node id
root_id	int(10) unsigned	NO	MUL			cluster node id (usually 1) where this genetree is attached
left_index	int(10)	NO	MUL			left index of the tree-traversal binary search
right_index	int(10)	NO	MUL			right index of the tree-traversal binary search
distance_to_parent	double	NO		1		branch length between this node and parent node

E.g. the rows:

mysql> select * from protein_tree_node where node_id=10;
+---------+-----------+---------+------------+-------------+--------------------+
| node_id | parent_id | root_id | left_index | right_index | distance_to_parent |
+---------+-----------+---------+------------+-------------+--------------------+
|      10 |    707637 |       1 |       7645 |        7646 |           0.001496 |
+---------+-----------+---------+------------+-------------+--------------------+

corresponds to the node_id=10 with a branch length of 0.001496. This the right_index-left_index=1 value indicates that is an external node (leaf)

protein_tree_member

This tables stores the relationship between the protein_tree_node and the member tables.

protein_tree_member description
Field	Type	Null	Key	Default	Description
node_id	int(10) unsigned	NO	PRI		external reference to protein_tree_node.node_id
member_id	int(10) unsigned	NO	MUL		external reference to member.member_id
method_link_species_set_id	int(10) unsigned	NO			method_link_species_set_id
cigar_line	mediumtext	YES		NULL	cigar string coding the alignment
cigar_start	int(10)	YES		NULL	defines the first alignment aminoacid
cigar_end	int(10)	YES		NULL	defines the last alignment aminoacid

E.g. the rows:

mysql> select * from protein_tree_member where node_id=10;
+---------+-----------+----------------------------+------------------------------+-------------+-----------+
| node_id | member_id | method_link_species_set_id | cigar_line                   | cigar_start | cigar_end |
+---------+-----------+----------------------------+------------------------------+-------------+-----------+
|      10 |    416753 |                      40046 | 106D53MD9M4D4MD42MD47MD47M8D |        NULL |      NULL |
+---------+-----------+----------------------------+------------------------------+-------------+-----------+

corresponds to the node_id=10.

N.B.The cigar_start and cigar_end fields will be NULL in multiple sequence alignments (only used in pairwise alignments).

protein_tree_tag

This tables stores various tags for nodes in protein_tree_node.

protein_tree_tag description
Field	Type	Null	Key	Default	Description
node_id	int(10) unsigned	NO	MUL		node unique ID
tag	varchar(50)	YES	MUL	NULL	tag
value	mediumtext	YES		NULL	value

E.g. the rows:

mysql> select * from protein_tree_tag where node_id=707631;
+---------+----------------------------+------------------+
| node_id | tag                        | value            |
+---------+----------------------------+------------------+
|  707631 | Bootstrap                  | 70               |
|  707631 | Duplication                | 0                |
|  707631 | Sitewise_dNdS_runtime_msec | 58504.8859863281 |
|  707631 | Sitewise_dNdS_subroot_id   | 8                |
|  707631 | taxon_alias                | Primates         |
|  707631 | taxon_id                   | 9443             |
|  707631 | taxon_name                 | Primates         |
+---------+----------------------------+------------------+

corresponds to the node_id=707631 and shows all the tags associated with this internal node.

ncbi_taxa_node

This tables stores the phylogenetic structure of the NCBI taxonomy DB.

ncbi_taxa_node description
Field	Type	Null	Key	Default	Description
taxon_id	int(10) unsigned	NO	PRI		taxon ID
parent_id	int(10) unsigned	NO	MUL		parent taxon id
rank	char(32)	NO	MUL		rank in the tree of life (family, genus, species, ...)
genbank_hidden_flag	tynyint(1)	NO		0	genbank flag
left_index	int(10)	NO	MUL		left index of the tree-traversal binary search
right_index	int(10)	NO	MUL		right index of the tree-traversal binary search
root_id	int(10)	NO		1	cluster node id (usually 1) where this taxonomy node is attached

E.g. the rows:

mysql> select * from ncbi_taxa_node limit 10;
+----------+-----------+--------------+---------------------+------------+-------------+---------+
| taxon_id | parent_id | rank         | genbank_hidden_flag | left_index | right_index | root_id |
+----------+-----------+--------------+---------------------+------------+-------------+---------+
|        1 |         0 | no rank      |                   0 |          1 |      891068 |       1 |
|        2 |    131567 | superkingdom |                   0 |       7665 |      234070 |       1 |
|        6 |    335928 | genus        |                   0 |      97634 |       97669 |       1 |
|        7 |         6 | species      |                   1 |      97635 |       97638 |       1 |
|        9 |     32199 | species      |                   1 |     123547 |      123678 |       1 |
|       10 |    135621 | genus        |                   0 |     129052 |      129111 |       1 |
|       11 |        10 | species      |                   1 |     129075 |      129076 |       1 |
|       13 |    203488 | genus        |                   0 |      50174 |       50197 |       1 |
|       14 |        13 | species      |                   1 |      50179 |       50182 |       1 |
|       16 |     32011 | genus        |                   0 |      70484 |       70531 |       1 |
+----------+-----------+--------------+---------------------+------------+-------------+---------+

correspond to some taxon_ids in the NCBI taxonomy DB

ncbi_taxa_name

This tables stores the names of the NCBI taxonomy entries.

ncbi_taxa_name description
Field	Type	Null	Key	Default	Description
taxon_id	int(10) unsigned	NO	PRI		external reference to ncbi_taxa_node.taxon_id
name	varchar(255)	YES	MUL	NULL	Name of the taxon
name_class	varchar(50)	YES	MUL	NULL	class of name

E.g. the rows:

mysql> select * from ncbi_taxa_name where taxon_id=9606;
+----------+--------------+---------------------+
| taxon_id | name         | name_class          |
+----------+--------------+---------------------+
|     9606 | Homo sapiens | scientific name     |
|     9606 | human        | genbank common name |
|     9606 | man          | common name         |
|     9606 | Human        | ensembl alias name  |
|     9606 | human        | ensembl common name |
+----------+--------------+---------------------+

correspond to the human taxon_id names in the NCBI taxonomy DB

homology

Contains all the genomic homologies found. There are two homology_member entries for each homology entry for now, but both the schema and the API can handle more than just pairwise relations.

homology table description
Field	Type	Null	Key	Default	Extra	Description
homology_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
stable_id	varchar(40)	YES		NULL		stable ID of the pairwise homology relationship
method_link_species_set_id	int(10) unsigned		MUL			external reference to method_link_species_set.method_link_species_set_id
description	varchar(40)	YES		NULL		describes the type of homology found: ortholog_one2one for one to one orthologs apparent_ortholog_one2one for apparent one to one orthologs ortholog_one2many for one to many orthologs ortholog_many2many for many to many orthologs between_species_paralog for between species paralogs
subtype	varchar(40)	NO				The subtype defines the taxonomic level of the relationship found (taxon_name).
dn	float(10,5)	YES		NULL		number of nonsynonymous substitutions per nonsynonymous site
ds	float(10,5)	YES		NULL		number of synonymous substitutions per synonymous site
n	float(10,1)	YES		NULL		number of nonsynonymous sites
s	float(10,1)	YES		NULL		number of synonymous sites
lnl	float(10,3)	YES		NULL		maximum likelihood test value
threshold_on_ds	float(10,5)	YES		NULL		used by the EnsEMBL Web Browser to decide whether or not to display dN/DS ratio
ancestor_node_id	int(10) unsigned	NO				ancestor node_id of the relationship
tree_node_id	int(10) unsigned	NO	MUL			root node_id for the genetree where this relationship lies

dN, dS, N, S and lnL are statistical values given by the codeml program of the Phylogenetic Analysis by Maximum Likelihood (PAML) package.

E.g. the row

mysql> select * from homology where homology_id=79;
+-------------+-----------+----------------------------+------------------+-...
| homology_id | stable_id | method_link_species_set_id | description      | 
+-------------+-----------+----------------------------+------------------+-...
|          79 | NULL      |                      22467 | ortholog_one2one | 
+-------------+-----------+----------------------------+------------------+-...

...+------------+---------+---------+------+------+----------+-----------------+------------------+--------------+
   | subtype    | dn      | ds      | n    | s    | lnl      | threshold_on_ds | ancestor_node_id | tree_node_id |
...+------------+---------+---------+------+------+----------+-----------------+------------------+--------------+
   | Catarrhini | 0.14610 | 0.21260 | 82.1 | 37.9 | -222.752 |         0.17120 |              284 |          284 |
...+------------+---------+---------+------+------+----------+-----------------+------------------+--------------+

defines a one to one orthology at the taxonomic level Catarrhini (Apes and old world monkeys).

N.B.At the moment there are no stable ids for homologies.

homology_member

Contains the sequences corresponding to every genomic homology relationship found. There are two homology_member entries for each pairwise homology entry. As written in the homology table section, both schema and API can deal with more than pairwise relationships.

The original alignment is not stored but it can be retrieved using the cigar_line field and the original sequences. The cigar line defines the sequence of matches or mismatches and deletions in the alignment.

First peptide sequence:  SERCQVVVISIGPISVLSMILDFY

Second peptide sequence: SDRCQVLVISILSMIGLDFY

```
First corresponding cigar line:  20MD4M
```

Second corresponding cigar line: 11M5D9M

The alignment will be:

Example of alignment reconstruction
First peptide cigar line	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	M	D	M	M	M	M
First aligned peptide	S	E	R	C	Q	V	V	V	I	S	I	G	P	I	S	V	L	S	M	I	-	L	D	F	Y
Second aligned peptide	S	D	R	C	Q	V	L	V	I	S	I	-	-	-	-	-	L	S	M	I	G	L	D	F	Y
Second peptide cigar line	M	M	M	M	M	M	M	M	M	M	M	D	D	D	D	D	M	M	M	M	M	M	M	M	M

homology_member table description
Field	Type	Null	Key	Default	Description
homology_id	int(10) unsigned		PRI	0	external reference to homology.homology_id
member_id	int(10) unsigned		PRI	0	external reference to member.member_id.It refers to the corresponding gene (ENSEMBL_GENE).
peptide_member_id	int(10) unsigned	YES		NULL	external reference to member.member_id.It refers to the peptide/protein (ENSEMBL_PEP).
peptide_align_feature_id	int(10) unsigned	YES		NULL	external reference to peptide_align_feature.peptide_align_feature_id
cigar_line	mediumtext	YES		NULL	an internal description of the alignment. It contains mathces/mismatches (M) and delations (D)and refers to the corresponding peptide_member_id sequence.
cigar_start	int(10)	YES		NULL	defines the first aligned aminoacid
cigar_end	int(10)	YES		NULL	defines the last aligned aminoacid
perc_cov	int(10)	YES		NULL	defines the percentage of the peptide which has been aligned
perc_id	int(10)	YES		NULL	defines the percentage of identity between both homologues
perc_pos	int(10)	YES		NULL	defines the percentage of positivity (similarity) between both homologues

E.g. the rows

mysql> select * from homology_member where homology_id = 296648;
+-------------+-----------+-------------------+--------------------------+------------+-···
| homology_id | member_id | peptide_member_id | peptide_align_feature_id | cigar_line |
+-------------+-----------+-------------------+--------------------------+------------+-···
|      296648 |       685 |               722 |                     NULL | 77M        |
|      296648 |    406456 |            406463 |                     NULL | 77M        |
+-------------+-----------+-------------------+--------------------------+------------+-···

 ···-+-------------+-----------+----------+---------+----------+
     | cigar_start | cigar_end | perc_cov | perc_id | perc_pos |
 ···-+-------------+-----------+----------+---------+----------+
     |           1 |        77 |       30 |      79 |       87 |
     |          91 |       167 |       38 |      79 |       87 |
 ···-+-------------+-----------+----------+---------+----------+

refer to the two homologue sequences defined by the homology.homology_id 296648. The gene corresponding to the first sequence can be retrieved using the member.member_id 685 and the corresponding peptide using the member.member_id 722. Gene and peptide sequence of the second homologue can retrieved in the same way.

N.B.At the moment the peptide_align_feature_ids are NULL because they are only indirectly used in the homology prediction but left there for compatibility with the old BRH system.

sitewise_aln

Contains the site wise dN/dS values for the codon alignments.

sitewise_aln table description
Field	Type	Null	Key	Default	Extra	Description
sitewise_id	int(10) unsigned	NO	PRI	NULL	auto_increment	internal unique ID
aln_position	int(10) unsigned	NO	MUL			alignment position of the codon/aminoacid
node_id	int(10) unsigned	NO	MUL			root node_id for the subtree used in the analysis. External reference to protein_tree_node.node_id
tree_node_id	int(10) unsigned	NO				root node_id for the tree. External reference to protein_tree_node.node_id
omega	float(10,5)	YES		NULL		Omega (dn/ds) value
omega_lower	float(10,5)	YES		NULL		Lower bound of support interval (confidence interval) for omega.
omega_upper	float(10,5)	YES		NULL		Upper bound of support interval (confidence interval) for omega.
threshold_on_branch_ds	float(10,5)	YES		NULL		Synonymous length used in the analysis at which a branch is considered to be subject to saturation of synonymous mutation.
type	varchar(10)	NO				describes the type of site found: positive1 for positively selected site at uncorrected 95% probability positive2 for positively selected site at uncorrected 99% probability positive3 for positively selected site at corrected 95% probability positive4 for positively selected site at corrected 99% probability negative1 for negatively selected site at uncorrected 95% probability negative2 for negatively selected site at uncorrected 99% probability negative3 for negatively selected site at corrected 95% probability negative4 for negatively selected site at corrected 99% probability constant for site with no changes all_gaps for site with only gaps (due to the use of subalignments) single_character for site with only 1 site and the remaining positions being gaps synonymous for site with only synonymous changes default for site that are none of the above

E.g. the row

mysql> select * from sitewise_aln where sitewise_id=1;
+-------------+--------------+---------+--------------+-...
| sitewise_id | aln_position | node_id | tree_node_id |
+-------------+--------------+---------+--------------+-...
|           1 |           31 |    1827 |         1827 |
+-------------+--------------+---------+--------------+-...

...+---------+-------------+-------------+------------------------+-----------+
   | omega   | omega_lower | omega_upper | threshold_on_branch_ds | type      |
...+---------+-------------+-------------+------------------------+-----------+
   | 9.23330 |     3.22020 |    23.21050 |                1.50000 | positive3 |
...+---------+-------------+-------------+------------------------+-----------+

defines a positively selected position with an omega value omega=9.23330 with a confidence interval of (3.2,23.2) calculated using a threshold_on_branch_ds=1.5 for the genetree with root 1827 (in this case a full genetree, not a subalignment as node_id=tree_node_id).

family

Contains all the group homologies found. There are several family_member entries for each family entry.

family table description
Field	Type	Null	Key	Default	Extra	Description
family_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
stable_id	varchar(40)		UNI			stable family ID
method_link_species_set_id	int(10) unsigned			0		external reference to method_link_species_set.method_link_species_set_id
description	varchar(255)	YES	MUL	NULL		description of the family as found using the Longest Common String (LCS) of the descriptions of the member proteins.
description_score	double	YES		NULL		Scores the accuracy of the annotation (max. 100)

E.g. the row

mysql> select * from family where family_id=4000;
+-----------+-------------------+----------------------------+-...
| family_id | stable_id         | method_link_species_set_id |
+-----------+-------------------+----------------------------+-...
|      4000 | fam51v00000004000 |                      30017 |
+-----------+-------------------+----------------------------+-...

...+--------------------------------------------------------------------+-------------------+
   | description                                                        | description_score |
...+--------------------------------------------------------------------+-------------------+
   | NUCLEAR PORE COMPLEX NUP205 NUCLEOPORIN NUP205.205 KDA NUCLEOPORIN |               100 |
...+--------------------------------------------------------------------+-------------------+

defines a family homology found which stable ID is fam51v00000004000 and the description of this family is "NUCLEAR PORE COMPLEX NUP205 NUCLEOPORIN NUP205.205 KDA NUCLEOPORIN" scored with a 100.

family_member

Contains the proteins corresponding to protein family relationship found. There are several family_member entries for each family entry.

family_member table description
Field	Type	Null	Key	Default	Description
family_id	int(10) unsigned		PRI	0	external reference to family.family_id
member_id	int(10) unsigned		PRI	0	external reference to member.member_id
cigar_line	mediumtext	YES		NULL	internal description of the multiple alignment (see homology_member table)

E.g. the rows

mysql> SELECT * FROM family_member WHERE family_id = 13252;
+-----------+-----------+------------+
| family_id | member_id | cigar_line |
+-----------+-----------+------------+
|     13252 |     69013 | NULL       |
|     13252 |     69028 | 26D348M    |
|     13252 |    217503 | NULL       |
|     13252 |    217511 | 374M       |
|     13252 |    823691 | 26D348M    |
+-----------+-----------+------------+

refer to the five members of the protein family 13252. The proteins can be retieved using the member_ids. The multiple alignment can be restored using the cigar_lines.

domain

Not used by now

domain table description
Field	Type	Null	Key	Default	Extra	Description
domain_id	int(10) unsigned		PRI	NULL	auto_increment	internal unique ID
stable_id	varchar(40)
method_link_species_set	int(10) unsigned			0		external reference to method_link_species_set.method_link_species_set_id
description	varchar(255)	YES		NULL

domain_member

Not used by now

domain_member table description
Field	Type	Null	Key	Default
domain_id	int(10) unsigned		MUL	0
member_id	int(10) unsigned		MUL	0
member_start	int(10)	YES		NULL
member_end	int(10)	YES		NULL

EnsEMBL Compara DB Schema Documentation

Introduction

List of tables

General Tables

meta

taxon

genome_db

method_link

method_link_species_set

Tables For Genomic Alignments

dnafrag

genomic_align_block

genomic_align

genomic_align_group

synteny_region

dnafrag_region

Tables For Orthologues and Protein Clusters

member

sequence

analysis

analysis_description

peptide_align_feature

protein_tree_node

protein_tree_member

protein_tree_tag

ncbi_taxa_node

ncbi_taxa_name

homology

homology_member

sitewise_aln

family

family_member

domain

domain_member