Slides from a short tutorial on querying Chado dabatases using SQL, given for the Pathogen Genomics group at the Wellcome Trust Sanger Institute on 12th February 2009.

1. Querying Chado
Monday, February 16, 2009

2. Overview
• Relational databases
• Chado
• Writing queries
• Saving the results
• More examples
Monday, February 16, 2009

3. Relational database
• Data are organised in tables:
• The columns of the table represent attributes,
• The rows represent entities.
Monday, February 16, 2009

4. A conventional genomic database
organism
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

5. A conventional genomic database
organism
Primary key
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

6. A conventional genomic database
organism
Primary key Foreign key
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

7. A conventional genomic database
organism
Attribute
Primary key Foreign key
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

8. A conventional genomic database
organism
organism_id genus species strain
1 Staphylococcus aureus MRSA252
2 Plasmodium falciparum 3D7
3 Schistosoma mansoni
Attribute
Primary key Foreign key
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

9. A conventional genomic database
organism
organism_id genus species strain
1 Staphylococcus aureus MRSA252
2 Plasmodium falciparum 3D7
3 Schistosoma mansoni
gene
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
3 2 PFA00005
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

10. A conventional genomic database
organism
organism_id genus species strain
1 Staphylococcus aureus MRSA252
2 Plasmodium falciparum 3D7
3 Schistosoma mansoni
transcript
gene
exon
gene_id organism_id locus_tag
1 1 SAR0001
2 1 SAR0002
chromosome
3 2 PFA00005
&c
4 2 PFB00010
5 3 Smp_012250
6 3 Smp_152680
Monday, February 16, 2009

11. The core of Chado
Organism
organism_id
genus
species CV
cv_id
name
Feature
feature_id
CVterm
organism_id
cvterm_id
type_id
cv_id
uniquename
name
name
residues
Monday, February 16, 2009

12. The core of Chado
Organism
organism_id
genus
species CV
cv_id
name
Feature
feature_id
CVterm
organism_id
cvterm_id
type_id
cv_id
uniquename
name
name
residues
Monday, February 16, 2009

13. Connecting to the database
• Make sure you have an account on the database,
• Log onto pcs4,
• Type “chado”,
• Enter your database password.
Monday, February 16, 2009

14. Connecting to the database
Welcome to psql 8.2.5, the PostgreSQL interactive terminal.
• Make sure you have an account on the database,
Type: copyright for distribution terms
h for help with SQL commands
• Log ontohelp with psql commands
? for pcs4,
g or terminate with semicolon to execute query
Type to quit
q “chado”,
•
malaria_workshop=>
• Enter your database password.
Monday, February 16, 2009

15. Example queries
d cv
Monday, February 16, 2009

16. Example queries
d for ‘describe’
d cv
Monday, February 16, 2009

17. Example queries
d cv
select * from cv;
Monday, February 16, 2009

18. Example queries
d cv
select * from cv;
* means ‘aquot;
columns’
Monday, February 16, 2009

19. Example queries
d cv
select * from cv;
Name of
* means ‘aquot;
table
columns’
Monday, February 16, 2009

20. Example queries
d cv Queries end with
a semicolon
select * from cv;
Name of
* means ‘aquot;
table
columns’
Monday, February 16, 2009

21. Example queries
d cv
select * from cv;
d cvterm
Monday, February 16, 2009

22. Example queries
d cv
select * from cv;
d cvterm
select name from cvterm
where cv_id = 10;
Monday, February 16, 2009

23. Example queries
d cv
select * from cv;
d cvterm the terms like this is pretty baffling.
Just seeing
If you want to understand the structure of the
ontology better,from download OBO-Edit
you can cvterm
select name
'om oboedit.org, and the sequence ontology
where cv_id sequenceontology.org
'om = 10;
Monday, February 16, 2009

24. Example queries
select name from cvterm
where cv_id = 10;
select cvterm.name
from cvterm
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence';
Monday, February 16, 2009

25. Example queries
select name from cvterm
where cv_id = 10;
select cvterm.name
from cvterm
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence';
select species from organism where
genus = 'Staphylococcus';
Monday, February 16, 2009

26. Count the genes in MRSA252
select count(*)
from feature gene
where gene.type_id in (
select cvterm.cvterm_id
from cvterm
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence'
and cvterm.name = 'gene'
)
and gene.organism_id in (
select organism_id
from organism
where genus = 'Staphylococcus'
and species = 'aureus (MRSA252)'
);
Monday, February 16, 2009

27. Editing queries
• Now type e (for “edit”),
• Change “gene” to “pseudogene”:
• The query will run again, and count the
pseudogenes.
Monday, February 16, 2009

28. More Chado tables
• Locations are stored in the table featureloc.
Featureloc
featureloc_id
refers to the gene
feature_id
refers to the chromosome
srcfeature_id
fmin
} interbase coordinates
fmax
1 (forward) or -1 (reverse)
strand
locgroup
} both 0 for the principal location
rank
Monday, February 16, 2009

29. More Chado tables
• Locations are stored in the table featureloc.
Interbase coordinates
Featureloc
featureloc_id
ACGGTCCATACGGTCCATACGGTCCATCGGTTA
refers to the gene
feature_id
refers to the chromosome
0 1 2 3srcfeature_id
45 etc.
fmin
} interbase coordinates
fmax
13–18(forward) or -1 (reverse)
1
strand
locgroup
} both 0 for the principal location
rank
Monday, February 16, 2009

30. More Chado tables
• Locations are stored in the table featureloc.
Featureloc
featureloc_id
refers to the gene
feature_id
refers to the chromosome
srcfeature_id
fmin
} interbase coordinates
fmax
1 (forward) or -1 (reverse)
strand
locgroup
} both 0 for the principal location
rank
Monday, February 16, 2009

31. Location example
select avg(geneloc.fmax - geneloc.fmin)
from feature gene
join featureloc geneloc
on geneloc.feature_id = gene.feature_id
where gene.type_id in (
select cvterm.cvterm_id
Find the mean gene length of MRSA252
from cvterm
join cv on cv.cv_id on the forward strand.
genes = cvterm.cv_id
where cv.name = 'sequence'
and cvterm.name = 'gene'
)
and gene.organism_id in (
select organism_id
from organism
where genus = 'Staphylococcus'
and species = 'aureus (MRSA252)'
)
and geneloc.locgroup = 0
and geneloc.rank = 0
and geneloc.strand = 1;
Monday, February 16, 2009

32. Location example
select avg(geneloc.fmax - geneloc.fmin)
from feature gene
join featureloc geneloc
on geneloc.feature_id = gene.feature_id
where gene.type_id in (
select cvterm.cvterm_id
from cvterm
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence'
and cvterm.name = 'gene'
)
and gene.organism_id in (
select organism_id
from organism
where genus = 'Staphylococcus'
and species = 'aureus (MRSA252)'
)
and geneloc.locgroup = 0
and geneloc.rank = 0
and geneloc.strand = 1;
Monday, February 16, 2009

33. Another location example
select chromosome.uniquename as chromosome
, count(*) as quot;number of genesquot;
from feature gene
join featureloc geneloc
on geneloc.feature_id = gene.feature_id
join feature chromosome
on geneloc.srcfeature_id = chromosome.feature_id
where gene.type_id in (
select cvterm.cvterm_id
How many genes are on each
from cvterm
chromosome in Plasmodium falciparum?
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence'
and cvterm.name = 'gene'
)
and gene.organism_id in (
select organism_id
from organism
where genus = 'Plasmodium'
and species = 'falciparum'
)
and geneloc.locgroup = 0
and geneloc.rank = 0
group by chromosome.uniquename
;
Monday, February 16, 2009

34. Another location example
select chromosome.uniquename as chromosome
, count(*) as quot;number of genesquot;
from feature gene
join featureloc geneloc
on geneloc.feature_id = gene.feature_id
join feature chromosome
on geneloc.srcfeature_id = chromosome.feature_id
where gene.type_id in (
select cvterm.cvterm_id
from cvterm
join cv on cv.cv_id = cvterm.cv_id
where cv.name = 'sequence'
and cvterm.name = 'gene'
)
and gene.organism_id in (
select organism_id
from organism
where genus = 'Plasmodium'
and species = 'falciparum'
)
and geneloc.locgroup = 0
and geneloc.rank = 0
group by chromosome.uniquename
;
Monday, February 16, 2009

35. Transcripts and exons
Feature_relationship
subject_id
} feature
object_id
type_id cvterm
• Each exon is related to a transcript,
• Each transcript is related to a gene,
• Each polypeptide is related to a transcript,
• Annotation is attached to the polypeptide.
Monday, February 16, 2009

36. Annotation
Products
Feature_cvterm Most other things
feature_id
cvterm_id
Featureprop
feature_id
type_id
value
Monday, February 16, 2009

37. Lots more examples
• Live and direct!
Monday, February 16, 2009