GeneOntologyDbManager is a C++ tool that is part of my experimental Variation Toolkit.
This program is a set of tools for GeneOntology, it is based on the sqlite3 library.
Download
Download the sources from Google-Code using
subversion:....
svn checkout http://variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only
... or update the sources of an existing installation...
cd variationtoolkit
svn update
... and edit the
variationtoolkit/congig.mk file.
Dependencies
Compilation
Define "
SQLITE_LIB" and
"
SQLITE_CFLAGS" in
config.mk (see
HowToInstall )
$ cd variationtoolkit/src/
$ make ../bin/godbmgr
if ! [ -z "-lsqlite3" ] ;then g++ -o ../bin/godbmgr godatabasemgr.cpp xsqlite.cpp application.o xstream.o xxml.o -g `xml2-config --cflags ` /usr/include/sqlite3.h -lz -lsqlite3 `xml2-config --libs` ; else g++ -o ../bin/godbmgr godatabasemgr.cpp -DNOSQLITE -O3 -Wall ; fi
Usage
godbmgr (program-name) -f database.sqlite [options] (file1.vcf file2... | stdin )
Sub-Program: loadrdf
Loads the RDF/XML GO database (
http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz) into the
sqlite3 database.
Usage
godbmgr loadrdf -f database.sqlite (stdin|file)
Options
Example
$ curl -s "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
gunzip -c |\
godbmgr loadrdf -f database.sqlite
list the content of the database:
$ sqlite3 -separator ' ' -header database.sqlite 'select * from TERM where acn="GO:0000007"'
acn xml
GO:0000007 <go:term xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.geneontology.org/go#GO:0000007">
<go:accession xmlns:go="http://www.geneontology.org/dtds/go.dtd#">GO:0000007</go:accession>
<go:name xmlns:go="http://www.geneontology.org/dtds/go.dtd#">low-affinity zinc ion transmembrane transporter activity</go:name>
<go:definition xmlns:go="http://www.geneontology.org/dtds/go.dtd#">Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.</go:definition>
<go:is_a xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="http://www.geneontology.org/go#GO:0005385"/>
</go:term>
$ sqlite3 -separator ' ' -header database.sqlite 'select * from TERM2REL where acn="GO:0000007"'
acn rel target
GO:0000007 is_a GO:0005385
Sub-Program: loadgoa
inserts the database for GOA into a
sqlite3 database (e.g:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz)
Usage
godbmgr loadgoa -f database.sqlite (stdin|file)
Options
Examples
$ curl -s "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz" |\
gunzip -c |\
godbmgr loadgoa -f database.sqlite
list the content of the database:
$ sqlite3 -line database.sqlite 'select * from GOA where term="GO:0005385" limit 2'
DB = UniProtKB
DB_Object_ID = B3KU87
DB_Object_Symbol = SLC30A6
term = GO:0005385
DB_Object_Name = cDNA FLJ45816 fis, clone NT2RP7019682, highly similar to Homo sapiens solute carrier family 30 (zinc transporter), member 6 (SLC30A6), mRNA
Synonym = B3KU87_HUMAN|SLC30A6|hCG_23082|IPI01009565|B7WP49
DB_Object_Type = protein
DB = UniProtKB
DB_Object_ID = B5MCR8
DB_Object_Symbol = SLC30A6
term = GO:0005385
DB_Object_Name = Solute carrier family 30 (Zinc transporter), member 6, isoform CRA_b
Synonym = B5MCR8_HUMAN|SLC30A6|hCG_23082|IPI00894292
DB_Object_Type = protein
Sub-Program: desc
print the descendants (children) of a given GO node.
Usage
godbmgr desc -f db.sqlite [options] term1 term2 ... termn
Options
Examples
Default output
$ godbmgr desc -f database.sqlite "GO:0005385"
GO:0000006
GO:0000007
GO:0005385
GO:0015341
GO:0015633
GO:0016463
GO:0022883
xml/rdf output
$ godbmgr desc -f database.sqlite -t xml "GO:0005385" | head
<go:go xmlns:go='http://www.geneontology.org/dtds/go.dtd#' xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
<rdf:RDF>
<go:term xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.geneontology.org/go#GO:0000006">
<go:accession xmlns:go="http://www.geneontology.org/dtds/go.dtd#">GO:0000006</go:accession>
<go:name xmlns:go="http://www.geneontology.org/dtds/go.dtd#">high affinity zinc uptake transmembrane transporter activity</go:name>
<go:definition xmlns:go="http://www.geneontology.org/dtds/go.dtd#">Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force. In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.</go:definition>
<go:is_a xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="http://www.geneontology.org/go#GO:0005385"/>
</go:term>
<go:term xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.geneontology.org/go#GO:0000007">
<go:accession xmlns:go="http://www.geneontology.org/dtds/go.dtd#">GO:0000007</go:accession>
GOA output
$godbmgr desc -f database.sqlite -t goa "GO:0005385"
UniProtKB B3KU87 SLC30A6 GO:0005385 cDNA FLJ45816 fis, clone NT2RP7019682, highly similar to Homo sapiens solute carrier family 30 (zinc transporter), member 6 (SLC30A6), mRNA B3KU87_HUMAN|SLC30A6|hCG_23082|IPI01009565|B7WP49 protein
UniProtKB B5MCR8 SLC30A6 GO:0005385 Solute carrier family 30 (Zinc transporter), member 6, isoform CRA_b B5MCR8_HUMAN|SLC30A6|hCG_23082|IPI00894292 protein
(..)
UniProtKB Q99726 SLC30A3 GO:0015633 Zinc transporter 3 ZNT3_HUMAN|ZNT3|SLC30A3|IPI00293793|Q8TC03protein
TSV output
$ godbmgr desc -f database.sqlite -t tsv "GO:0022857" |\
cut -c 1-100 |\
head
#go:accession go.name go.def
GO:0000006 high affinity zinc uptake transmembrane transporter activity Catalysis of the transfer of
GO:0000007 low-affinity zinc ion transmembrane transporter activity Catalysis of the transfer of a s
GO:0000064 L-ornithine transmembrane transporter activity Catalysis of the transfer of L-ornithine f
GO:0000095 S-adenosylmethionine transmembrane transporter activity Catalysis of the transfer of S-ad
GO:0000099 sulfur amino acid transmembrane transporter activity Catalysis of the transfer of sulfur
GO:0000100 S-methylmethionine transmembrane transporter activity Catalysis of the transfer of S-meth
GO:0000102 L-methionine secondary active transmembrane transporter activity Catalysis of the transfe
GO:0000227 oxaloacetate secondary active transmembrane transporter activity Catalysis of the transfe
GO:0000269 toxin export channel activity Enables the energy independent passage of toxins, sized les
(...)
Sub-Program: asc
prints the ascendants (parents) of a given node.
Usage
godbmgr asc -f db.sqlite [options] term1 term2 ... termn
Options
Examples
Default output
$ godbmgr asc -f database.sqlite "GO:0022857"
GO:0003674
GO:0005215
GO:0022857
all
xml/rdf output
$ godbmgr asc -f database.sqlite -t xml "GO:0022857" | head
<go:go xmlns:go='http://www.geneontology.org/dtds/go.dtd#' xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
<rdf:RDF>
<go:term xmlns:go="http://www.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.geneontology.org/go#GO:0003674">
<go:accession xmlns:go="http://www.geneontology.org/dtds/go.dtd#">GO:0003674</go:accession>
<go:name xmlns:go="http://www.geneontology.org/dtds/go.dtd#">molecular_function</go:name>
<go:synonym xmlns:go="http://www.geneontology.org/dtds/go.dtd#">GO:0005554</go:synonym>
<go:synonym xmlns:go="http://www.geneontology.org/dtds/go.dtd#">molecular function</go:synonym>
<go:synonym xmlns:go="http://www.geneontology.org/dtds/go.dtd#">molecular function unknown</go:synonym>
<go:definition xmlns:go="http://www.geneontology.org/dtds/go.dtd#">Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.</go:definition>
<go:comment xmlns:go="http://www.geneontology.org/dtds/go.dtd#">Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.</go:comment>
GOA output
$godbmgr desc -f database.sqlite -t goa "GO:0005385"
UniProtKB B3KU87 SLC30A6 GO:0005385 cDNA FLJ45816 fis, clone NT2RP7019682, highly similar to Homo sapiens solute carrier family 30 (zinc transporter), member 6 (SLC30A6), mRNA B3KU87_HUMAN|SLC30A6|hCG_23082|IPI01009565|B7WP49 protein
UniProtKB B5MCR8 SLC30A6 GO:0005385 Solute carrier family 30 (Zinc transporter), member 6, isoform CRA_b B5MCR8_HUMAN|SLC30A6|hCG_23082|IPI00894292 protein
(..)
UniProtKB Q99726 SLC30A3 GO:0015633 Zinc transporter 3 ZNT3_HUMAN|ZNT3|SLC30A3|IPI00293793|Q8TC03protein
TSV output
$ godbmgr asc -f database.sqlite -t tsv "GO:0022857"
#go:accession go.name go.def
GO:0003674 molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
GO:0005215 transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
GO:0022857 transmembrane transporter activity Enables the transfer of a substance from one side of a membrane to the other.
all all .
Sub-program: goa
Annotate a TSV file with the GOA annotation.
Usage
godbmgr goa -f db.sqlite [options] (stdin|files)
Options
- -f (filename) the sqlite3 database
- -c (column index) REQUIRED. The observed column.
Example
$ echo -e "#MyGene\nHello\nNOTCH2" |\
godbmgr goa -c 1 -f database.sqlite |\
head -n 4 |\
verticalize
>>> 2
$1 #MyGene Hello
$2 DB .
$3 DB_Object_ID .
$4 DB_Object_Symbol .
$5 term .
$6 DB_Object_Name,Synonym .
$7 DB_Object_Type .
$8 ??? .
<<< 2
>>> 3
$1 #MyGene NOTCH2
$2 DB UniProtKB
$3 DB_Object_ID Q04721
$4 DB_Object_Symbol NOTCH2
$5 term GO:0001709
$6 DB_Object_Name,Synonym Neurogenic locus notch homolog protein 2
$7 DB_Object_Type NOTC2_HUMAN|NOTCH2|IPI00297655|Q5T3X7|Q99734|Q9H240
$8 ??? protein
<<< 3
>>> 4
$1 #MyGene NOTCH2
$2 DB UniProtKB
$3 DB_Object_ID Q04721
$4 DB_Object_Symbol NOTCH2
$5 term GO:0004872
$6 DB_Object_Name,Synonym Neurogenic locus notch homolog protein 2
$7 DB_Object_Type NOTC2_HUMAN|NOTCH2|IPI00297655|Q5T3X7|Q99734|Q9H240
$8 ??? protein
Sub-Program: grep
filters the line having an identifier (gene...) that is a children of a given GO term.
Usage
godbmgr grep -f db.sqlite [options] (stdin|files)
Options
- -f (filename) the sqlite3 database
- -c (column index) REQUIRED. The column containing a GO:acn
- -v inverse selection
- -t (GO:acn) add a GO term in the filter (One is REQUIRED).
- -r (rel) add a go relationship (http://www.obofoundry.org/ro/) (OPTIONAL, default: it adds "is_a").
Example
$
$ echo -e "#MyACN\nGO:0003674\nGO:0001618\n" |\
godbmgr grep -f database.sqlite -c 1 -t GO:0004872 -t GO:0004879
#MyACN
GO:0001618
$ echo -e "#MyACN\nGO:0003674\nGO:0001618\n" |\
godbmgr grep -f database.sqlite -c 1 -t GO:0004872 -t GO:0004879 -v
#MyACN
GO:0003674
That's it,
Pierre
