Biomedical Engineering Reference
In-Depth Information
# Functional Classification Catalogue Version 2.1 09.01.2007
01 METABOLISM
01.01 amino acid metabolism
01.01.03 assimilation of ammonia, metabolism of the glutamate group
01.01.03.01 metabolism of glutamine
01.01.03.01.01 biosynthesis of glutamine
01.01.03.01.02 degradation of glutamine
01.01.03.02 metabolism of glutamate
01.01.03.02.01 biosynthesis of glutamate
01.01.03.02.02 degradation of glutamate
01.01.03.03 metabolism of proline
01.01.03.03.01 biosynthesis of proline
01.01.03.03.02 degradation of proline
Figure 9.1
A subset of a functional category in FunCat (ftp://ftpmips.gsf.de/catalogue/
funcat-2.1_scheme).
address the lack of consistent annotations for gene products in different databases. GO began
as a collaboration between FlyBase [38], the
Saccharomyces
Genome Database (SGD) [39]
and the Mouse Genome Database (MGD) [40], but has grown to include annotations from
a large number of databases, such as WormBase [41], The Institute for Genomic Research
(TIGR, now the J. Craig Venter Institute) databases and the Zebrafish Information Network
(ZFIN) [42]. In recent years, GO gained popularity quickly and has been used in a large
number of studies on function prediction.
PROTOCOL 9.1 Obtaining Gene Ontology Annotations
for Function Prediction
Requirements
•
Internet access to download data and software
•
Programming or scripting language such as C, C++, Perl, Matlab.
Method
1 The GO annotation scheme can be downloaded from http://www.geneontology
.org/GO.downloads.ontology.shtml. The ontology can be downloaded in several file
formats, including the standard OBO format, SQL database dumps, RDF and OWL.
2 Download GO annotations of genomes of interest from a variety, including
Mus
musculus
,
Caenorhabditis elegans
and
Homo sapiens
from http://www.geneontology
.org/GO.current.annotations.shtml
a
3 Each record in an annotation file contains a gene identifier, the GO term identifier and
the reference to a database or publication from which the annotation is derived among,
other information. See http://www.geneontology.org/GO.format.annotation.shtml for a
complete description of the file format.
