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Methods for Creating GO Annotations
Emily Dimmer
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge
UK
The core information needed for a
GO annotation
1. Database object (protein)
e.g. Q9ARH1
2. GO term ID
e.g. GO:0004674
3. Reference ID
e.g. PubMed ID: 12374299
GOA:InterPro
4. Evidence code
e.g. TAS
The core information needed for a
GO annotation
1. Database object (protein)
e.g. Q9ARH1
2. GO term ID
e.g. GO:0004674
3. Reference ID
e.g. PubMed ID: 12374299
GOA:InterPro
4. Evidence code
e.g. TAS
The core information needed for a
GO annotation
1. Database object (protein)
e.g. Q9ARH1
2. GO term ID
e.g. GO:0004674
3. Reference ID
e.g. PubMed ID: 12374299
GOA:InterPro
4. Evidence code
e.g. TAS
The core information needed for a
GO annotation
1. Database object (protein)
e.g. Q9ARH1
2. GO term ID
e.g. GO:0004674
3. Reference ID
e.g. PubMed ID: 12374299
GOA:InterPro
4. Evidence code
e.g. TAS
GO Evidence Codes
• Every GO annotation includes an Evidence Code that gives
information about the evidence from which the annotation has been
made.
Code
Definition
IEA
Inferred from Electronic Annotation
IDA
Inferred from Direct Assay
IEP
Inferred from Expression Pattern
IGI
Inferred from Genetic Interaction
IMP
Inferred from Mutant Phenotype
IPI
Inferred from Physical Interaction
ISS
Inferred from Sequence Similarity
TAS
Traceable Author Statement
NAS
Non-traceable Author Statement
RCA
Reviewed Computational Analysis
IC
Inferred from Curator
ND
No Data
Manually
annotated
Additional fields can be used to further
clarify an annotation
• Qualifiers
(NOT, contributes_to, colocalizes_with)
• ‘with’ data
to provide users with more information on the
method/experiment applied.
Annotations using the ‘NOT’ qualifier
hSNF2H
Rsf-1
NOT
ATPase activity GO:0016887
IDA
ATPase activity GO:0016887
IDA
Loyola et al. Mol Cell Biol. 2003 Oct;23(19):6759-68.
Annotations using the ‘contributes_to’ qualifier
A protein which is part of a complex
can be annotated to terms in that
describe:
1. Its individual action
2. the action of the whole complex
(Molecular Function terms)
To differentiate between these two types of annotations, if
a protein does not possess the activity itself, the
annotation has the contributes_to qualifier added
Annotations using the ‘contributes_to’ qualifier
Ring1B ubiquitin-protein ligase activity
IDA
Bmi-1 ubiquitin-protein ligase activity
IDA
Ring1A ubiquitin-protein ligase activity
IDA contributes_to
Pc3
IDA
ubiquitin-protein ligase activity
Cao et al. Mol Cell. 2005 Dec 22;20(6):845-54.
contributes_to
contributes_to
Annotations using the ‘colocalizes_with’ qualifier
• Used with cellular component terms
• To describe proteins that are transiently or
peripherally associated with an organelle or
complex
CENP-E condensed chromosome kinetochore IDA colocalizes_with
Meyer et al. J Cell Biol. 1997 Feb 24;136(4):775-88.
Annotations using additional identifiers in the
‘with’ column
• Provides further information to support the evidence code
used in an annotation
When transferring annotations based on sequence similarity…
Protein
GO term
Evidence
Reference
With
For protein binding annotations…
Protein
GO term
Evidence
Reference
With
There are two main types of GO
annotation:

Electronic Annotation

Manual Annotation
both these methods have their
advantages
They can be easily distinguished by the
‘evidence code’ used.
Electronic Annotation
Fatty acid biosynthesis
GO:Fatty acid biosynthesis
( Swiss-Prot Keyword)
EC:6.4.1.2
(EC number)
(GO:0006633)
GO:acetyl-CoA carboxylase
activity
(GO:0003989)
IPR000438: Acetyl-CoA
carboxylase carboxyl
transferase beta subunit
(InterPro entry)
MF_00527: Putative 3methyladenine DNA
glycosylase
GO:acetyl-CoA carboxylase
activity
(GO:0003989)
GO:DNA repair
(HAMAP)
•
(GO:0006281)
Very high-quality
•However
these annotations often use high-level GO terms and
provide little detail.
Camon et al. BMC Bioinformatics. 2005; 6 Suppl 1:S17
Mappings of external concepts to GO
http://www.geneontology.org/GO.indices.shtml
InterProScan
http://www.ebi.ac.uk/InterProScan
Output from InterProScan…
Manual Annotation
• High–quality, specific annotations made using:
• Peer-reviewed papers
• A range of evidence codes to categorize
the types of evidence found in a paper
• very time consuming and requires trained
biologists
Finding GO terms … …for chicken TaxREB107protein (Q8UWG7)
nucleoli
cytoplasmic
increased troponin I reporter gene
activity
positive modulator of skeletal muscle gene
expression
Component:
cytoplasm
GO:0005737
Component:
nucleolus
GO:0005730
positive regulation of transcription
GO:0045941
Process:
Process: positive regulation of skeletal muscle development
GO:0048643
http://www.geneontology.org/GO.annotation.shtml
Aids for GO manual annotation
Many are on the GO Consortium tools page:
http://www.geneontology.org/GO.tools.shtml
GoPubMed gives an overview over literature abstracts taken from
PubMed and categorizes them with Gene Ontology terms:
GoPubMed
http://gopubmed.org
GoPubMed
http://gopubmed.org
http://www.ebi.ac.uk/Rebholz-srv/whatizit
Whatizit
UniProt Ac’s
GO terms
http://www.ebi.ac.uk/Rebholz-srv/whatizit
Searching for GO terms
http://www.ebi.ac.uk/ego
http://www.godatabase.org
http://www.geneontology.org/GO.tools.html
…and more varieties of browsers available on the GO Tools page:
http://www.geneontology.org/GO.tools.html
http://www.ebi.ac.uk/ego
Exact match
http://www.ebi.ac.uk/ego
GO annotation editors
• The GO Consortium is aware there is a need for
a light-weight, generic GO annotation tool.
• enhanced spreadsheets (e.g. Excel)
• Protein2GO (GOA)
Enhanced Spreadsheets
• quick and cheap to start with
• however difficult to maintain/update a reasonable
sized set of annotations
protein2go
Protein2GO
Protein2GO
Protein2GO
Protein2GO
Protein2GO
Protein2GO
Protein2GO
How users can view GO annotations
Download and parse
an entire gene
association file…
…or look at annotations
for a protein using one of
the GO browsers or a
database that integrates
GO annotations.
QuickGO : http://www.ebi.ac.uk/ego
http://www.geneontology.org/GO.current.annotations.shtml
http://www.ebi.ac.uk/goa
Acknowledgements
Nicky Mulder
Head of InterPro
Evelyn Camon
Daniel Barrell
Rachael Huntley
GOA Coordinator
GOA Programmer
GOA Curator
David Binns & John Maslen
QuickGO, Protein2GO tools
Achuthanunni C. Balakrishnan Text-2-GO
Jorge Duarte
IPI sets
Midori Harris
Jane Lomax
Amelia Ireland
Jennifer Clarke
GO Editor
GO Curator
GO Curator
GO Curator
Rolf Apweiler
Head of Sequence Database Group
The Gene Ontology Consortium and 1.5 members of GOA currently supported by an
P41 grant from the National Human Genome Research Institute (NHGRI) [grant
HG002273], GOA is also supported by core EMBL funding.