Download Introduction to GO Annotation

GO Annotations: What are they
and how are they made?
Rama Balakrishnan
Saccharomyces Genome Database
Stanford University
Why GO?
• Comparisons between species
– Gets powerful if we have broader species coverage
• Terminology used to describe your species
becomes more accessible
• Genome-wide analyses
– Can be used to figure out if there is anything common
in your microarray cluster
How can this be accomplished?
• By providing Annotations (i.e. link genes to GO
terms)
• By providing Content (controlled vocabularies to the
ontologies)
• Sharing tools, scripts and other resources
I want to Annotate my Genome. Where do I
start?
• GO website
http://www.geneontology.org
– Check the Annotation Documentation, Teaching Resources section on the GO
website
• http://www.geneontology.org/GO.current.annotations.shtml
• http://www.geneontology.org/GO.teaching.resources.shtml
–
–
–
–
Attend one of the annotation camps
Annotation mailing list
Source Forge tracker for annotation related issues
Farmanimals mailing list (new)
• A GO consortium member can mentor a new comer if need be
What tools/infrastructure do you need to
record annotations?
• Excel spread sheet (simple, easy, small scale)
OR
• FileMaker Pro, Access
– Simple databases, scales very well
• ORACLE or MySQL
Lets Get Started!
• What is an annotation?
• Annotation approaches
• Strategies for identifying literature to
annotate
• Strategies for reading a paper for
annotation
• Strategies for annotating a gene and a
genome
What is a GO annotation?
• A annotation is a piece of information
associated with a gene product
• A gene product is usually a protein but can
be a functional RNA
• A GO annotation is a Gene Ontology term
associated with a gene product
Approaches for annotation of a genome
1. Automated/Electronic approaches
2. Manual approaches
3. Combinatorial approach
Anatomy of a GO annotation
Reference
Gene Product
IMP, IGI, IPI,
ISS, IDA, IEP,
TAS, NAS, ND,
RCA, IC, IEA
Evidence Code
GO Term
Literature Source
1. PubMed
- National Library of Medicine, National Institutes of
Health
- http://ncbi.nlm.nih.gov
2. Agricola
- United States Department of Agriculture, National
Agricultural Library
- http://agricola.nal.usda.gov
3. Embase
- Elsevier
- http://www.embase.com
4. Biosis
- Thomson
- http://www.biosis.org
5. Unpublished
- abstract in your own database
- unpublished abstract submitted to GO references
collection
Evidence types
•
•
•
•
•
•
•
•
•
•
ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
•
IEA: Inferred from electronic annotation
Electronic Annotation
• First pass annotations relatively quickly
• Annotation derived without human validation
– Sequence similarity, e.g. Blast search ‘hits’
– Mapping file, e.g. interpro2go, ec2go, etc.
• Useful For:
– genomes that don’t have extensive literature
– groups with limited curatorial resources
Electronic Annotation
• Typically based on sequence similarity
• Document the method used in a abstract
• Internal Reference
- unpublished abstract in your own database
- unpublished abstract submitted to GO references
collection
• Annotation is not reviewed by human
• IEA evidence code
Example IEA Annotations from
dictyBase
Example unpublished reference
Manual annotation
•
•
•
•
Created by scientific curators
Time intensive
Utilizes published literature
Manatee (offered by TIGR)
Combinatorial Approach,
e.g. using sequence similarity
1.
Alignments published in literature
2.
Analysis using full length protein
3.
Analysis using protein domains
Additional annotation information
• WITH/FROM: describes the evidence code
– IPI, IGI, IMP, IEP, ISS, IEA, IC, NAS
– Contains the interacting or similar gene product
• QUALIFIER: describes the GO term
– NOT
– contributes to
– colocalizes with
Example Annotation
nek2
PMID: 11956323
Reference
Gene Product
IDA
centrosome
GO:0005813
Inferred from
Direct Assay
GO Term
Evidence Code
What to Search For in Published Literature?
1. Species name
2. Gene/gene product names:
daf-12, spo11, Sonic hedgehog
3. Process AND species:
embryonic development AND elegans
4. Function AND species:
transcription factor AND mays
5. Cellular component AND species (genus):
plasma membrane AND Drosophila
GO Annotation: GMOD Tools for Enhancing
Information Retrieval
GMOD – Generic Software Components for Model Organism Databases
- http://www.gmod.org/home
- Literature search tools:
PubSearch – http://www.gmod.org/?q=node/44
PubFetch - http://www.gmod.org/?q=node/84
Textpresso – http://www.textpresso.org
- full text of articles
- semantic categories
GO Annotation: Strategies for Identifying
Literature for Curation
1. Primary research literature with new experimental data
- Mutant phenotypes – process
- Activity assays – function
- Localization studies – component
2. Computational analyses
- Phylogenetic analysis – function (ISS)
- Domain analysis
3. Review articles
- TAS evidence
Which parts of the paper are most
important?
• Introductory information
• Abstract
• Experimental Results
• Results: Figures, Tables, Text
• Materials and Methods
• Explanatory text (use with caution)
• (Introduction) – mostly TAS information
• (Discussion)
How is it different from reading papers
as a bench scientist?
• Don’t be swayed by the speculations or theories
that may appear in the Discussion.
• Focus on the actual results vs. the possible
implications of those results.
• Read for details and contact authors if key
identifiers are missing.
How to search for a GO term?
• Web based tools– AmiGO browser (http://www.godatabase.org)
– QuickGO (http://www.ebi.ac.uk/ego/)
• Downloadable tool
(https://sourceforge.net/projects/geneontology/)
– OBO-Edit
– Download the ontology file
Extracting Information from a paper
Sample text from PMID: 12374299
In this study, we report the isolation and molecular
characterization of the B. napus PERK1 cDNA, that is predicted to
encode a novel receptor-like kinase. We have shown that like
other plant RLKs, the kinase domain of PERK1 has serine/threonine
kinase activity, In addition, the location of a PERK1-GTP fusion
protein to the plasma membrane supports the prediction that
PERK1 is an integral membrane protein…these kinases have been
implicated in early stages of wound response…
Example Manual Annotations from SGD
Strategies for annotating
• Approaches
• Updating GO annotations
Annotation from published literature
1. Focus on known genes
2. Identify literature relevant to that gene
a. using gene names, species name
3. Complete annotation set for a gene
a. annotate available experimental data
b. annotations to root nodes indicate nothing is known
Updating GO annotations
• Ongoing process
– New experimental data
– More specific annotation
• Replace obsolete terms
• Rerun computational methods
– InterProScan and interpro2go
I don’t see terms in the ontology that
describe the biology of my species.
• Send an email to the GO mailing list
• Source Forge (SF) tracker for term related issues
https://sourceforge.net/projects/geneontology/
• Content meetings
– Organized by the consortium if the ontology related issues can’t
be resolved over email/SF
– Look for announcements on the GO website, mailing lists
I have my annotations, what next?
•
•
•
Prepare to submit your annotations to the GO consortium
Follow file format
Information on Annotation file format can be found at:
http://www.geneontology.org/GO.annotation.shtml#file
•
A file in this format is called gene_association file
DB: Source of the ID in column 2
Examples- SGD, MGI, UniProt
ID for the gene or gene_product
Examples - FBgn0015331, MGI:99240,
SPAC9.03c
Symbol like Brr2, DDX21_HUMAN that
means something to a biologist, not an ID
Object_Type - gene, transcript,
protein, protein_structure, or
complex, should match the ID
Sample gene-associations file
Optional column
DB source
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
DB Object ID
S000004660
S000004660
S000004660
S000004660
S000000289
S000000289
S000000289
S000000289
S000000289
S000003916
S000003916
S000003916
S000005275
S000005275
S000005275
S000005525
S000005525
S000005525
S000001837
S000001837
S000001837
S000000704
S000000704
S000000704
Object Symbol Qualifier
GOID
AAC1
GO:0005743
AAC1
GO:0005471
AAC1
GO:0006839
AAC1
GO:0009060
AAC3
GO:0005743
AAC3
GO:0005471
AAC3
GO:0009061
AAC3
GO:0009061
AAC3
GO:0009061
AAD10
GO:0008372
AAD10
GO:0018456
AAD10
GO:0006081
AAD14
GO:0008372
AAD14
GO:0018456
AAD14
GO:0006081
AAD15
GO:0008372
AAD15
GO:0018456
AAD15
GO:0006081
AAD16
GO:0008372
AAD16
GO:0018456
AAD16
GO:0006081
AAD3
GO:0008372
AAD3
GO:0018456
AAD3
GO:0006081
DB:reference
SGD_REF:S000050955|PMID:2167309
SGD_REF:S000050955|PMID:2167309
SGD_REF:S000050955|PMID:2167309
SGD_REF:S000050955|PMID:2167309
SGD_REF:S000045889|PMID:2165073
SGD_REF:S000045889|PMID:2165073
SGD_REF:S000045889|PMID:2165073
SGD_REF:S000052497|PMID:1915842
SGD_REF:S000045889|PMID:2165073
SGD_REF:S000069584
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000069584
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000069584
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000069584
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000069584
SGD_REF:S000042151|PMID:10572264
SGD_REF:S000042151|PMID:10572264
Optional column
Ev_code
TAS
IDA
IGI
IGI
ISS
ISS
IGI
IGI
IEP
ND
ISS
ISS
ND
ISS
ISS
ND
ISS
ISS
ND
ISS
ISS
ND
ISS
ISS
With/From
Aspect DB object Name
Synonym
C
ADP/ATP translocator
YMR056C
F
ADP/ATP translocator
YMR056C
SGD:S000000126
P
ADP/ATP translocator
YMR056C
SGD:S000000126
P
ADP/ATP translocator
YMR056C
SGD:S000000126|SGD:S000004660
C
ADP/ATP translocator
YBR085W|ANC3
SGD:S000000126|SGD:S000004660
F
ADP/ATP translocator
YBR085W|ANC3
SGD:S000000126
P
ADP/ATP translocator
YBR085W|ANC3
SGD:S000000126|SGD:S000004660
P
ADP/ATP translocator
YBR085W|ANC3
P
ADP/ATP translocator
YBR085W|ANC3
C
aryl-alcohol dehydrogenase
YJR155W(putative)
F
aryl-alcohol dehydrogenase
YJR155W(putative)
P
aryl-alcohol dehydrogenase
YJR155W(putative)
C
aryl-alcohol dehydrogenase
YNL331C(putative)
F
aryl-alcohol dehydrogenase
YNL331C(putative)
P
aryl-alcohol dehydrogenase
YNL331C(putative)
C
aryl-alcohol dehydrogenase
YOL165C(putative)
F
aryl-alcohol dehydrogenase
YOL165C(putative)
P
aryl-alcohol dehydrogenase
YOL165C(putative)
C
YFL057C
F
YFL057C
P
YFL057C
C
aryl-alcohol dehydrogenase
YCR107W
(putative)
F
aryl-alcohol dehydrogenase
YCR107W
(putative)
P
aryl-alcohol dehydrogenase
YCR107W
(putative)
Object_type
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
gene
Taxon ID
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
taxon:4932
Date
20010118
20010213
20040226
20040226
20040226
20040226
20040226
20040226
20040226
20010119
20020902
20020902
20010119
20020902
20020902
20010119
20020902
20020902
20020902
20020902
20020902
20010119
20020902
20020902
Assigned by
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
SGD
How do I share my gene_associations file?
• Provide them to the larger community by submitting your
annotations to the GO project
• What information should I submit to GO?
– gene-association file
– Contact email address
• Where should I submit the data?
– Send the file to Mike Cherry or send an email to the GO mailing
list
– [email protected]
Databases contributing annotations
– dictyBase (Dictyostelium discoideum)
– FlyBase (Drosophila melanogaster)
– GeneDB (Schizosaccharomyces pombe, Plasmodium falciparum, Leishmania
major and Trypanosoma brucei)
– UniProt Knowledgebase (Swiss-Prot/TrEMBL/PIR-PSD) and InterPro databases
– Gramene (grains, including rice, Oryza)
– Mouse Genome Database (MGD) and Gene Expression Database (GXD) (Mus
musculus)
– Rat Genome Database (RGD) (Rattus norvegicus)
– Reactome
– Saccharomyces Genome Database (SGD) (Saccharomyces cerevisiae)
– The Arabidopsis Information Resource (TAIR) (Arabidopsis thaliana)
– The Institute for Genomic Research (TIGR): databases on several bacterial
species
– WormBase (Caenorhabditis elegans)
– Zebrafish Information Network (ZFIN): (Danio rerio)
Species coverage
• All major eukaryotic model organism
species
• Human via GOA group at UniProt
• Several bacterial and parasite species
through TIGR and GeneDB at Sanger
– many more in pipeline
Annotation coverage
Annotation coverage
Resources the GO project offer to help
you get started
• GO website
– http://www.geneontology.org
– Lots of documentation
– Tools, tutorials and software
• GO mailing list
• [email protected]
• GO project on Source Forge (SF)
– https://sourceforge.net/projects/geneontology/
• AmiGO web application (http://www.godatabase.org)
• GO database