Transcript AmiGO

CRIBI Genomics group
Erika Feltrin
PhD student in
Biotechnology
6 months at EBI
grup.bio.unipd.it
Tools for browsing ontologies
www.geneontology.org/GO.tools.shtml
GO tools
• Consortium Tools
– developed within the Gene Ontology Consortium
– FREE to academics
– you can receive support in using them by writing to the GO helpdesk
• Non-Consortium Tools
– Many tools have been created outside of the consortium for use with
the GO ontologies
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Tools for searching and browsing GO
Annotation tools
Tools for gene expression/microarray analysis
Other tools
www.geneontology.org/GO.tools.shtml
Searching for GO terms
• BROWSER
– AmiGO
http://amigo.geneontology.org
– QuickGO
http://www.ebi.ac.uk/ego
– OLS
http://www.ebi.ac.uk/ontology-lookup
– MGI Browser
http://www.informatics.jax.org
• EDITOR
– OBO-Edit
http://oboedit.org/
…and more varieties of tools available on the GO Tools page
www.geneontology.org/GO.tools.shtml
AmiGO
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Official Gene Ontology HTML based application
Freely available from GO website
Can be installed locally
Used to browse, query and visualize GO data
What can I do using AmiGO?
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browse the GO ontology and view terms
search for a gene or gene product (or a list) and view the GO term
associations
search for GO terms and view the genes or gene products they are
annotated to
perform a sequence identity BLAST search and view the GO term
associations for the genes or proteins returned
amigo.geneontology.org
AmiGO
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AmiGO
AmiGO search interface
amigo.geneontology.org
AmiGO
• Searching features
select to search for
GO terms
select to search for
annotated genes
tick this box to
search for only
exactly matching
strings
amigo.geneontology.org
AmiGO
Filtering Functions
• functions for filtering what
data is displayed in
AmiGO
• selecting ‘All’ then clicking
‘Submit Query’ will show
genes for all datasources
annotated to term
• currently only Uniprot
data is being shown
amigo.geneontology.org
AmiGO- browsable GO tree
• the tree can be expanded to show ‘child’ terms by clicking on the
+ symbol before the term
• expanded node, can be closed again by clicking the ― icon
amigo.geneontology.org
AmiGO
Some ‘child’
terms of
biological
process
•
number of genes
annotated to term,
and its children
indicates relationship of term to its parent.
P = part_of
I = is_a
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AmiGO
Uniprot
All
19,627
219,941
13,101
140,556
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AmiGO – Graphical view
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AmiGO
Term Search Result
List of GO terms
matching search string
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AmiGO
• Gene associations
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AmiGO
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• Term information
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Amigo
• Term information
amigo.geneontology.org
AmiGO
• Term lineage
amigo.geneontology.org
AmiGO
• Term lineage
view shows two different
paths up the tree for term
‘mitochondrial membrane’
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AmiGO
• External references
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AmiGO
links between term and objects in other external databases
e.g InterPro numbers, Pfam ID and ProDom ID
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AmiGO
• Term associations
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AmiGO
• Genes annotated to term, with annotation information
gene symbol/name. Links to
page showing all
annotations to gene
source of annotation i.e. the
database that created the
annotation
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Bax gene
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AmiGO
• Evidence code information
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AmiGO – Blast
You can use your sequence as
Blast query sequence
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Searching for genes
Enter gene to search for here, check the Gene Symbol/Name box
Click ‘Submit Query’
You have this Gene Products Search Results
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AmiGO – Advanced Search
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AmiGO – BLAST search
The AmiGO BLAST server
searches the sequences
from the GO protein
sequence database,
which comprises protein
sequences of genes and
gene products that have
been annotated to a GO
term and submitted to the
GO Consortium.
amigo.geneontology.org
QuickGO
• QuickGO is another GO browser, developed at EBI
• QuickGO is a fast Gene Ontology browser.
• It is now integrated with the InterPro browser. It displays
GO Terms and assignments of GO Terms to UniProt proteins.
www.ebi.ac.uk/ego
QuickGO
www.ebi.ac.uk/ego
QuickGO
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select the field to search on e.g.
GO id, UniProt identifier. Seaches
name/synonym by defaut
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select ontology, i.e. biological
process, molecular function,
cellular component, to search.
Seaches all by default.
www.ebi.ac.uk/ego
QuickGO
• Other matches to search string
• Click term name to select
• Exact match
www.ebi.ac.uk/ego
QuickGO
• Term details
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Term ID
Name
Definitions
Hierarchy
www.ebi.ac.uk/ego
QuickGO – Graphical View
• Alternative paths
through tree
• View of term
location in tree
www.ebi.ac.uk/ego
Ontology Lookup Service - OLS
• The OLS provides a web service interface to
query multiple ontologies from a single location
with a unified output format
• The OLS can integrate any ontology available in
the Open Biomedical Ontology (OBO) format
www.ebi.ac.uk/ontology-lookup
OLS
• You can query ontologies that you need
www.ebi.ac.uk/ontology-lookup
OLS
• Search for Term Name
– enter a partial search term and you will see suggested terms that
match what are entering in the form.
www.ebi.ac.uk/ontology-lookup
OLS
• Search for Term ID
www.ebi.ac.uk/ontology-lookup
OLS
• Get information for the term
www.ebi.ac.uk/ontology-lookup
OLS
• Browse an ontology by clicking on the “browse” button
www.ebi.ac.uk/ontology-lookup
MGI GO browser
www.informatics.jax.org
MGI GO browser
• Query result
www.informatics.jax.org
Tool for ontology development
OBO-edit
www.oboedit.org
OBO-Edit
OBO-Edit – An Ontology Editor for Biologists
John Day-Richter et al. Bioinformatics (2007)
• OBO-Edit is an open source ontology editor written in Java and
developed by the Berkeley Bioinformatics and Ontologies Project
• It is funded by the Gene Ontology Consortium.
• OBO-Edit is optimized for the OBO biological ontology file format.
• OBO-Edit Working Group, a team of OE users responsible for bug
testing, the generation of documentation and the future of OE
• Contributions to the OBO-Edit codebase are always welcome.
www.oboedit.org
OBO-Edit
• OBO-Edit working group meets every week on Thursday
for discussing about new OE features, bugs and other
OE related topics using Webex technology
www.oboedit.org
OBO-Edit
www.oboedit.org
OBO-Edit
• OBO- Edit wiki page
– It is a central repository
for OBO-Edit developer
info, announcements, and
technical information
wiki.geneontology.org/index.php/OBO-Edit
OBO-Edit interface
www.oboedit.org
Acknowledgements
GO Editorial Office
Midori Harris
Jennifer Deegan
CRIBI@University of Padua
prof. Giorgio Valle
GOA project
Emily Dimmer
http://grup.bio.unipd.it/
Thank you for attention!!!
www.geneontology.org