Grup.bio.unipd.it CRIBI Genomics group Erika Feltrin PhD student in Biotechnology 6 months at EBI

grup.bio.unipd.it

CRIBI Genomics group

Erika Feltrin

PhD student in Biotechnology

6 months at EBI

www.geneontology.org/GO.tools.shtml

Tools for browsing ontologies


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

• Tools for searching and browsing GO• Annotation tools • Tools for gene expression/microarray analysis • Other tools


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

amigo.geneontology.org

AmiGO

• 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?

• 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


AmiGO

AmiGO search interface


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

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- 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

• indicates relationship of term to its parent.

P = part_of

I = is_a

number of genes annotated to term, and its children

Some ‘child’ terms of biological process


AmiGO

All

219,941

140,556

Uniprot

19,627

13,101


AmiGO – Graphical view


AmiGO

Term Search Result

List of GO terms matching search

string


AmiGO

• Gene associations


AmiGO


AmiGO

• Term information


Amigo

• Term information


AmiGO

• Term lineage


AmiGO

• Term lineage

view shows two different paths up the tree for term ‘mitochondrial membrane’


AmiGO

• External references


links between term and objects in other external databases

e.g InterPro numbers, Pfam ID and ProDom ID

AmiGO


AmiGO

• Term associations


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


Bax gene


AmiGO

• Evidence code information


AmiGO – Blast

You can use your sequence as Blast query sequence


Searching for genes

You have this Gene Products Search Results

Enter gene to search for here, check the Gene Symbol/Name box

Click ‘Submit Query’


AmiGO – Advanced Search


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.

www.ebi.ac.uk/ego

• 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.

QuickGO

www.ebi.ac.uk/ego

QuickGO

www.ebi.ac.uk/ego

QuickGO

• select the field to search on e.g. GO id, UniProt identifier. Seaches name/synonym by defaut

• select ontology, i.e. biological process, molecular function, cellular component, to search. Seaches all by default.

www.ebi.ac.uk/ego

QuickGO

• Exact match

• Other matches to search string• Click term name to select

www.ebi.ac.uk/ego

QuickGO

• Term details– 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/ontology-lookup

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

http://obo.sourceforge.net/


OLS

• You can query ontologies that you need


OLS

• Search for Term Name– enter a partial search term and you will see suggested

terms that match what are entering in the form.


OLS

• Search for Term ID


OLS

• Get information for the term


OLS

• Browse an ontology by clicking on the “browse” button

www.informatics.jax.org

MGI GO browser

www.informatics.jax.org

MGI GO browser

• Query result

www.oboedit.org

Tool for ontology development

OBO-edit

www.oboedit.org

OBO-Edit

OBO-Edit – An Ontology Editor for BiologistsOBO-Edit – An Ontology Editor for BiologistsJohn Day-Richter et al. Bioinformatics (2007)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

www.oboedit.org

OBO-Edit interface

www.oboedit.org

Acknowledgements

CRIBI@University of Padua

prof. Giorgio Vallehttp://grup.bio.unipd.it/

GO Editorial Office

Midori Harris

Jennifer Deegan

GOA project

Emily Dimmer

http://grup.bio.unipd.it/



www.geneontology.org

Thank you for attention!!!

Documents

Grup.bio.unipd.it CRIBI Genomics group Erika Feltrin PhD student in Biotechnology 6 months at EBI