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

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 –AmiGOhttp://amigo.geneontology.org –QuickGOhttp:// –OLShttp:// –MGI Browserhttp:// EDITOR –OBO-Edithttp://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.geneontology.org AmiGO

amigo.geneontology.org 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 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.geneontology.org AmiGO All 219, ,556 Uniprot 19,627 13,101

amigo.geneontology.org AmiGO – Graphical view

amigo.geneontology.org AmiGO Term Search Result List of GO terms matching search string

amigo.geneontology.org AmiGO Gene associations

amigo.geneontology.org AmiGO

amigo.geneontology.org AmiGO Term information

amigo.geneontology.org 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’

amigo.geneontology.org AmiGO External references

amigo.geneontology.org links between term and objects in other external databases e.g InterPro numbers, Pfam ID and ProDom ID AmiGO

amigo.geneontology.org AmiGO Term associations

amigo.geneontology.org 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

amigo.geneontology.org Bax gene

amigo.geneontology.org AmiGO Evidence code information

amigo.geneontology.org AmiGO – Blast You can use your sequence as Blast query sequence

amigo.geneontology.org 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.geneontology.org AmiGO – Advanced Search

amigo.geneontology.org 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.

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

QuickGO

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.

QuickGO Exact match Other matches to search string Click term name to select

QuickGO Term details –Term ID –Name –Definitions –Hierarchy

QuickGO – Graphical View Alternative paths through tree View of term location in tree

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) formatOpen Biomedical Ontology

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

MGI GO browser

MGI GO browser Query result

Tool for ontology development OBO-edit

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.

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

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

Acknowledgements of Padua prof. Giorgio Valle GO Editorial Office Midori Harris Jennifer Deegan GOA project Emily Dimmer

Thank you for attention!!!