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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 • • • • 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 • • • • 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 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 amigo.geneontology.org AmiGO Uniprot All 19,627 219,941 13,101 140,556 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 AmiGO links between term and objects in other external databases e.g InterPro numbers, Pfam ID and ProDom ID 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 Enter gene to search for here, check the Gene Symbol/Name box Click ‘Submit Query’ You have this Gene Products Search Results 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. 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 • 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 • Other matches to search string • Click term name to select • Exact match 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/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