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

2. www.geneontology.org/GO.tools.shtml Tools for browsing ontologies

3. 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

4. www.geneontology.org/GO.tools.shtml Searching for GO terms BROWSER –AmiGOhttp://amigo.geneontology.org –QuickGOhttp://www.ebi.ac.uk/ego –OLShttp://www.ebi.ac.uk/ontology-lookup –MGI Browserhttp://www.informatics.jax.org EDITOR –OBO-Edithttp://oboedit.org/ …and more varieties of tools available on the GO Tools page

5. 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

6. amigo.geneontology.org AmiGO

7. amigo.geneontology.org AmiGO AmiGO search interface

8. 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

9. 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

10. 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

11. 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

12. amigo.geneontology.org AmiGO All 219,941 140,556 Uniprot 19,627 13,101

13. amigo.geneontology.org AmiGO – Graphical view

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

15. amigo.geneontology.org AmiGO Gene associations

16. amigo.geneontology.org AmiGO

17. amigo.geneontology.org AmiGO Term information

18. amigo.geneontology.org Amigo Term information

19. amigo.geneontology.org AmiGO Term lineage

20. amigo.geneontology.org AmiGO Term lineage view shows two different paths up the tree for term ‘mitochondrial membrane’

21. amigo.geneontology.org AmiGO External references

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

23. amigo.geneontology.org AmiGO Term associations

24. 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

25. amigo.geneontology.org Bax gene

26. amigo.geneontology.org AmiGO Evidence code information

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

28. 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’

29. amigo.geneontology.org AmiGO – Advanced Search

30. 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.

31. 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

32. www.ebi.ac.uk/ego QuickGO

33. 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.

34. www.ebi.ac.uk/ego QuickGO Exact match Other matches to search string Click term name to select

35. www.ebi.ac.uk/ego QuickGO Term details –Term ID –Name –Definitions –Hierarchy

36. www.ebi.ac.uk/ego QuickGO – Graphical View Alternative paths through tree View of term location in tree

37. 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) formatOpen Biomedical Ontology

38. www.ebi.ac.uk/ontology-lookup OLS You can query ontologies that you need

39. 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.

40. www.ebi.ac.uk/ontology-lookup OLS Search for Term ID

41. www.ebi.ac.uk/ontology-lookup OLS Get information for the term

42. www.ebi.ac.uk/ontology-lookup OLS Browse an ontology by clicking on the “browse” button

43. www.informatics.jax.org MGI GO browser

44. www.informatics.jax.org MGI GO browser Query result

45. www.oboedit.org Tool for ontology development OBO-edit

46. 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.

47. 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

48. www.oboedit.org OBO-Edit

49. 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

50. www.oboedit.org OBO-Edit interface

51. Acknowledgements CRIBI@University of Padua prof. Giorgio Valle http://grup.bio.unipd.it/ GO Editorial Office Midori Harris Jennifer Deegan GOA project Emily Dimmer

52. www.geneontology.org Thank you for attention!!!