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CRIBI Genomics group

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

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CRIBI Genomics group

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

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

  3. 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

  4. 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

  5. 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.geneontology.org

  6. AmiGO amigo.geneontology.org

  7. AmiGO AmiGO search interface amigo.geneontology.org

  8. AmiGO • Searching features select to search for GO terms tick this box to search for only exactly matching strings select to search for annotated genes amigo.geneontology.org

  9. 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

  10. 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

  11. indicates relationship of term to its parent. P = part_of I = is_a number of genes annotated to term, and its children AmiGO Some ‘child’ terms of biological process amigo.geneontology.org

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

  13. AmiGO – Graphical view amigo.geneontology.org

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

  15. AmiGO • Gene associations amigo.geneontology.org

  16. AmiGO amigo.geneontology.org

  17. AmiGO • Term information amigo.geneontology.org

  18. Amigo • Term information amigo.geneontology.org

  19. AmiGO • Term lineage amigo.geneontology.org

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

  21. AmiGO • External references amigo.geneontology.org

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

  23. AmiGO • Term associations amigo.geneontology.org

  24. 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 amigo.geneontology.org

  25. Bax gene amigo.geneontology.org

  26. AmiGO • Evidence code information amigo.geneontology.org

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

  28. You have this Gene Products Search Results Enter gene to search for here, check the Gene Symbol/Name box Click ‘Submit Query’ Searching for genes amigo.geneontology.org

  29. AmiGO – Advanced Search amigo.geneontology.org

  30. 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

  31. 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

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

  33. 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 www.ebi.ac.uk/ego

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

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

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

  37. 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

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

  39. 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

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

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

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

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

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

  45. Tool for ontology developmentOBO-edit www.oboedit.org

  46. 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

  47. 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

  48. OBO-Edit www.oboedit.org

  49. 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

  50. OBO-Edit interface www.oboedit.org

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