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Tools to Browse and Analyze Gene Ontologies: A Comprehensive Overview

Explore an extensive array of tools designed for navigating and analyzing Gene Ontologies. This resource, developed within the Gene Ontology Consortium, offers free access to a variety of applications for academics. Users can visit AmiGO, QuickGO, and OLS for searching, filtering, and visualizing GO terms and gene associations. Additionally, learn about non-consortium tools and how to use them effectively. Get support through the GO helpdesk and enhance your research with powerful gene annotation and expression analysis tools.

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Tools to Browse and Analyze Gene Ontologies: A Comprehensive Overview

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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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