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GO Outreach

GO Outreach. Rama Balakrishnan Saccharomyces Genome Database (SGD) Stanford University. What do GO annotations buy you?. Comparisons between species Possible only if we have broader species coverage Biology of your species becomes more accessible Analyzing microarray data

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GO Outreach

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  1. GO Outreach Rama Balakrishnan Saccharomyces Genome Database (SGD) Stanford University

  2. What do GO annotations buy you? • Comparisons between species • Possible only if we have broader species coverage • Biology of your species becomes more accessible • Analyzing microarray data • Can be used to figure out if there is anything common in your cluster

  3. How can you contribute to GO?ORHow can you participate in the GO project? • By providing Annotations • By providing Content (controlled vocabularies to the ontologies) • Tools and other resources

  4. Accurate GO annotations are crucial for GO to succeed • Comparison is possible only if all groups annotate consistently • What does an annotation include? • Gene name, reference, GO term, evidence code • How do you extract the information you need to make an annotation? • Where to start? • Check the Documentation, Teaching Resources section on the GO website http://www.geneontology.org/GO.current.annotations.shtml http://www.geneontology.org/GO.teaching.resources.shtml • Attend one of the annotation camps • Annotation mailing list • Source Forge tracker for annotation related issues • Farmanimals mailing list (new!) • A GO consortium member can mentor a new comer if need be

  5. What tools do you need to make annotations? • Excel spread sheet (simple, easy, small scale) OR • FileMaker Pro, Access • Simple databases, scales very well

  6. How do you generate an annotation? DB: Your project name Examples- SGD, MGI, UniProt • The GO project recommends a format for each annotation for consistency sake • Information on Annotation file format can be found at: http://www.geneontology.org/GO.annotation.shtml#file ID for the gene or gene_product Examples - FBgn0015331, MGI:99240, SPAC9.03c Symbol like Brr2, DDX21_HUMAN that means something to a biologist,not an ID Object_Type - gene, transcript, protein, protein_structure, or complex, should match the ID

  7. Gene-associations fileWhat does it look like? Optional column Optional column

  8. I did some annotations, what next? • Provide them to the larger community by submitting your annotations to the GO project • What information should I submit to GO? • gene-association file • Contact email address • Where should I submit the data? • Send the file to Mike Cherry or send an email to the GO mailing list

  9. How can I see my annotations?

  10. I don’t see terms in the ontology that describe the biology of my species. • Source Forge (SF) tracker for term related issues https://sourceforge.net/tracker/?func=add&group_id=36855&atid=440764 • Send an email to the GO mailing list • Content meetings • Organized by the consortium if the ontology related issues can’t be resolved over email/SF • Look for announcements on the GO website, mailing lists

  11. Resources the GO project offer to help you get initiated • Subscribing to the GO mailing list • gofriends@geneontology.org • Visit the GO website • http://www.geneontology.org • Lots of documentation • Following the GO project on Source Forge (SF) • https://sourceforge.net/tracker/?func=add&group_id=36855&atid=440764 • AmiGO web application • GO database • Tools, tutorials and software

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