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 – Can be used to figure out if there is anything common in your cluster
How can you contribute to GO? OR How can you participate in the GO project? • By providing Annotations • By providing Content (controlled vocabularies to the ontologies) • Tools and other resources
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
What tools do you need to make annotations? • Excel spread sheet (simple, easy, small scale) OR • File. Maker Pro, Access – Simple databases, scales very well
How do you generate an annotation? • • 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 DB: Your project name Examples- SGD, MGI, Uni. Prot ID for the gene or gene_product Examples - FBgn 0015331, MGI: 99240, SPAC 9. 03 c Symbol like Brr 2, DDX 21_HUMAN that means something to a biologist, not an ID Object_Type - gene, transcript, protein_structure, or complex, should match the ID
Gene-associations file What does it look like? Optional column
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
How can I see my annotations?
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
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 • Ami. GO web application • GO database • Tools, tutorials and software
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