GO Outreach

Rama BalakrishnanSaccharomyces 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

• FileMaker 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, UniProt

ID for the gene or gene_productExamples - 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

Gene-associations fileWhat does it look like?

DB source DB Object ID Object Symbol Qualifier GOID DB:reference Ev_code With/From Aspect DB object Name Synonym Object_type Taxon ID Date Assigned bySGD S000004660 AAC1 GO:0005743 SGD_REF:S000050955|PMID:2167309 TAS C ADP/ATP translocatorYMR056C gene taxon:4932 20010118 SGDSGD S000004660 AAC1 GO:0005471 SGD_REF:S000050955|PMID:2167309 IDA F ADP/ATP translocatorYMR056C gene taxon:4932 20010213 SGDSGD S000004660 AAC1 GO:0006839 SGD_REF:S000050955|PMID:2167309 IGI SGD:S000000126 P ADP/ATP translocatorYMR056C gene taxon:4932 20040226 SGDSGD S000004660 AAC1 GO:0009060 SGD_REF:S000050955|PMID:2167309 IGI SGD:S000000126 P ADP/ATP translocatorYMR056C gene taxon:4932 20040226 SGDSGD S000000289 AAC3 GO:0005743 SGD_REF:S000045889|PMID:2165073 ISS SGD:S000000126|SGD:S000004660C ADP/ATP translocatorYBR085W|ANC3 gene taxon:4932 20040226 SGDSGD S000000289 AAC3 GO:0005471 SGD_REF:S000045889|PMID:2165073 ISS SGD:S000000126|SGD:S000004660F ADP/ATP translocatorYBR085W|ANC3 gene taxon:4932 20040226 SGDSGD S000000289 AAC3 GO:0009061 SGD_REF:S000045889|PMID:2165073 IGI SGD:S000000126 P ADP/ATP translocatorYBR085W|ANC3 gene taxon:4932 20040226 SGDSGD S000000289 AAC3 GO:0009061 SGD_REF:S000052497|PMID:1915842 IGI SGD:S000000126|SGD:S000004660P ADP/ATP translocatorYBR085W|ANC3 gene taxon:4932 20040226 SGDSGD S000000289 AAC3 GO:0009061 SGD_REF:S000045889|PMID:2165073 IEP P ADP/ATP translocatorYBR085W|ANC3 gene taxon:4932 20040226 SGDSGD S000003916 AAD10 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative)YJR155W gene taxon:4932 20010119 SGDSGD S000003916 AAD10 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative)YJR155W gene taxon:4932 20020902 SGDSGD S000003916 AAD10 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative)YJR155W gene taxon:4932 20020902 SGDSGD S000005275 AAD14 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative)YNL331C gene taxon:4932 20010119 SGDSGD S000005275 AAD14 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative)YNL331C gene taxon:4932 20020902 SGDSGD S000005275 AAD14 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative)YNL331C gene taxon:4932 20020902 SGDSGD S000005525 AAD15 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative)YOL165C gene taxon:4932 20010119 SGDSGD S000005525 AAD15 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative)YOL165C gene taxon:4932 20020902 SGDSGD S000005525 AAD15 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative)YOL165C gene taxon:4932 20020902 SGDSGD S000001837 AAD16 GO:0008372 SGD_REF:S000069584 ND C YFL057C gene taxon:4932 20020902 SGDSGD S000001837 AAD16 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F YFL057C gene taxon:4932 20020902 SGDSGD S000001837 AAD16 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P YFL057C gene taxon:4932 20020902 SGDSGD S000000704 AAD3 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative)YCR107W gene taxon:4932 20010119 SGDSGD S000000704 AAD3 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative)YCR107W gene taxon:4932 20020902 SGDSGD S000000704 AAD3 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative)YCR107W gene taxon:4932 20020902 SGD

Optional columnOptional 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 issueshttps://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

• AmiGO web application • GO database• Tools, tutorials and software