AmiGO: Use Cases

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Use Cases for AmiGO development

1) - query for 'proof reading'. i expect to see hits like 'proof reading during DNA replication'. 'proofreading' can be one word or split with a space. Interface should handle with and without space, with and without hyphen - query for 'error free' I expect to see terms like error free DNA repair etc. Terms in the ontology have a hyphen. Interface should be able to handle the hyphen.

2) -query for tRNA. tRNA is an exact synonym for triplet codon-amino acid adaptor acitivity. But this term doesn't come as a hit in the first page. May be a summary page that breaks down the hits by category will work. Also, exact match hit (in the term name or synonym) should be listed first on the summary page. - search exact synonyms by default when doing a term name search (since they're supposed to mean exactly the same thing, and often there are several equally-used names for the same concept, and it's pot luck which one gets picked for the GO name)

-query for 'tRNA yeast'- gives no results now. Intention was to retrieve yeast tRNA genes.

3) search for non-adjacent words search for 'metabolism glucose' returns any terms with metabolism and glucose in them, instead of no results

4) use standard search engine syntax, e.g. "glucose metabolism" searches for the exact string glucose -metabolism searches for terms with the word glucose but without the word metabolism glucose (biosynthesis,metabolism) searches for glucose and either biosynthesis or metabolism

Use the search syntax employed by google or some other common search engine

Be able to use these syntax options in a basic (i.e. not advanced) search so that you don't have to wait for the advanced search page to load up every time

5) Enable wild card searches, e.g. regulation of gluc* metabolism (possibly) 26 proteasome doesn't pull out anything. It is missing an 'S' next to 26. Google would for example suggest Did you mean 26S proteasome? Is that possible with AmiGO?

6)) query for 'trim' using the Gene Name/symbol searches the gene product field also and while there are few genes names that match the string 'TRIM', you get all sorts of hits (heteroTRIMeric, TRIMethylamine methyltransferase, TRIM5 and so on). Another case where a summary of hits will help I think.

I think all of the above can be thought of as search using ALL words, ANY words or EXACT MATCH and append wild card to all words, any word etc.

Other User needs [edit]

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7) accurate gene_product counts after applying filters.

8) search for a term name or gene_product name by kingdom for example, tRNA fungi, tRNA plants, tRNA bacteria etc (PAG meeting)

9) I have a set of genes and I would like to get the GO terms in all aspects for these. How do I do it in bulk? (this came in as an email to go-help)

10) I am trying to figure out GO annotations of the 388 genes (Soybean ESTs) (this also came as an email to go-help). How can I do it in bulk?

11) Clicking on some of the higher level nodes like 'cellular physiological process' takes several minutes and typically a server error is displayed.

12) the species names are all abbreviated in the small boxes (for example, F. catus, G. violaceus). Often we don't know what these stand for (is it a bacteria or plant and so on). Can you display the full names?- PAG meeting

13) Download button to download results