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[go-friends] Is there a standard format for GO term enrichment results?

Robinson, Peter peter.robinson at charite.de
Wed Aug 17 11:25:17 PDT 2011


Hi Chris,
I assume that with the following you mean the study set (e.g., diff regulated genes) and the population set (e.g., all genes in microarray or genome)

# Input token list + token type (e.g. symbol)
# Background token list + token type (if provided)

In that case, given the ontology and association files, it is possible to reconstruct the mapping and list of unmatched tokens and this does not need to be part of the output format explicitly:
#Token-gene ID mapping (plus unmatched tokens)

Or have I misunderstood what you mean and the above is meant to apply to tools that also do extra work to match wierd tokens to gene symbols?

#Algorithm parameters (cut-offs, algorithm selected, etc)
=> This is difficult given the wide range of algorithms. Does OBI have a vocabulary to cover everything? 
=> Probably it would be good to have a separate field for the multiple-testing correction used and the methods etc.

#List of results - for each result:

    * term ID
    * optional term metadata
    * list of gene IDs (+ optional gene metadata)
    * scoring metadata (p-vals, rank, etc)
=> Here, there is no absolute reason to include a list of genes for each term, as this can be reconstructed assuming that everything else in the file is correct and comprehensive.

In any case, this would be a useful thing to have and we would add such a feature to the ontologizer.

best wishes Peter


PD Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566042
peter.robinson at charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
________________________________________
Von: go-friends-bounces at lists.stanford.edu [go-friends-bounces at lists.stanford.edu] im Auftrag von Chris Mungall [cjmungall at lbl.gov]
Gesendet: Mittwoch, 17. August 2011 20:10
An: gofriends friends
Betreff: [go-friends] Is there a standard format for GO term enrichment results?

Hi gofriends,

Within the GO consortium we are considering providing a unified interface to a number of heterogeneous term enrichment tools. In order to facilitate this we would need to have a standard output format and/or API for the tool results. I think the standardizing on a format would be easier than an API.

I asked this question on the biostar forum:
        http://biostar.stackexchange.com/questions/11269/is-there-a-standard-format-for-go-term-enrichment-results

But I thought I would also ask here, as I know a number of tool providers are subscribed.

Thanks
Chris
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