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

Chris Mungall cjmungall at lbl.gov
Thu Aug 18 09:27:40 PDT 2011


On Aug 18, 2011, at 9:15 AM, Calin Voichita wrote:

> Hi Chris,
> 
> We would also be interested to add such a feature to our Onto-Express tool.

Great!

> As Peter pointed out the list of genes for for each term is redundant
> information given the association and ontology versions and should be
> excluded.

See my response to Peter

> However, the Token-gene ID mapping we believe is required, as
> some tools allow input tokens that are not available in the gene
> association file. For example, our tool allow the input of other IDs,
> like affymetrix probe IDs.

Yes, that was the idea.

> With regards the algorithm parameters, it is true that is difficult to
> cover the range of algorithms. Also, some tools may use heuristics for
> multiple comparison or not well know algorithms; a description of the
> methods or reference to the methods should be included.

Well I probably fall to the more extreme end of the ontologize-everything camp.

> As the results may contain multiple scoring indexes (e.g., two types of
> p-values) a contextual description of these should be the starting point.

Agreed

Thanks for your comments,
Chris

> Best regards,
> Calin
> 
> -- 
> Calin Voichita
> Ph.D. Candidate
> Intelligent Systems and Bioinformatics Laboratory (ISBL)
> Department of Computer Science	- Wayne State University
> Phone: +1 (313) 577 5070	Fax:   +1 (313) 577 6868
> Detroit, MI 48202, USA
> http://vortex.cs.wayne.edu
> 
> 
> -------- Original Message  --------
> Subject: Re: [go-friends] Is there a standard format for GO term
> enrichment	results?
> From: Robinson, Peter <peter.robinson at charite.de>
> To: Chris Mungall <cjmungall at lbl.gov>, gofriends friends
> <gofriends at genome.stanford.edu>
> Date: Wed 17 Aug 2011 02:25:17 PM EDT
> 
>> 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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