[Bioc-devel] ANN: BioC Developer's Meeting/agenda/discussion

Gordon Smyth smyth at wehi.edu.au
Mon Jul 25 06:43:37 CEST 2005

At 04:24 AM 18/07/2005, Robert Gentleman wrote:
>Life would be much simpler with an ontology, but that does not seem likely 
>to appear in any short order but perhaps we could decide if we like the 
>terms that Vince has used, and if there are any other extensions. In some 
>sense these belong either in ctv, or some other place so that new 
>developers have easy access to them (and no I don't think we should use 
>the KEYWORDS file in R; I have to say I find that mechanism distinctly 
>unhelpful). Gordon, do you have input on the hierarchy of terms?

Well, I've already made some input I think. I personally think that a 
fairly broad and relaxed grouping, not unlike the grouping already on the 
BioC faq page is best. I think that a detailed ontology is, by its very 
nature, likely to have the opposite effect to that intended. An ontology 
will tend to emphasise package differences rather than overlaps and will 
reward package fragmentation rather than reducing the number of packages. A 
package ontology needs to be done very well indeed, but someone who has 
taken time to understand all the packages well, otherwise it risks being a 
hindrance rather than a help. I don't think that the list of terms that 
Vince currently has will do the job.

1. The terms in the ontology need to stay fairly broad. Drilling down into 
small topics with just one or two packages in them tends to hide package 
overlaps, not display them.

2. In order to be useful to users, the ontologies needs to focus on 
processes that users want to do, not on mathematical concepts. A user 
doesn't seek to fit a linear model for example, but they might want to 
analyse a microarray experiments with multiple RNA sources. They certainly 
don't start out wanting to fit an Error Model ...

>  And do you think it would be useful to have package developers add 
> themselves in and out, or should this be done by the maintainer?
>Initially there were some arguments against developers doing it, as we 
>might want to have the view managed by an expert in the field who could 
>also give recommendations.

The idea of an expert in the field editing the work of the developers 
really fills me with trepidation. Who are the experts if not the developers 
themselves? I don't think that anyone could claim to know what all the 
packages do. I think that the Harvard and Seattle BioC maintainers should 
be very cautious about putting themselves forward as experts in this sense.

If the "task view" remains a relaxed view like what is currently in the 
BioC faq web page, then I am happy for it to be done by a BioC maintainer. 
If a detailed package ontology is envisaged, then it needs to be done by 
the package developers themselves.


>  Best wishes
>   Robert

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