[Bioc-devel] What to do with Francesco Ferrari?

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Jan 17 21:23:19 CET 2008

Do you know if there is a publication in a peer-reviewed journal
describing or making use of this remapping?

I would be willing to try to use one to see what is so different
about them if you can make a copy available on gopher2, for example.

I think we don't want to just redistribute something that does not
cohere meaningfully with basic bioc practices, but if setting the
annotation field on the data object and annotate:lookUp can be used
with this alternate annotation, it might be reasonable to take it.

If there is nothing in the literature to lend credence to this
remapping, perhaps we could say we'd like to wait until there is.
But this might be unfair given other things that have been taken.

Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Thu, 17 Jan 2008, Marc Carlson wrote:

> So I have some correspondence from a guy named Francesco Ferrari.
> He has made 6 packages that he would like to have available here at
> Bioconductor.  Two each of the CDF packages, the probe packages and the
> corresponding annotation packages.  These were made for two remapped
> platforms from their custom "gene cards" database.
> Because they are based on the gene cards databases, the annotation
> packages are extremely different from an annotation package that you
> would make using AnnBuilder.  They didn't use Annbuilder to make these
> packages either.  These packages are fully custom jobs.
> He claims that he will fully support these packages and update them
> every 6 months with fresh content (using his own methods).  He also
> claims to have done everything he can to make them seem the same as the
> other annotation packages, although because of the contents this is
> quite impossible.  He has very few of the same environments in common
> with the packages that we make here, although it is clear that he has
> made a strong effort to keep the interface similar.  He has also
> expressed a willingness to make the packages so that they can work with
> the new DB-based design.
> So the question I have is what are we going to tell this guy?  Should we
> offer to host his bizarre annotation packages?  Or is this situation
> another dangerous time-sucking vortex?  And if we do host them, how will
> we keep them sorted from the other ones?
> Last summer there were some other annotation packages that were more
> subtly different, and we hosted those with the addition of some
> alternate biocviews.  Those packages were more classic annotation
> packages that were just labeling a different item in the genome (CpG
> islands instead of genes).  Where is the line?  How different from our
> normal annotation packages is something normally allowed to be?
> Advice welcome,
>     Marc
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