[Bioc-devel] biocViews preprocessing term

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Tue Sep 2 20:12:40 CEST 2008

yes in specific, and although you did not ask it does
appear that we need some renovation of the biocViews

alas i am not really clear on how modifications to the
vocabulary impact the build system.  i will take a look
at this and make a proposal momentarily.

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 Tue, 2 Sep 2008, Florian Hahne wrote:

> Hi Vince,
> the cellHTS and cellHTS2 package provide (mostly) preprocessing
> functionality for cell-based assays, and assigning the biocViews term
> "Preprocessing" seems to be reasonable. However, in the ontology this is
> defined as "Microarray -> Preprocessing;", and that's not really what we
> want. Shouldn't there be a general "Preprocessing" term independent of
> micro arrays. I guess this will also become interesting for many of the
> other emerging new technologies like deep sequencing. With the current
> design, it seems this is not possible, since terms have to be
> unambiguous. Is there any reasonable way of dealing with this problem
> other than adding a new term like "General Preprocessing"? And wouldn't
> it be useful to allow for terms like "Technology -> FlowCytometry
> ->Preprocessing;"
> Florian
> --
> Florian Hahne, PhD
> Computational Biology Program
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-3148
> fhahne at fhcrc.org

More information about the Bioc-devel mailing list