[BioC] mislinked task views?

Wacek Kusnierczyk Waclaw.Marcin.Kusnierczyk at idi.ntnu.no
Tue May 19 10:38:06 CEST 2009

Vincent Carey wrote:
> It is true that the biocViews/inst/dot/biocViewsVocab.dot indicates two
> paths to
> BiologicalDomains (via Software and ExperimentData).  For consistent HTML
> generation such a structure should probably not be allowed.

it's not a problem of html generation.  there is nothing wrong in an
html page being linked to from more than one 'parent', and accessible
through more than one path.

it's a problem of the hierarchy of topics, each of which resides on a
separate html page.  if these pages are generated automatically, then
there is a problem in the underlying specification of categories.  since
the categories 'software' and 'experiment data' seem to be disjoint, it
seems to make no sense to have nodes that have both as parents, and it
certainly makes no sense to see 'experimental data' as the only parent
when one chooses a subcategory in 'software'.

thanks for the response.


> Also, it appears that many tags in the vocabulary are not used.  Thus there
> are several empty views.  It is hoped that this sparsity will diminish with
> time.
> On Wed, May 13, 2009 at 12:52 PM, Wacek Kusnierczyk <
> Waclaw.Marcin.Kusnierczyk at idi.ntnu.no> wrote:
>> hello,
>> there is a minor problem with links in the hierarchy of tasks at bioc
>> views [1].  the top category is subdivided into software, annotation
>> data, and experiment data.  clicking on software/biological domains
>> leads to a task view where the are no packages, and the parent category
>> is experiment data rather than software.
>> vQ
>> [1] http://www.bioconductor.org/packages/release/BiocViews.html
>> --
>> -------------------------------------------------------------------------------
>> Wacek Kusnierczyk, MD PhD
>> Email: waku at idi.ntnu.no
>> Phone: +47 73591875, +47 72574609
>> Department of Computer and Information Science (IDI)
>> Faculty of Information Technology, Mathematics and Electrical Engineering
>> (IME)
>> Norwegian University of Science and Technology (NTNU)
>> Sem Saelands vei 7, 7491 Trondheim, Norway
>> Room itv303
>> Bioinformatics & Gene Regulation Group
>> Department of Cancer Research and Molecular Medicine (IKM)
>> Faculty of Medicine (DMF)
>> Norwegian University of Science and Technology (NTNU)
>> Laboratory Center, Erling Skjalgsons gt. 1, 7030 Trondheim, Norway
>> Room 231.05.060
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