[Bioc-devel] biocViews now checked in

James W. MacDonald jmacdon at med.umich.edu
Fri Nov 4 17:30:29 CET 2005

On the biocViews pages, some of the packages have a description in 
square brackets next to the names, and some have [NA]. Is this dependent 
on the length of the Description line in the DESCRIPTION file, or is 
there some other mechanism to get this information appended to the name?



Vincent Carey 525-2265 wrote:
>>What's the current status of biocViews? I seem to remember several emails
>>with instructions about including a biocViews tag in package DESCRIPTION
>>files, and I took some trouble to do this in the limma package for the BioC
>>1.7 release. So I'm a bit surprised to find no mention at all of the limma
>>package in the Task Views link from http://www.bioconductor.org/download/,
>>despite the fact that the tag in limma includes terms such as
>>"DifferentialExpression" which have an entry in the Task Views.
> the biocViews HTML documents had not been refreshed for some time.
> i just refreshed them and limma is visible.  the design of the
> HTML generation system is still immature.  eventually it will be
> taken care of at the repository level.  for now i must create the
> HTML by running the vignette and moving the generated HTML to
> the URL known to the web page.
>>What does one do to get a package in the Task Views list? Reading the
>>biocViews vignette didn't tell me and I couldn't find any instructions
>>archived in the bioc-devel mailing list (although perhaps I've missed them
>>because I don't know a way to search this archive).
> add a biocViews field to the DESCRIPTION file.  terms currently in
> the ontology:
>  "Microarray"
>  "NoViewProvided"            "Visualization"
>  "Statistics"                "GraphsAndNetworks"
>  "Technology"                "Annotation"
>  "Infrastructure"            "OneChannel"
>  "TwoChannel"                "DataImport"
>  "QualityControl"            "Preprocessing"
>  "Transcription"             "DNACopyNumber"
>  "SNPsAndGeneticVariability" "DifferentialExpression"
>  "Clustering"                "Classification"
>  "MultipleComparisons"       "TimeCourse"
>  "Proteomics"                "MassSpectrometry"
>  "SAGE"                      "CellBasedAssays"
>  "Genetics"                  "GO"
>  "Pathways"                  "ProprietaryPlatforms"
>  "ReportWriting"
> package authors can  use any collection of these terms.
> the hierarchical relations among terms can be assessed
> by looking at the views page
> http://www.biostat.harvard.edu/~carey/bcv2/index.html
> or at the link near the bottom of the downloads page
> at the bioc portal.
> sorry for any misunderstanding.  comments on the vocabulary
> or the deployment of the view system are welcome.
>>At 07:46 AM 26/07/2005, Vincent Carey 525-2265 wrote:
>>>biocViews, with vignette and man pages, is now checked in to
>>>the svn archive of bioconductor
>>>clearly we need to reformulate the vocabulary and reannotate
>>>relative to what is in the package.  i welcome all comments/
>>>Bioc-devel at stat.math.ethz.ch mailing list
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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