[Bioc-devel] biocViews now checked in

[James W. MacDonald]

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?

Best,

Jim



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.
> 
> 
>>Gordon
>>
>>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/
>>>contributions
>>>
>>>_______________________________________________
>>>Bioc-devel at stat.math.ethz.ch mailing list
>>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> 
> _______________________________________________
> 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
734-647-5623