[Bioc-devel] biocViews now checked in

[Vincent Carey 525-2265]

i am fixing this now.  basically the Title field from the description
is being stuck there now.  i have just refreshed the HTML.  be sure to
refresh your browser; the NAs will go away for almost all packages (some GTK
dependent ones are not processed yet), and the package links will actually
work to get us to the download pages on the repository server

sorry for all the bumps.  this is the second version of the software.
there will be more.  we want view sets for metadata and for
experimental data.  we may be able to link views to installation.

as the repository management resources evolve, behavior of the
view generation software must adapt.  we are still making use of
infrastructure in the CRAN ctv package, and would like to have a good
symbiosis with ctv.  but the role of the task ontology in bioc is
currently unique to biocViews.

thanks for your patience

---
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 Fri, 4 Nov 2005, James W. MacDonald wrote:

> 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
>
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