[Bioc-devel] biocViews now checked in

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

--
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