biocViews

Introduction

Packages being added to the Bioconductor Project require biocViews in their DESCRIPTION file.

(Note that the field name "biocViews" is case-sensitive and must begin with a lower-case 'b'.)

biocViews are "keywords" which are used to describe a given package. They are broadly divided into three categories, representing the type of packages present in the Bioconductor Project -

  1. Software

  2. Annotation Data

  3. Experiment Data

Motivation

One can use biocViews for two broad purposes.

  1. A researcher might want to identify all packages in the Bioconductor Project which are related to a specific purpose. For example, one may want to look for all packages related to Copy Number Variants.

  2. During development, a package contributor can "tag" his package with biocViews so that when someone is looking for packages (like in scenario 1), they can easily find his package.

Devel and Release branch of biocViews

The biocViews for the release branch of Bioconductor can be used to search for packages that belong to the current release of Bioconductor Project and can be viewed at:Release

The devel branch of biocViews contains the latest biocViews and can be used to search for packages that are under the development in Bioconductor Project. The biocViews and packages present here will become part of the next release. The biocViews for the devel branch of Bioconductor can be viewed at :Devel

Using biocViews to search for packages

Researchers are often directed to the release and devel page when they are looking to find new packages. The tree structure in each category can be expanded to explore packages in both release and devel.

The devel branch has a small check box under the tree structure which states "Developers: check this box to toggle the visibility of childless biocViews."

When this checkbox is unselected, one can view only the biocViews which have packages assigned to them.

biocViews during development

Add BiocViews to your new package

It is recommended to visit the devel branch of biocViews when you're in the process of adding biocViews to your new package.

The devel branch has a small check box under the tree structure which states "Developers: check this box to toggle the visibility of childless biocViews." When this checkbox is selected, package contributors can view the full comprehensive list of biocViews. This list also contains biocViews that are not tagged with any package.

We believe that by constantly revising and adding new biocViews to the tree in the devel branch, we give package contributors the power to contribute richer and diverse packages for the analysis and comprehension of high-throughput genomic data.

Please Note:

  1. Since your package will belong to any one part of Bioconductor Project(Software, Annotation Data or Experiment Data), you are allowed only to add biocViews from any one of these categories.

  2. Please do not modify any of these biocViews when adding them to your package (eg: spelling, lower-case, uppper-case) as these biocViews are checked during the build process by the Bioconductor Project and the package reviewer.

biocViews during build

When you submit your new package for review , your package is checked and built by the Bioconductor Project.

We check the following for biocViews:

  1. Package contributor has added biocViews.

  2. biocViews are valid.

  3. Package contributor has added biocViews from only one of the categories.

If you recieve a "RECOMMENDED" direction for any of these biocViews after you have submitted your package, you can try correcting them on your own following the directions given here or ask your package reviewer for more information.

Fred Hutchinson Cancer Research Center