biocViews

Introduction

Packages added to the Bioconductor Project require a biocViews: field in their DESCRIPTION file. The field name “biocViews” is case-sensitive and must begin with a lower-case ‘b’.

biocViews terms are “keywords” 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

biocViews are available for the release and devel branches of Bioconductor. The devel branch has a check box under the tree structure which, when checked, displays biocViews that are defined but not used by any package, in addition to biocViews that are in use.

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” their package with biocViews so that when someone looking for packages (like in scenario 1) can easily find their package.

biocViews during new package development

Visit the devel branch of biocViews when you are in the process of adding biocViews to your new package. Identify as many terms as appropriate from the hierarchy. Prefer ‘leaf’ terms at the end of the hierarchy, over more inclusive terms. Remember to check the box displaying all available terms.

Please Note:

  1. Your package will belong to only one part of Bioconductor Project (Software, Annotation Data or Experiment Data), so choose only only biocViews from that category.

  2. biocViews listed in your package must match exactly (e.g., spelling, capitalization) the terms in the biocViews hierarchy.

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 receive 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