Update the biocViews Vocabulary

Overview

The biocViews package contains a vocabulary of terms that can be used as valid entries in the biocViews field within a package's DESCRIPTION file.

This document describes the process of updating the vocabulary definition. The policy for changes to the vocabulary is to send a brief proposal to the bioc-devel mailing list requesting comment. If no objections are raised within a week's time, then go ahead with the change.

When considering changes to the vocabulary, it is important to understand that the vocabulary is structured as a directed acyclic graph (DAG). In its current implementation, we have links from general terms to more specific terms. For example, TaskViews -> Software, describes Software as being a more specific term in the vocabulary than TaskViews.

Step 1: Modify biocViewsVocab.dot

The source file for the vocabulary is biocViews/inst/dot/biocViewsVocab.dot. This file describes the vocabulary DAG in dot syntax. You can learn more about dot here.

Generally, if you follow the example of the existing vocabulary, you should be ok.

Step 2: Generate a GXL file from the dot file

After making the desired edits to biocViewsVocab.dot, you need to generate a GXL version. GXL is an XML markup for graphs and the graph package knows how to import GXL.

The graphviz tools come with a utility function dot2gxl that you should use to convert the dot file to GXL. Here is an example:

dot2gxl biocViewsVocab.dot > biocViewsVocab.gxl

Step 3: Update the biocViews vocab graph instance

1. Start R
2. load the graph package

3. Use the following code:

   library(graph)
   con <- file("biocViewsVocab.gxl", open="r")
   biocViewsVocab <- fromGXL(con)
   close(con)
   save(biocViewsVocab, file="biocViewsVocab.rda", compress=TRUE)

4. Copy the resulting rda file over the one in the data/ subdir of the biocViews package.