Upgrading biocViews with EDAM

Vince Carey

Harvard Medical School
Source: vignettes/challenges/EDAMviews.Rmd

Abstract

The EDAM ontology should be useful for improving the organization of Bioconductor resources. This challenge considers how to integrate information in the ontology with biocViews terms. It may be possible to reconceptualize the role of biocViews in project infrastructure in the context of this challenge.

Difficulty

Advanced.

Challenge leader(s)

Date added

This challenge was created on October 30, 2021

Topics

  • Challenges

Duration

A minimum of 2 month(s) is recommended for this challenge.

Repositories

A list of GitHub repositories that participate in this challenge.

No repository currently addresses this challenge.

Guidelines

Note

This task can impact several aspects of Bioconductor and R packages for genomics.

  • First, use of EDAM to tag Bioconductor packages and resources may aid in the processes of publicizing and discovering software and data
  • Second, an EDAMviews tag may be added as an endorsed field for package DESCRIPTION
  • Third, EDAM may integrate into the presentation of Bioconductor resources in the same manner as biocViews does presently; see the search box for software.

Evaluate EDAM and compare to biocViews

Investigate the biocViews vocabulary, and the EDAM ontology. For motivation, consider the display derived from the EDAM browser:

How can we take advantage of this terminology and concept structure?

  • Are there terms in biocViews for which EDAM terms are ready-to-use substitutes?
  • Are there concepts in biocViews that are lacking in EDAM that should be proposed for additions?