Software BiocViews missing from many packages

[Shians]

pkg_list <- BiocPkgTools::biocPkgList()
has_software_tag <- sapply(pkg_list$biocViews, function(b_view) "Software" %in% b_view))
table(has_software_tag)
## FALSE  TRUE 
## 1301   348 

So only 348 packages have the Software biocView. But on bioconductor.org almost every has the software biocView.

[seandavi]

Thanks, Shian. It looks like those are likely added based on the "repo" and are not present in the original DESCRIPTION tags. We can add the top-level biocViews terms for each available repo (AnnotationData, Software, ExperimentData) at download time to fix the issue.

In the slightly longer term, we can probably address this on Bioconductor to make sure that the DESCRIPTION files match up with the website.

[seandavi]

I think the issue here is that the BiocViews in package listing are just the leaf nodes in the DAG. I need to use the biocViews package to expand to include all ancestors. That entails instantiating the graph of terms from biocViews and then computing the ancestors of all the BiocViews for each package. Software is a root node, so it will be included for all software packages with biocViews terms.

[rioualen]

Hi there,
Been toying around with biocViews annotations for a while now, and I put up a list of packages and/or terms that have some sort of issue (also mentioned to @lshep) - you can check out the google sheet

NB: only been working with software packages specifically

[lshep]

I think the reason issues also pop up is 1. biocViews didn't always exists so there might be legacy packages that don't have the term 2. after a package is accepted into Bioconductor there is no validity check on views as the check only exists in BiocCheck which is not run on accepted packages only incoming packages