Add existing mapped entries from bioconductor to bio.tools

vjcitn / biocEDAM

preliminary investigation of biocViews in relation to EDAM ontology

https://vjcitn.github.io/biocEDAM/

1 stars 0 forks source link

Open hmenager opened 4 months ago

hmenager commented 4 months ago

I'll elaborate later on that, but the bio.tools data are in https://github.com/research-software-ecosystem/content, in data/*/*.biotools.json

hmenager commented 4 months ago

and what about other projects that might have done the same for bioconductor packages:

vjcitn commented 1 month ago

OK, I am trying to understand this issue. I checked out

https://github.com/research-software-ecosystem/content.git

which seems to be 5.2GB (maybe I should have used --depth 1)

There are 40000 folders in content/data.

To find the folders that refer to bioconductor assets is not completely clear:

a folder for package p may hold bioconda_bioconductor-[p].yaml
a folder for package p may have [p].biotools.json with "BioConductor" in the collectionID field

vjcitn commented 1 month ago

I would say there is something problematic in the biotools.json content in that it has a download component that

"url": "http://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.2.0.tar.gz"

but that version tag is inappropriate for the current release ... this is irrelevant for this EDAM project but is noteworthy