Obtain metadata for software packages in Bioconductor
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Donghui ▴ 10
@22411967
Last seen 3 days ago
United States

I'm working on a free research discovery tool meta.org. We're looking into ways to index the software packages list here

https://www.bioconductor.org/packages/release/bioc/

To do, I'll need to collect metadata about each package such as name, maintainer, title, description, link to code repository, citations etc.

1) Does Bioconductor provide software metadata in structured formats? for example, XML, JSON. It will be harder to 'scrape' info from this page https://www.bioconductor.org/packages/release/bioc/ 2) Is there a programmatic access such as an API to get this type of data?

I checked https://github.com/Bioconductor but couldn't find what I need there.

Thank you for pointing me to the right direction.

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Mike Smith ★ 5.0k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

You can take a look at the BiocPkgTools package (https://www.bioconductor.org/packages/BiocPkgTools/), specifically the function biocPkgList(). That should provide you with an R data.frame containing most of the information that you're looking for. You can then convert to JSON etc if needed.

I'm not sure you can get the citations for all packages via that mechanism - that might be a nice addition for BiocPkgTools to have.

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thank you Mike Smith this is helpful!

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