Question

Does a given Bioconductor version always use the same version of a database, e.g. GO.db?

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rebeliscu • 0

@rebeliscu-19945

Last seen 2.0 years ago

United States

I'd like to know whether the version of a database used in a given Bioconductor package will always be the same, given the same version of Bioconductor. In other words, is the version of Bioconductor synonymous with a given version of a database that a package is based upon?

For example:

Will Bioconductor 3.14 GO.db package always be based on "Gene Ontology http://current.geneontology.org/ontology/gobasic.obo With a date stamp from the source of: 2021-09-01" (per GO.db manual)?

Or is there a possibility that the GO.db package will reference an updated version of the GO ontology within the same version of Bioconductor?

Thanks in advance!

GO.db versioning • 1.1k views

ADD COMMENT • link updated 2.3 years ago by James W. MacDonald 65k • written 2.3 years ago by rebeliscu • 0

score 1 · Answer 1 · 2022-01-07

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 5 hours ago

United States

Yes. All annotation packages are generated for each release and remain static. If you try to install GO.db in two years, using R-4.1.2/Bioc_3.14, you will get the same exact package you have right now.

ADD COMMENT • link 2.3 years ago James W. MacDonald 65k

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Fantastic, thank you! And I apologize if this information is stated elsewhere...

ADD REPLY • link 2.3 years ago rebeliscu • 0

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It's probably posted somewhere, but that's fine. It's not uncommon for questions to be asked when the answer might be found elsewhere.

I should point out that this isn't 100% true. A few releases ago we realized that GO had stopped updating the data we were downloading from them (the old SQL dumps they previously provided) and the only updated data were the OBO files. This happened after the release, and we had to quickly generate code to parse the OBO files, and then re-released GO.db. So hypothetically one could have the original 'bad' version of GO.db and then go back and update to get the re-released good version. But in normal situations what I said above is true.

ADD REPLY • link 2.3 years ago James W. MacDonald 65k

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I see. Was the version of the GO.db package updated so as to be able to differentiate between the 'bad' and 'good' version of GO.db, from the same Bioconductor release?

ADD REPLY • link 2.3 years ago rebeliscu • 0

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Yes. If you had that version of Bioc installed, and did BiocManager::install(), it would automatically download and install the corrected version.

ADD REPLY • link 2.3 years ago James W. MacDonald 65k

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FWIW, the same thing happens for any bugfixes that happen during the release cycle. If someone realizes there is a pernicious bug in their package they will fix the bug, increment the version, and push to the Git repo. That will cause the package builder to make a new package (with the incremented version) and if you had that package installed and did BiocManager::install(), you would be told that there is a new version, and would you like to install it. The correct answer is almost always yes.

ADD REPLY • link 2.3 years ago James W. MacDonald 65k