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UniProtKeywords
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- Repository: https://github.com/jokergoo/UniProtKeywords
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Hi @jokergoo
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: UniProtKeywords
Type: Package
Title: Keywords from the UniProt database
Version: 0.99.0
Date: 2022-06-27
Authors@R: person("Zuguang", "Gu", email = "[email protected]", role = c("aut", "cre"),
comment = c('ORCID'="0000-0002-7395-8709"))
Depends: R (>= 4.2)
Imports: utils
Suggests: knitr, rmarkdown, markdown, testthat
biocViews: AnnotationData, Organism, Homo_sapiens
Description: UniProt database provides a list of controlled vocabulary represented as keywords
for genes or proteins. This is useful for summarizing gene functions in a compact way. This package
provides data of keywords hierarchy and gene-keywords relations.
VignetteBuilder: knitr
URL: https://github.com/jokergoo/UniProtKeywords, https://www.uniprot.org/keywords/
BugReports: https://github.com/jokergoo/UniProtKeywords/issues
License: MIT + file LICENSE
NeedsCompilation: no
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/UniProtKeywords to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2665150c27acc50915cab60559e4d427360400d6
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/UniProtKeywords to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 277e9c2cc5e5f8b332165d37f05d41c2ebf38961
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/UniProtKeywords to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
It's a nice package but I am somewhat concerned about the arbitrary nature of the resource that it is built on. "Keywords", not an ontology, not clear what kind of versioning is done, and so forth. It works, if you can add some details on provenance and updating policy that will be great.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
Thanks! Sure I will add more information of the version of the data and other related things.
Dear @jokergoo ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
do not close the issue -- we will process it and add it to the daily builder but it must remain open until then. I was away on holiday last week; I will process the issues in the next day or two.
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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("UniProtKeywords"). The package 'landing page' will be created at
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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
Hi @jokergoo Shouldn't this use the UniProt API rather than a static file in the package? Best, Marcel
Hi Marcel, I think the API is only convenient for getting record for e.g. single protein/gene?
You can get the table with the URL that they provide on the website: E.g., (with pagination)
https://rest.uniprot.org/keywords/search?compressed=true&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29&size=500