dhimmel / biorxiv-licenses Goto Github PK

Currently, altair visualizations don't appear in mybinder.org notebooks. I believe this is because we removed the vega nbextension because it didn't install properly (35954f7).

Filed an issue to see if this is possible: binder-project/binder#87.

I used the following workflow (will only work if you're me):

if [ ! -d .git ] ; then
  git init
  git remote add origin https://github.com/dhimmel/biorxiv-licenses.git
  git config --global user.email "[email protected]"
  git config --global user.name "Daniel Himmelstein"
fi

# Add files you want and commit
git add
git commit --message "Your description"
git branch --set-upstream-to=origin/master master

git pull --rebase
# If there's a conflict
git checkout --ours Dockerfile
git checkout --theirs # Files modified by your commits here
# Add files with desired changes
git add 
git rebase --continue

# Push to github (enter username and password when prompted)
git push

Note I don't recommend this -- there are conflicts and it's hard to resolve. Also the binder can be out of date unless you recently rebuilt it.

@OmnesRes initially provided us with biorxiv_data.txt via Twitter (in 54db073). In a series of commits, I modified this file to create biorxiv-prepubmed.tsv which uses a simpler format. It would be great to script the creation of biorxiv-prepubmed.tsv so we could run in the future and make this study reproducible.

@OmnesRes is the generation of this dataset possible via public APIs? Do you have code that you used to create biorxiv_data.txt? I'm happy to help you create a pull request to add this functionality.

I think it would be really interesting to look at license preferences over time, but dates with preprints are tricky.

The date in PrePubMed is not necessarily the date of the first version of the preprint. PrePubMed began indexing articles in April 2016. For any article added to bioRxiv after that date the date in PrePubMed should be the date of the first version of the preprint. For articles before this date PrePubMed indexed the version that was newest, not the earliest possible version. As a result, someone theoretically could have submitted a preprint in 2014 and chosen their license in 2014, but then updated their article in February 2016, and PrePubMed will have the date of February 2016. It is possible to reindex the dates to get the date of the first version, but this is assuming that users do not change the license when they upload a new version.