We’ve been using a few of the data releases as they’ve become available and we have started making our own analysis tools in combination with our internally produced data. Are there any plans for making the quarterly DepMap Public releases downloadable in a semi-automated fashion so that it’s easier to keep using up to date data? For example, could there be a single link that would point to the most recently released “Achilles_gene_effect.csv” file on figshare?
We deposit all of our public data onto figshare which has a very nice API.
If made it more visible what the figshare id/link is, would that address this need?
For example, here’s the link for the 21Q1 release: public_21q1
And one can then retrieve the contents programmatically using the information from their API call: https://api.figshare.com/v2/articles/13681534
(Figshare’s API docs can be seen here for more info: Figshare documentation )
This does help us somewhat, although I don’t see a way to automatically detect and/or incorporate when 2021Q2 is released without visiting the Downloads page periodically. Do you know of a good way to use the Figshare API to search for new quarterly DepMap releases? I looked into using the search endpoints with “Broad Depmap” as an author but it doesn’t look like that’s an acceptable search field.
Thanks for your help,
No, I don’t know a way to automate that fully. However, if you sign up for the DepMap mailing list, we do email out a notification when new data is released.
This would be a nice feature to have. You could for instance have a link that redirects to the latest Figshare url. For example, https://depmap.org/portal/download/latest/Achilles_gene_effect would redirect to https://ndownloader.figshare.com/files/27902046 or something similar.
This is absolutely doable. Both GDSC and Sanger have a “stable” link to the latest dataset.
It would be extremely helpful if DepMap also provided links of this type.