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jump-cellpainting / datasets

Images and other data from the JUMP Cell Painting Consortium
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update "Does JUMP contain X compound/gene?" link on FAQ #110

Closed AnneCarpenter closed 2 months ago

AnneCarpenter commented 2 months ago

On this page it says Data

Does JUMP contain X compound/gene? We have done our best to ensure that if you can check if your compound is available here.

but that URL just goes to the issues of this repo rather than a place to check for your compound/gene.

(side note: typo in "Frequently Asqued Questions" in the sidebar -> Asked)

AnneCarpenter commented 2 months ago

Also wanted to check whether the code here points to the latest JUMP recommended versions of the datasets (feel free to tag Niranj for this if more suited): https://broadinstitute.github.io/2023_12_JUMP_data_only_vignettes/howto/tutorial_basic.html

(if it will be hard to commit to keeping it up to date, we could instead put a big warning here that says go here [URL] to find the latest location of the latest profiles to use)

afermg commented 2 months ago

Also wanted to check whether the code here points to the latest JUMP recommended versions of the datasets (feel free to tag Niranj for this if more suited): https://broadinstitute.github.io/2023_12_JUMP_data_only_vignettes/howto/tutorial_basic.html

It is! I made sure of that last week. Shantanu double-checked here. The one thing that may still change is the newest CRISPR profile that Niranj produced. I am still waiting for the link on that one though. I generally try to keep the links to the minimum, so in case of doubt (https://broadinstitute.github.io/2023_12_JUMP_data_only_vignettes/howto/tutorial_basic.html) is the correct one.

afermg commented 2 months ago

On this page it says Data

Does JUMP contain X compound/gene? We have done our best to ensure that if you can check if your compound is available here.

but that URL just goes to the issues of this repo rather than a place to check for your compound/gene.

(side note: typo in "Frequently Asqued Questions" in the sidebar -> Asked)

Many thanks for pointing those issues out! The repeated thing indicates a search-and-replace gone wrong. I've fixed all these issues now. The Question links to broad.io/babel webtool (which is our closest thing to a knowledge graph atm) and also to the metadata files.

afermg commented 2 months ago

(if it will be hard to commit to keeping it up to date, we could instead put a big warning here that says go here [URL] to find the latest location of the latest profiles to use)

It will be a challenge, but as far as I understand we expect these to be the final profiles. The notebook in that tutorial is run in the background at every commit, so I (or whoever is in charge after me) will get notified if it fails. I think these commits solve the issues. Many thanks for double-checking Anne! that's loads of help. I will close the issue to focus on the other ones but feel free to reopen it if you find something out of place.

niranjchandrasekaran commented 1 month ago

The one thing that may still change is the newest CRISPR profile that Niranj produced. I am still waiting for the link on that one though.

@afermg the newest CRISPR profile is the one that you are already using (the one that Shantanu confirmed on Slack). You are all set when it comes to using the latest ORF and CRISPR profiles.

afermg commented 1 month ago

Then we are good to go. Thanks @niranjchandrasekaran!