Merge pull request #62 from broadinstitute/AnneCarpenter-patch-1

Adding link to zenodo resources, updating definitions

explanations/data_description.md

@@ -91,10 +91,25 @@ From 12 sources (data-generating centers):
 
 
 
-4. **Assembled Subsets**  
-
-   - Combined datasets in parquet format  
-   - URLs available in [profile index](https://github.com/jump-cellpainting/datasets/blob/main/manifests/profile_index.csv)
+4. **Index **
+   You can find the profile : https://github.com/jump-cellpainting/datasets/blob/main/manifests/profile_index.csv
+
+   - Parquet tables in which profiles were preprocessed with varying optimized pipelines.
+   - The "Interpretable" tables means that they are processed to the point where features retain their original mapping from the original features' names (relating to size, shape, intensity, etc.). 
+
+
+
+6. **Processed JUMP reference tables (JUMP_rr tables)**
+   [This](https://zenodo.org/records/14046034) dataset provides multiple precomputed analysis tables to make JUMP data exploration accessible:
+
+  - 'X_features.parquet' contains a ranking of the features that distinguish a given perturbation from negative controls.
+  - 'X_gallery.parquet' is for visualization of the images with all channels collapsed into one.
+  - 'X_cosinesim...parquet' contains the pairwise cosine similarity of all perturbations within a given dataset (i.e., orf, crispr). This allows searching for the closest matches for each perturbation of interest or looking at all relationships in a heatmap.
+  - 'X...significance...parquet' is the statistical significance for the phenotypic activity of a given sample (see broad.io/crispr_feature for a formal definition). It shows which perturbations yielded a phenotype distinguishable from negative controls.
+  - 'full' tables contain all the data points from the resulting analysis. Their non-full counterpart contains a subset comprised of the most significant entries, meant for in-browser consumption and queries. 
+  - Many of the above tables can be interactively viewed using [JUMPrr tools](https://github.com/broadinstitute/monorepo/tree/main/libs/jump_rr#quick-data-access)
+
+
 
 ## Data Access