Update README.md

README.md

@@ -38,6 +38,42 @@ human protein pairs interact directly or indirectly.
     Huttlin et al. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. 2015 Jul 16;162(2):425-40. doi: 10.1016/j.cell.2015.06.043.
     Reimand et al. g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9. doi: 10.1093/nar/gkw199.
 
+## Description of dataset files
+  |-- **full**
+    |-- **humap3_full_feature_matrix_20220625.csv.gz**
+      This is the full feature matrix that contains all 26 million proteins pairs that DirectContacts2 makes 
+      predictions on and the 324 features from >25,000 proteomic mass spectrometry experiments. The feature 
+      matrix was originally developed in hu.MAP3.0.
+  |-- **reference_interactions**
+    |-- **benchmark_test_INTRAandINTER_complex_NegativePairs_20250619.csv**
+      These are the test set negatives that contains both intra- and inter-complex negative pairs. The file
+      contains a pair of proteins (defined by UniProt acession) per line. The set of structures (PDBs) these
+      interactions come from all have at least 5 subunits.
+    |-- **benchmark_test_IntraComplex_NegativePairs_pdbsize5_20240326.txt**
+      These are the test set negatives that contain only intra-complex negative pairs and are the negatives used
+      in the test feature matrix provided when reading in the test feature matrix using the *datasets* package.
+      The other feature matrix is provided under this same directory (*reference_interactions). All PDBs that
+      these interactions come from have at least 5 protein subunits. The file is structured with one pair of 
+      proteins (defined by UniProt acession) per line.
+    |-- **benchmark_test_IntraComplex_PositivePairs_pdbsize5_20240326.txt**
+      These are the test set positives, which are only intra-complex pairs. The PDB structures from which the 
+      interactions are derived all have at least 5 subunits. The file is structured with one pair of 
+      proteins (defined by UniProt acession) per line.
+    |-- **benchmark_train_INTERandINTRA_complex_NegativePairs_pdbsize3_20240326.txt**
+      These are the training set negatives, which contain both inter- and intra-complex pairs. The set of 
+      structures (PDBs) these interactions come from all have at least 3 subunits. The file is structured with 
+      one pair of proteins (defined by UniProt acession) per line.
+    |-- **benchmark_train_IntraComplex_PositivePairs_pdbsize3_20240326.txt**
+      These are the test set positives, which are only intra-complex pairs. The PDB structures from which the 
+      interactions are derived all have at least 3 subunits. The file is structured with one pair of 
+      proteins (defined by UniProt acession) per line.
+  |-- **test**
+    |-- **test_FeatureMatrix_pdbsize5_only_INTRA_complex_NegativePairs_20240326.csv.gz**
+      This is the feature matrix for the test set of interactions.
+  |-- **train**
+    |-- **train_FeatureMatrix_pdbsize3_20240326.csv.gz**
+      This is the feature matrix for the training set of interactions.
+      
 ## Associated code 
   Additional code examples can be found on our [GitHub](https://github.com/KDrewLab/DirectContacts2_analysis.git), including:
   importing the [DirectContacts2 model](https://huggingface.co/DrewLab/DirectContacts2_AutoGluon) to make predictions, importing the