Update README.md

README.md

 # Embeddings in DR
 
 
-1.  Supplementary `data.xlsx` descriptionExcel file, available in the present Gitlab repository, with different sheets that contain the data used in the analysis.
+1.  Supplementary [`data.xlsx](https://medal.ctb.upm.es/internal/gitlab/disnet/sequences/embeddings-in-dr/blob/master/data.xlsx)` descriptionExcel file, available in the present Gitlab repository, with different sheets that contain the data used in the analysis.
 
 <n>
 
@@ -66,47 +66,49 @@ The distance value for each protein pair filtered by PANTHERdb class is included
 
 ```
 embeddings/
-├── Global_embedding.ipynb 
-│   └── **Script to execute protein sequence embedding retrieval for all methods**
 ├── OneHot.tsv
-│   └── **Final embeddings in One Hot encoding**
+│   └── Final embeddings in One Hot encoding.
 ├── SGT.tsv 
-│   └── **Final embeddings in Sequence Graph Transform encoding**
+│   └── Final embeddings in Sequence Graph Transform encoding.
 ├── ProtBERT.tsv
-│   └── **Final embeddings in Pretrained BERT (Pro-Trans model) Transformer encoding**
+│   └── Final embeddings in Pretrained BERT (Pro-Trans model) Transformer encoding.
 └── SeqVec.tsv
-    └── **Final embeddings in Pretrained CNN + biLSTM (SeqVec model) encoding**
+    └── Final embeddings in Pretrained CNN + biLSTM (SeqVec model) encoding.
     
     
 distances/
 ├── OneHot.npy
-│   └── **Cosine distance matrix from all protein pair embeddings retrieved from One-Hot encoding**
+│   └── Cosine distance matrix from all protein pair embeddings retrieved from One-Hot encoding. Rows and columns are ordered according to the protein lists provided in the next directory (proteins.csv).
 ├── SGT.npy
-│   └── **Cosine distance matrix from all protein pair embeddings retrieved from SGT encoding**
+│   └── Cosine distance matrix from all protein pair embeddings retrieved from SGT encoding. Rows and columns are ordered according to the protein lists provided in the next directory (proteins_sgt.csv).
 ├── ProtBERT.npy
-│   └── **Cosine distance matrix from all protein pair embeddings retrieved from BERT encoding**
+│   └── Cosine distance matrix from all protein pair embeddings retrieved from BERT encoding. Rows and columns are ordered according to the protein lists provided in the next directory (proteins.csv).
 └── SeqVec.npy
-    └── **Cosine distance matrix from all protein pair embeddings retrieved from SeqVec encoding**
+    └── Cosine distance matrix from all protein pair embeddings retrieved from SeqVec encoding. Rows and columns are ordered according to the protein lists provided in the next directory (proteins.csv).
     
     
 proteins/
 ├── protein_list/
 │   ├── protein_names.csv
-│   │   └── **List of total protein IDs (Uniprot ID), name and descriptions.**
+│   │   └── List of total protein IDs (Uniprot ID), name and descriptions.
 │   ├── proteins.csv
-│   │   └── **Total protein IDs retrieved for embeddings in all embedding methods except SGT after length filtering**
+│   │   └── Total protein IDs retrieved for embeddings in all embedding methods except SGT after length filtering.
 │   └── proteins_sgt.csv
-│       └── **Total protein IDs retrieved for embeddings generation in SGT**
+│       └── Total protein IDs retrieved for embeddings generation in SGT.
 ├── proteins_DR/
 │   ├── CSBJ-ND.tsv
-│   │   └── **List of total protein pairs linked to disease pairs that share the same repurposed pharmaceutical indication, from repurpousing data gathered in Literature[1]**
+│   │   └── List of total protein pairs linked to disease pairs that share the same repurposed pharmaceutical indication, from repurpousing data gathered in Literature [1].
 │   └── repoDB.tsv
-│       └── **List of total protein pairs linked to disease pairs that share the same repurposed pharmaceutical indication, from repurpousing data gathered from repoDB[2]**
+│       └── List of total protein pairs linked to disease pairs that share the same repurposed pharmaceutical indication, from repurpousing data gathered from RepoDB [2].
 └── proteins_DR_different_class/
     ├── CSBJ-ND.tsv
-    │   └── **Protein pair lists from protein_DR/CSBJ-ND.tsv, limited to protein pairs that do not share the same protein functional class (Filtered subset)**
+    │   └── Protein pair lists from protein_DR/CSBJ-ND.tsv, limited to protein pairs that do not share the same protein functional class (Filtered subset).
     └── repoDB.tsv
-        └── **Protein pair lists from protein_DR/repoDB.tsv, limited to protein pairs that do not share the same protein functional class (Filtered subset
+        └── Protein pair lists from protein_DR/repoDB.tsv, limited to protein pairs that do not share the same protein functional class (Filtered subset).
+
+DR/
+└── disease_protein.csv
+    └── List of disease - protein associations to be used in the search for new repurposing hypotheses. These data comes from DisGeNET.
 ```
 ---