From 34d0481cb17112e661965d1a5962cb231e92a6df Mon Sep 17 00:00:00 2001
From: NATALIA GARCIA SANCHEZ <natalia.garcia.sanchez@alumnos.upm.es>
Date: Sun, 25 Feb 2024 23:26:52 +0000
Subject: [PATCH] Update README.md

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 README.md | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 51 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index d4d1755..30f2df0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 # Embeddings in DR
 
-Additional `data.xlsx` descriptionExcel file with different sheets that contain the data used in the analysis.
+
+1.  Supplementary `data.xlsx` descriptionExcel file, available in the present Gitlab repository, with different sheets that contain the data used in the analysis.
 <n>
 - **DR cases – repoDB**
 
@@ -46,4 +47,52 @@ The distance value for each protein pair is included for every embedding method.
 
 - **PP by class – Distances**
 
-The distance value for each protein pair filtered by PANTHERdb class is included forevery embedding method. We indicated if the protein pair belongede to repoDB, Literature or both datasets.
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+The distance value for each protein pair filtered by PANTHERdb class is included forevery embedding method. We indicated if the protein pair belongede to repoDB, Literature or both datasets.
+
+
+2. Supplementary files for protein data used in the study, sequence embeddings from the four reviewed methods and protein pair distances, available in [](https://drive.upm.es/s/egBAv71on4AgBdn?path=%2Fdata)
+
+**File folder structure **
+
+embeddings/
+├── Global_embedding.ipynb 
+│   └── **Script to execute protein sequence embedding retrieval for all methods**
+├── OneHot.tsv
+│   └── **Final embeddings in One Hot encoding**
+├── SGT.tsv 
+│   └── **Final embeddings in Sequence Graph Transform encoding**
+├── ProtBERT.tsv
+│   └── **Final embeddings in Pretrained BERT (Pro-Trans model) Transformer encoding**
+└── SeqVec.tsv
+    └── **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**
+├── SGT.npy
+│   └── **Cosine distance matrix from all protein pair embeddings retrieved from SGT encoding**
+├── ProtBERT.npy
+│   └── **Cosine distance matrix from all protein pair embeddings retrieved from BERT encoding**
+└── SeqVec.npy
+    └── **Cosine distance matrix from all protein pair embeddings retrieved from SeqVec encoding**
+    
+    
+proteins/
+├── protein_list/
+│   ├── protein_names.csv
+│   │   └── **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**
+│   └── proteins_sgt.csv
+│       └── **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]**
+│   └── 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]**
+└── 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)**
+    └── 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)**
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2.24.1