diff --git a/data/.gitignore b/data/.gitignore
index 8b13789..0cbfe16 100644
--- a/data/.gitignore
+++ b/data/.gitignore
@@ -1 +1,15 @@
+# This gitignore contains all those data files, which are not kept on the repo
+# and thus have to be downloaded automatically or manually (in case registration
+# or journal access is needed)
+
+# The temporary download folder:
+tmp/
+
+
+################
+#  PPIs
+#################
+
+#  Bossi & Lehner PPI file
+ppis/CRG.integrated.human.interactome.txt
 
diff --git a/data/README.md b/data/README.md
new file mode 100644
index 0000000..4d53e6e
--- /dev/null
+++ b/data/README.md
@@ -0,0 +1,13 @@
+Data Sources
+============
+
+Protein-Protein Interaction Networks
+------------------------------------
+
+### Bossi & Lehner composite PPI network
+
+From the supplementary section of the paper ["Tissue specificity and the human protein interaction network"](http://www.ncbi.nlm.nih.gov/pubmed/19357639).
+
+This can be automatically downloaded via the download_data.sh script.
+
+
diff --git a/data/download_data.sh b/data/download_data.sh
new file mode 100755
index 0000000..3913da2
--- /dev/null
+++ b/data/download_data.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# This script downloads all publicly available data into the correct folders.
+# Run this before using the pipeline.
+# Don't forget to download the data, that is not publicly available (see README.md for 
+# sources and further explainations)
+
+# A few settings
+TMP_FOLDER=tmp
+
+
+# make tmp folder
+rm -R $TMP_FOLDER
+mkdir -p $TMP_FOLDER
+
+
+####################
+#   PPI networks 
+###################
+
+# 1.) Bossi & Lehner:
+BOSSI_URL=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683721/bin/msb200917-s2.zip
+BOSSI_ZIP=$TMP_FOLDER/bossi-lehner-suppl.zip
+
+curl -o $BOSSI_ZIP $BOSSI_URL
+unzip $BOSSI_ZIP -d $TMP_FOLDER
+cp $TMP_FOLDER/CRG-human-interactome/CRG.integrated.human.interactome.txt ppis/
+
+