diff README.rst @ 4:f294fd77b143 draft

planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty

--- a/README.rst	Wed Mar 07 09:56:25 2018 -0500
+++ b/README.rst	Wed Mar 14 12:22:51 2018 -0400
@@ -13,9 +13,11 @@
 
 -------------------------------------------------
 
-This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) regarding the expression profiles of human genes both on the mRNA and protein level. 
+This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) 
+regarding the expression profiles of human genes both on the mRNA and protein level. 
 
-A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), if it's not the case, please use the ID_Convert tool from ProteoRE.
+A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), 
+if it's not the case, please use the ID_Convert tool from ProteoRE.
 
 The resources from Human Protein Atlas that can be queried are the following: 
 
@@ -29,4 +31,25 @@
 
   The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable").
 
-  The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
\ No newline at end of file
+  The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
+
+-----
+
+**Reliability score**
+
+Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect 
+to the definitions from HPA:
+
+Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene 
+have obtained enhanced validation based on orthogonal or independent antibody validation method.
+
+Supported - Consistency with RNA-seq and/or protein/gene characterization data, 
+in combination with similar staining pattern if independent antibodies are available.
+
+Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of, 
+protein/gene characterization data. Alternatively, consistency with protein/gene characterization data 
+in combination with inconsistency with RNA-seq data. If independent antibodies are available, 
+the staining pattern is partly similar or dissimilar.
+
+Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, 
+in combination with dissimilar staining pattern if independent antibodies are available.