diff --git a/tools/data_source/encode_import_all_latest_datasets.xml b/tools/data_source/encode_import_all_latest_datasets.xml
index 237cf29e860..f07173f9c00 100644
--- a/tools/data_source/encode_import_all_latest_datasets.xml
+++ b/tools/data_source/encode_import_all_latest_datasets.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 For detailed information about data deposition and partitioning, click here_.
 
 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
diff --git a/tools/data_source/encode_import_chromatin_and_chromosomes.xml b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
index 9985f645c74..bf0dd376d98 100644
--- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml
+++ b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 For detailed information about data deposition and partitioning, click here_.
 
 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
diff --git a/tools/data_source/encode_import_gencode.xml b/tools/data_source/encode_import_gencode.xml
index 9b64d3cc55b..2767c4b654c 100644
--- a/tools/data_source/encode_import_gencode.xml
+++ b/tools/data_source/encode_import_gencode.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 These are the datasets used for partitioning files.
 
 For detailed information about data deposition and partitioning, click here_.
diff --git a/tools/data_source/encode_import_genes_and_transcripts.xml b/tools/data_source/encode_import_genes_and_transcripts.xml
index d93740d1c71..de1ce839c7e 100644
--- a/tools/data_source/encode_import_genes_and_transcripts.xml
+++ b/tools/data_source/encode_import_genes_and_transcripts.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 For detailed information about data deposition and partitioning, click here_.
 
 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
diff --git a/tools/data_source/encode_import_multi-species_sequence_analysis.xml b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
index d6cbed08adf..c89122be885 100644
--- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml
+++ b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 For detailed information about data deposition and partitioning, click here_.
 
 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
diff --git a/tools/data_source/encode_import_transcription_regulation.xml b/tools/data_source/encode_import_transcription_regulation.xml
index 83dceedd494..29efe16da3c 100644
--- a/tools/data_source/encode_import_transcription_regulation.xml
+++ b/tools/data_source/encode_import_transcription_regulation.xml
@@ -23,6 +23,13 @@
   </outputs>
   <code file="encode_import_code.py"/>
   <help>
+  
+.. class:: warningmark
+
+The data in this section is intended as a supplement for this manuscript_.  Use the **Get Data->UCSC Main** tool for current ENCODE data.
+
+.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
+
 For detailed information about data deposition and partitioning, click here_.
 
 .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups