Save the overrides to the RDF model.

They're designed to be loaded into the model before we start pulling data
from UCSC and our website.

Currently the file just defines submission to library URN/URL mappings
for the submissions whose submission name doesn't include the correct
library ID.

diff --git a/extra/ucsc_encode_submission/dt-overrides.turtle b/extra/ucsc_encode_submission/dt-overrides.turtle
new file mode 100644 (file)
index 0000000..fde9add
--- /dev/null
+++ b/extra/ucsc_encode_submission/dt-overrides.turtle
@@ -0,0 +1,158 @@
+##
+## Override submission ID to library URN names for our libraries
+## whose names either lack, or have the wrong library ID string 
+## embedded in them.
+##
+
+@base <file:///home/diane/proj/solexa/htsworkflow/extra/ucsc_encode_submission/no-lib.sparql> .
+@prefix encodeSubmit:<http://jumpgate.caltech.edu/wiki/UCSCSubmissionOntology#> .
+
+# woldlab-hepg2-rnaseq-2009dec
+<http://encodesubmit.ucsc.edu/pipeline/show/805>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10879> .
+
+# woldlab-hepg2-rnaseq-2009dec-part2
+<http://encodesubmit.ucsc.edu/pipeline/show/810>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10879> .
+
+# woldlab-hepg2-rnaseq-2009dec-part3\t 
+<http://encodesubmit.ucsc.edu/pipeline/show/869>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10879> .
+
+# woldlab-rnaseq-GM12878-rep1-stranded-2010Jan15
+<http://encodesubmit.ucsc.edu/pipeline/show/870>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11011> .
+
+# woldlab-hepg2-rnaseq-2010Jan-part4
+<http://encodesubmit.ucsc.edu/pipeline/show/897>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10879> .
+
+# woldlab-gm12878-directional-rep2-rnaseq-2010Jan06
+<http://encodesubmit.ucsc.edu/pipeline/show/898>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11010> .
+
+# woldlab-K562-directional-rnaseq-rep1-2010Jan6
+<http://encodesubmit.ucsc.edu/pipeline/show/903>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11010> .
+
+# woldlab-K562-directional-rnaseq-rep2-2010jan9
+<http://encodesubmit.ucsc.edu/pipeline/show/904>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11007> .
+
+# woldlab hESC 10886 rep1 2009Jan13
+<http://encodesubmit.ucsc.edu/pipeline/show/1026>
+  encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11286> .
+
+# woldlab 2010Jun15 1x75-Directional-NHEK-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1483>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11204> .
+
+# woldlab Jun18 1x75-Directional-H1-hESC-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1626>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11009> .
+
+# woldlab jun 18 1x75-Directional-GM12878-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1631>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11011> .
+
+# woldlab jun 18  1x75-Directional-GM12878-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1632>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11010> .
+
+# woldlab jun 18 1x75-Directional-H1-hESC-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1633>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10947> .
+
+# woldlab jun 18 1x75-Directional-HeLa-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1634>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11208> .
+
+# woldlab jun 18 1x75-Directional-HeLa-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1635>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11207> .
+
+# woldlab jun 18 1x75-Directional-HepG2-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1636>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11210> .
+
+# woldlab jun 18 1x75-Directional-K562-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1637>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11008> .
+
+# woldlab jun 18 1x75-Directional-HepG2-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1638>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11209> .
+
+# woldlab jun 18 1x75-Directional-HUVEC-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/1639>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11206> .
+
+# woldlab jun 18 1x75-Directional-HUVEC-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1645>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11205> .
+
+# woldlab jun 18 1x75-Directional-K562-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1646>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11007> .
+
+# woldlab June  2x75-GM12878-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/1856>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10515> .
+
+#2010 jul 9corrected fastqs 
+<http://encodesubmit.ucsc.edu/pipeline/show/1874>
+     encodeSubmit:ignore "1" .
+#    encodeSubmit:library_urn "
+
+# 2010-11-05 Correction 1x75-Directional-GM12878-Rep1.tgz
+<http://encodesubmit.ucsc.edu/pipeline/show/2926>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11010> .
+
+# 1x75-Directional-GM12878-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2930>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11010> .
+
+# 1x75-Directional-H1-hESC-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2931>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/10947> .
+
+# 1x75-Directional-H1-hESC-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2932>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11205> .
+
+# 1x75-Directional-HUVEC-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2933>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11206> .
+
+# 1x75-Directional-HUVEC-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2934>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11205> .
+
+# 1x75-Directional-HeLa-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2935>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11208> .
+
+# 1x75-Directional-HeLa-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2936>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11207> .
+
+# 1x75-Directional-HepG2-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2937>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11210> .
+
+# 1x75-Directional-HepG2-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2938>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11209> .
+
+# 1x75-Directional-K562-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2939>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11008> .
+
+# 1x75-Directional-K562-Rep2
+<http://encodesubmit.ucsc.edu/pipeline/show/2940>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11007> .
+
+# 1x75-Directional-NHEK-Rep1
+<http://encodesubmit.ucsc.edu/pipeline/show/2941>
+    encodeSubmit:library_urn <http://jumpgate.caltech.edu/library/11204> .
+