3ab97c0ed056b21d4c061f9cb0055f30391758ee
angie
  Wed Nov 29 14:07:07 2017 -0800
Updated refSeqFuncElems track to use NCBI's coloring and labeling scheme; also scrape PMIDs from note and function attributes.  refs #19638

diff --git src/hg/lib/refSeqFuncElems.as src/hg/lib/refSeqFuncElems.as
index 57934b6..b8e1149 100644
--- src/hg/lib/refSeqFuncElems.as
+++ src/hg/lib/refSeqFuncElems.as
@@ -1,19 +1,20 @@
 table refSeqFuncElems
-"Bed 6+ representation of the refSeq functional elements."
+"Bed 9+ representation of RefSeq functional elements."
     (
     string chrom;          "Reference sequence chromosome or scaffold"
     uint   chromStart;     "Start position in chromosome"
     uint   chromEnd;       "End position in chromosome"
-    string name;           "Numeric ID of the gene" 
+    string name;           "type of element"
     uint   score;          "unused; placeholder for BED format"
     char[1] strand;        "+ for forward strand, - for reverse strand"
     uint   thickStart;     "Start position in chromosome"
     uint   thickEnd;       "End position in chromosome"
+    uint reserved;         "Used as itemRgb: color based on type of element"
     string soTerm;         "Sequence ontology (SO) term"
     lstring note;          "A note describing the element"
-    lstring pubMedIds;     "PubMed ID (PMID) of associated publication(s)"
+    lstring geneIds;       "Entrez Gene ID of associated gene(s)"
+    lstring pubMedIds;     "PubMed ID of associated publication(s)"
     lstring experiment;    "Experimental evidence"
     lstring function;      "Predicted function"
-    string annotationID;   "Annotation release"
     lstring _mouseOver;    "Mouse over label"
     )