ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14
markd
  Mon Nov 30 16:35:39 2020 -0800
import of GENCODE V36

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index aa6bb63..08f1133 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -5401,53 +5401,132 @@
     mm10.wgEncodeGencodeAnnotationRemarkVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM25
 "Link together Gencode UniProt Support table with Attributes table"
     mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM25
 "Link together Gencode Exon Support table with Attributes table"
     mm10.wgEncodeGencodeExonSupportVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.90
 
 # end Gencode VM25
 
+# begin Gencode V35 (2020 reorganization quick change)
 identifier gencodeAnnotV35
 "Link together Gencode Annotation Table with Attributes table"
     $gbd.gencodeAttrsV35.transcriptId
     $gbd.gencodeGeneSymbolV35.transcriptId 
     $gbd.gencodePdbV35.transcriptId 
     $gbd.gencodePubMedV35.transcriptId 
     $gbd.gencodeRefSeqV35.transcriptId 
     $gbd.gencodeTagV35.transcriptId 
     $gbd.gencodeRefSeqV35.transcriptId minCheck=0.9
     $gbd.gencodeTranscriptSourceV35.transcriptId minCheck=0.9
     $gbd.gencodeTranscriptSupportV35.transcriptId 
     $gbd.gencodeTranscriptionSupportLevelV35.transcriptId 
     $gbd.gencodeUniProtV35.transcriptId 
     $gbd.gencodeAnnotationRemarkV35.transcriptId  minCheck=0.9
     $gbd.gencodeEntrezGeneV35.transcriptId 
     $gbd.gencodeExonSupportV35.transcriptId 
     $gbd.gencodeAnnotV35.name
 
 identifier gencodeAnnotV35Gene
 "Link together Gencode Annotation Table with Attributes table"
     $gbd.gencodeGeneSourceV35.geneId
     $gbd.gencodeAttrsV35.geneId
 
+# end Gencode V35 (2020 reorganization quick change)
+
+# begin Gencode V36 (2020 reorganization)
+
+identifier gencodeAnnotAttrsV36
+"Link together Gencode Annotation Table with Attributes table"
+    hg38.gencodeAttrsV36.transcriptId
+    hg38.gencodeAnnotV36.name
+
+# gencode association tables (joined through gencodeAttrsV36)
+identifier gencodeGeneSourceV36
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.gencodeGeneSourceV36.geneId
+    hg38.gencodeAttrsV36.geneId
+
+identifier gencodeToGeneSymbolV36
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.gencodeToGeneSymbolV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.20
+
+identifier gencodeToPdbV36
+"Link together Gencode Pdb table with Attributes table"
+    hg38.gencodeToPdbV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.015
+
+identifier gencodeToPubMedV36
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.gencodeToPubMedV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId  minCheck=0.63
+
+identifier gencodeToRefSeqV36
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.gencodeToRefSeqV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.05
+
+identifier gencodeTagV36
+"Link together Gencode Tag table with Attributes table"
+    hg38.gencodeTagV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.36
+    hg38.gencodeToRefSeqV36.transcriptId minCheck=0.9
+
+identifier gencodeTranscriptSourceV36
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.gencodeTranscriptSourceV36.transcriptId
+    hg38.gencodeAttrsV36.transcriptId
+
+identifier gencodeTranscriptSupportV36
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.gencodeTranscriptSupportV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.10
+
+identifier gencodeTranscriptionSupportLevelV36
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.gencodeTranscriptionSupportLevelV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.30
+
+identifier gencodeToUniProtV36
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.gencodeToUniProtV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.35
+
+identifier gencodeAnnotationRemarkV36
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.gencodeAnnotationRemarkV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.10
+
+identifier gencodeToEntrezGeneV36
+"Link together Gencode Entrez table with Attributes table"
+    hg38.gencodeToEntrezGeneV36.transcriptId dupeOk
+    hg38.gencodeToEntrezGeneV36.transcriptId minCheck=0.35
+
+identifier gencodeExonSupportV36
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.gencodeExonSupportV36.transcriptId dupeOk
+    hg38.gencodeAttrsV36.transcriptId minCheck=0.70
+
+# end Gencode V36 (2020 reorganization)
+
 identifier wgEncodeGencodeClassesV3Hg19
 "Link together Gencode gene model (Known) and class for July 2009 Data Version"
     hg19.wgEncodeGencodeClassesV3.name
     hg19.wgEncodeGencodeAutoV3.name unique
     hg19.wgEncodeGencodeManualV3.name unique
     hg19.wgEncodeGencodePolyaV3.name unique
 
 identifier acemblyName dependency
 "Link together Acembly gene model structure and peptide."
     $hg,$mm.acembly.name
     $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90
     hg17.acemblyPep.name unique minCheck=0.63
     $hg,$mm.acemblyClass.name full unique
 
 identifier ECgeneName dependency