0f6f8c5cdfc1c5385c814102a4fa59afb08d2849
markd
  Wed Jul 31 23:45:27 2024 -0700
import of GENCODE v47, v47lift37, and vM36 pre-releases

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 2959eb1..385ec3c 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -3939,30 +3939,124 @@
     hg38.wgEncodeGencodeAnnotationRemarkV46.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV46
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV46.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV46.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV46
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV46.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.50
 
 # end Gencode V46
 
+# begin Gencode V47
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV47
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV47
+identifier wgEncodeGencodeBasicAttrsV47
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV47.transcriptId
+    hg38.wgEncodeGencodeBasicV47.name
+
+identifier wgEncodeGencodeCompAttrsV47
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV47.transcriptId
+    hg38.wgEncodeGencodeCompV47.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV47
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV47.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV47.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV47)
+identifier wgEncodeGencodeGeneSourceV47
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV47.geneId
+    hg38.wgEncodeGencodeAttrsV47.geneId
+
+identifier wgEncodeGencodeGeneSymbolV47
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV47
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV47
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqV47
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV47
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV47.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV47
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV47
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV47.transcriptId
+    hg38.wgEncodeGencodeAttrsV47.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV47
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV47
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV47
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.28
+
+identifier wgEncodeGencodeAnnotationRemarkV47
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV47
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV47.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV47
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV47.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.50
+
+# end Gencode V47
+
 # begin Gencode V24lift37
 
 # gencode genepreds with no associations
 # wgEncodeGencodePolyaV24lift37
 # wgEncodeGencode2wayConsPseudoV24lift37
 
 # gencode genepreds with joining through wgEncodeGencodeAttrsV24lift37
 identifier wgEncodeGencodeBasicAttrsV24lift37
 "Link together Gencode Basic Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId
     hg19.wgEncodeGencodeBasicV24lift37.name
 
 identifier wgEncodeGencodeCompAttrsV24lift37
 "Link together Gencode Comprehensive Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId
@@ -5918,30 +6012,119 @@
     hg19.wgEncodeGencodeUniProtV46lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeAnnotationRemarkV46lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV46lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV46lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV46lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV46lift37.transcriptId minCheck=0.35
 
 # end Gencode V46lift37
 
+# begin Gencode V47lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV47lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV47lift37
+identifier wgEncodeGencodeBasicAttrsV47lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV47lift37.name
+
+identifier wgEncodeGencodeCompAttrsV47lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId
+    hg19.wgEncodeGencodeCompV47lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV47lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV47lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV47lift37)
+identifier wgEncodeGencodeGeneSourceV47lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV47lift37.geneId
+    hg19.wgEncodeGencodeAttrsV47lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV47lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV47lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV47lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqV47lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV47lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV47lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV47lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV47lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV47lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV47lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV47lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV47lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.28
+
+identifier wgEncodeGencodeAnnotationRemarkV47lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV47lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV47lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV47lift37.transcriptId minCheck=0.35
+
+# end Gencode V47lift37
+
 # begin Gencode VM2
 
 # gencode genepreds with no associations
 # wgEncodeGencodePolyaVM2
 # wgEncodeGencode2wayConsPseudoVM2
 
 # gencode genepreds with joining through wgEncodeGencodeAttrsVM2
 identifier wgEncodeGencodeBasicAttrsVM2
 "Link together Gencode Basic Table with Attributes table"
     mm10.wgEncodeGencodeAttrsVM2.transcriptId
     mm10.wgEncodeGencodeBasicVM2.name
 
 identifier wgEncodeGencodeCompAttrsVM2
 "Link together Gencode Comprehensive Table with Attributes table"
     mm10.wgEncodeGencodeAttrsVM2.transcriptId
@@ -8372,30 +8555,125 @@
 "Link together Gencode Annotation Remark table with Attributes table"
     mm39.wgEncodeGencodeAnnotationRemarkVM35.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM35
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM35.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM35.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM35
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM35.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.50
 
 # end Gencode VM35
+# begin Gencode VM36
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM36
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM36
+identifier wgEncodeGencodeBasicAttrsVM36
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId
+    mm39.wgEncodeGencodeBasicVM36.name
+
+identifier wgEncodeGencodeCompAttrsVM36
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId
+    mm39.wgEncodeGencodeCompVM36.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM36
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM36.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM36)
+identifier wgEncodeGencodeGeneSourceVM36
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM36.geneId
+    mm39.wgEncodeGencodeAttrsVM36.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM36
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM36
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.007
+
+identifier wgEncodeGencodePubMedVM36
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqVM36
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM36
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM36.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM36
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM36
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM36.transcriptId
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM36
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM36
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM36
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeAnnotationRemarkVM36
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM36
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM36.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM36
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM36.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.50
+
+# end Gencode VM36
+
+# end Gencode VM36
 
 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