1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e markd Tue Jul 29 12:15:26 2025 -0700 import of GENCODE Versions V49, V49lift37, and VM38 diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 1a388040333..b65695ec96d 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -4127,30 +4127,124 @@ hg38.wgEncodeGencodeAnnotationRemarkV48.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV48 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV48.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV48.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportV48 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV48.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.50 # end Gencode V48 +# begin Gencode V49 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaV49 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsV49 +identifier wgEncodeGencodeBasicAttrsV49 +"Link together Gencode Basic Table with Attributes table" + hg38.wgEncodeGencodeAttrsV49.transcriptId + hg38.wgEncodeGencodeBasicV49.name + +identifier wgEncodeGencodeCompAttrsV49 +"Link together Gencode Comprehensive Table with Attributes table" + hg38.wgEncodeGencodeAttrsV49.transcriptId + hg38.wgEncodeGencodeCompV49.name + +identifier wgEncodeGencodePseudoGeneAttrsV49 +"Link together Gencode PseudoGene Table with Attributes table" + hg38.wgEncodeGencodeAttrsV49.transcriptId + hg38.wgEncodeGencodePseudoGeneV49.name + +# gencode association tables (joined through wgEncodeGencodeAttrsV49) +identifier wgEncodeGencodeGeneSourceV49 +"Link together Gencode Gene Source table with Attributes table" + hg38.wgEncodeGencodeGeneSourceV49.geneId + hg38.wgEncodeGencodeAttrsV49.geneId + +identifier wgEncodeGencodeGeneSymbolV49 +"Link together Gencode gene symbol table with Attributes table" + hg38.wgEncodeGencodeGeneSymbolV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbV49 +"Link together Gencode Pdb table with Attributes table" + hg38.wgEncodeGencodePdbV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.007 + +identifier wgEncodeGencodePubMedV49 +"Link together Gencode Pubmed table with Attributes table" + hg38.wgEncodeGencodePubMedV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.40 + +identifier wgEncodeGencodeRefSeqV49 +"Link together Gencode RefSeq table with Attributes table" + hg38.wgEncodeGencodeRefSeqV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneV49 +"Link together Gencode RefSeq table with refGene track" + hg38.wgEncodeGencodeRefSeqV49.rnaAcc dupeOk chopAfter=. + hg38.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagV49 +"Link together Gencode Tag table with Attributes table" + hg38.wgEncodeGencodeTagV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.36 + +identifier wgEncodeGencodeTranscriptSourceV49 +"Link together Gencode Transcript Source table with Attributes table" + hg38.wgEncodeGencodeTranscriptSourceV49.transcriptId + hg38.wgEncodeGencodeAttrsV49.transcriptId + +identifier wgEncodeGencodeTranscriptSupportV49 +"Link together Gencode Transcript Support table with Attributes table" + hg38.wgEncodeGencodeTranscriptSupportV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.01 + +identifier wgEncodeGencodeTranscriptionSupportLevelV49 +"Link together Gencode Transcription Support Level table with Attributes table" + hg38.wgEncodeGencodeTranscriptionSupportLevelV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtV49 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeUniProtV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeAnnotationRemarkV49 +"Link together Gencode Annotation Remark table with Attributes table" + hg38.wgEncodeGencodeAnnotationRemarkV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneV49 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeEntrezGeneV49.transcriptId dupeOk + hg38.wgEncodeGencodeEntrezGeneV49.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeExonSupportV49 +"Link together Gencode Exon Support table with Attributes table" + hg38.wgEncodeGencodeExonSupportV49.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV49.transcriptId minCheck=0.50 + +# end Gencode V49 + # 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 @@ -6284,30 +6378,119 @@ hg19.wgEncodeGencodeUniProtV48lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.20 identifier wgEncodeGencodeAnnotationRemarkV48lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV48lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV48lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV48lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV48lift37.transcriptId minCheck=0.35 # end Gencode V48lift37 +# begin Gencode V49lift37 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaV49lift37 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsV49lift37 +identifier wgEncodeGencodeBasicAttrsV49lift37 +"Link together Gencode Basic Table with Attributes table" + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId + hg19.wgEncodeGencodeBasicV49lift37.name + +identifier wgEncodeGencodeCompAttrsV49lift37 +"Link together Gencode Comprehensive Table with Attributes table" + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId + hg19.wgEncodeGencodeCompV49lift37.name + +identifier wgEncodeGencodePseudoGeneAttrsV49lift37 +"Link together Gencode PseudoGene Table with Attributes table" + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId + hg19.wgEncodeGencodePseudoGeneV49lift37.name + +# gencode association tables (joined through wgEncodeGencodeAttrsV49lift37) +identifier wgEncodeGencodeGeneSourceV49lift37 +"Link together Gencode Gene Source table with Attributes table" + hg19.wgEncodeGencodeGeneSourceV49lift37.geneId + hg19.wgEncodeGencodeAttrsV49lift37.geneId + +identifier wgEncodeGencodeGeneSymbolV49lift37 +"Link together Gencode gene symbol table with Attributes table" + hg19.wgEncodeGencodeGeneSymbolV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbV49lift37 +"Link together Gencode Pdb table with Attributes table" + hg19.wgEncodeGencodePdbV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.007 + +identifier wgEncodeGencodePubMedV49lift37 +"Link together Gencode Pubmed table with Attributes table" + hg19.wgEncodeGencodePubMedV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.40 + +identifier wgEncodeGencodeRefSeqV49lift37 +"Link together Gencode RefSeq table with Attributes table" + hg19.wgEncodeGencodeRefSeqV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneV49lift37 +"Link together Gencode RefSeq table with refGene track" + hg19.wgEncodeGencodeRefSeqV49lift37.rnaAcc dupeOk chopAfter=. + hg19.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagV49lift37 +"Link together Gencode Tag table with Attributes table" + hg19.wgEncodeGencodeTagV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.36 + +identifier wgEncodeGencodeTranscriptSourceV49lift37 +"Link together Gencode Transcript Source table with Attributes table" + hg19.wgEncodeGencodeTranscriptSourceV49lift37.transcriptId + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId + +identifier wgEncodeGencodeTranscriptSupportV49lift37 +"Link together Gencode Transcript Support table with Attributes table" + hg19.wgEncodeGencodeTranscriptSupportV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.01 + +identifier wgEncodeGencodeTranscriptionSupportLevelV49lift37 +"Link together Gencode Transcription Support Level table with Attributes table" + hg19.wgEncodeGencodeTranscriptionSupportLevelV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtV49lift37 +"Link together Gencode UniProt Support table with Attributes table" + hg19.wgEncodeGencodeUniProtV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeAnnotationRemarkV49lift37 +"Link together Gencode Annotation Remark table with Attributes table" + hg19.wgEncodeGencodeAnnotationRemarkV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV49lift37.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneV49lift37 +"Link together Gencode UniProt Support table with Attributes table" + hg19.wgEncodeGencodeEntrezGeneV49lift37.transcriptId dupeOk + hg19.wgEncodeGencodeEntrezGeneV49lift37.transcriptId minCheck=0.35 + +# end Gencode V49lift37 + # 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 @@ -8926,30 +9109,124 @@ mm39.wgEncodeGencodeAnnotationRemarkVM37.transcriptId dupeOk mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM37 "Link together Gencode UniProt Support table with Attributes table" mm39.wgEncodeGencodeEntrezGeneVM37.transcriptId dupeOk mm39.wgEncodeGencodeEntrezGeneVM37.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportVM37 "Link together Gencode Exon Support table with Attributes table" mm39.wgEncodeGencodeExonSupportVM37.transcriptId dupeOk mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.50 # end Gencode VM37 +# begin Gencode VM38 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaVM38 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsVM38 +identifier wgEncodeGencodeBasicAttrsVM38 +"Link together Gencode Basic Table with Attributes table" + mm39.wgEncodeGencodeAttrsVM38.transcriptId + mm39.wgEncodeGencodeBasicVM38.name + +identifier wgEncodeGencodeCompAttrsVM38 +"Link together Gencode Comprehensive Table with Attributes table" + mm39.wgEncodeGencodeAttrsVM38.transcriptId + mm39.wgEncodeGencodeCompVM38.name + +identifier wgEncodeGencodePseudoGeneAttrsVM38 +"Link together Gencode PseudoGene Table with Attributes table" + mm39.wgEncodeGencodeAttrsVM38.transcriptId + mm39.wgEncodeGencodePseudoGeneVM38.name + +# gencode association tables (joined through wgEncodeGencodeAttrsVM38) +identifier wgEncodeGencodeGeneSourceVM38 +"Link together Gencode Gene Source table with Attributes table" + mm39.wgEncodeGencodeGeneSourceVM38.geneId + mm39.wgEncodeGencodeAttrsVM38.geneId + +identifier wgEncodeGencodeGeneSymbolVM38 +"Link together Gencode gene symbol table with Attributes table" + mm39.wgEncodeGencodeGeneSymbolVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbVM38 +"Link together Gencode Pdb table with Attributes table" + mm39.wgEncodeGencodePdbVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.007 + +identifier wgEncodeGencodePubMedVM38 +"Link together Gencode Pubmed table with Attributes table" + mm39.wgEncodeGencodePubMedVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.40 + +identifier wgEncodeGencodeRefSeqVM38 +"Link together Gencode RefSeq table with Attributes table" + mm39.wgEncodeGencodeRefSeqVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneVM38 +"Link together Gencode RefSeq table with refGene track" + mm39.wgEncodeGencodeRefSeqVM38.rnaAcc dupeOk chopAfter=. + mm39.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagVM38 +"Link together Gencode Tag table with Attributes table" + mm39.wgEncodeGencodeTagVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.36 + +identifier wgEncodeGencodeTranscriptSourceVM38 +"Link together Gencode Transcript Source table with Attributes table" + mm39.wgEncodeGencodeTranscriptSourceVM38.transcriptId + mm39.wgEncodeGencodeAttrsVM38.transcriptId + +identifier wgEncodeGencodeTranscriptSupportVM38 +"Link together Gencode Transcript Support table with Attributes table" + mm39.wgEncodeGencodeTranscriptSupportVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.01 + +identifier wgEncodeGencodeTranscriptionSupportLevelVM38 +"Link together Gencode Transcription Support Level table with Attributes table" + mm39.wgEncodeGencodeTranscriptionSupportLevelVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtVM38 +"Link together Gencode UniProt Support table with Attributes table" + mm39.wgEncodeGencodeUniProtVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeAnnotationRemarkVM38 +"Link together Gencode Annotation Remark table with Attributes table" + mm39.wgEncodeGencodeAnnotationRemarkVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneVM38 +"Link together Gencode UniProt Support table with Attributes table" + mm39.wgEncodeGencodeEntrezGeneVM38.transcriptId dupeOk + mm39.wgEncodeGencodeEntrezGeneVM38.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeExonSupportVM38 +"Link together Gencode Exon Support table with Attributes table" + mm39.wgEncodeGencodeExonSupportVM38.transcriptId dupeOk + mm39.wgEncodeGencodeAttrsVM38.transcriptId minCheck=0.50 + +# end Gencode VM38 + 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