438d43910f377e7abe8b81cb9b04acaadaca1b6d markd Thu Jul 18 13:04:33 2019 -0700 indicated that GENCODE gene/transcript status columns are obsolete diff --git src/hg/lib/encode/wgEncodeGencodeAttrs.sql src/hg/lib/encode/wgEncodeGencodeAttrs.sql index fd55ac2..5c0603f 100644 --- src/hg/lib/encode/wgEncodeGencodeAttrs.sql +++ src/hg/lib/encode/wgEncodeGencodeAttrs.sql @@ -1,30 +1,30 @@ # wgEncodeGencodeAttrs.sql was originally generated by the autoSql program, which also # generated wgEncodeGencodeAttrs.c and wgEncodeGencodeAttrs.h. This creates the database representation of # an object which can be loaded and saved from RAM in a fairly # automatic way. #Basic set of attributes associated with all Gencode transcripts. CREATE TABLE wgEncodeGencodeAttrs ( geneId varchar(255) not null, # Gene identifier geneName varchar(255) not null, # Gene name geneType varchar(255) not null, # BioType of gene - geneStatus varchar(255) not null, # Status of gene + geneStatus varchar(255) not null, # Status of gene (obsolete) transcriptId varchar(255) not null, # Transcript identifier transcriptName varchar(255) not null, # Transcript name transcriptType varchar(255) not null, # BioType of transcript - transcriptStatus varchar(255) not null, # Status of transcript + transcriptStatus varchar(255) not null, # Status of transcript (obsolete) havanaGeneId varchar(255) not null, # HAVANA identifier if gene is in HAVANA havanaTranscriptId varchar(255) not null, # HAVANA identifier if transcript is in HAVANA ccdsId varchar(255) not null, # CCDS identifier if transcript is in CCDS level int not null, # GENCODE level: 1 = experimental confirmed, 2 = manual, 3 = automated transcriptClass varchar(255) not null, # high level type of transcript proteinId varchar(255) not null, # Protein identifier (not loaded on many older versions of GENCODE) #Indices index(geneId), index(geneName), PRIMARY KEY(transcriptId), index(havanaGeneId), index(havanaTranscriptId), index(ccdsId), index(proteinId) );