The --symbol_col argument specifies column for standard_name. The default value is 2
The --systematic_col argument specifies column for systematic_name. The default value is 3
In the gene_info.gz file from Entrez, the third column is Symbol and the fourth is LocusTag. Here is the definition I found for LocusTag:
Locus tag corresponds to the systematic feature qualifier used by the international sequence collaboration (INSDC, DDBJ/EMBL/GenBank) and can be assigned by sequence submitters as a unique, systematic gene descriptor. When such a value is not available from submitted sequence, the identifier from a collaborating model organism database is used. Locus tag is often used to anchor a link to a database other than Gene. Locus tag may also be used as the preferred symbol if an official symbol has not been identified for a gene.
The Entrez Gene file Homo_sapiens.gene_info.gz doesn't have LocusTag. Both Homo_sapiens.gene_info.gz and gene_info.gz have a column Symbol_from_nomenclature_authority.
So what do standard_name and systematic_name refer to? And should these fields be renamed to from name to symbol?
"""
Bitbucket issue #5 (priority: minor) https://bitbucket.org/greenelab/adage-server/issues/13/determine-how-to-link-to-ml_source_file
@dhimmel commented: """ I'm tying to understand the difference between
standard_nameandsystematic_name. According tomanagement/commands/genes_load_geneinfo.py--symbol_colargument specifies column forstandard_name. The default value is 2--systematic_colargument specifies column forsystematic_name. The default value is 3In the
gene_info.gzfile from Entrez, the third column isSymboland the fourth isLocusTag. Here is the definition I found for LocusTag:The Entrez Gene file
Homo_sapiens.gene_info.gzdoesn't haveLocusTag. BothHomo_sapiens.gene_info.gzandgene_info.gzhave a columnSymbol_from_nomenclature_authority.So what do
standard_nameandsystematic_namerefer to? And should these fields be renamed to fromnametosymbol? """