Some annotation qualifiers can be nominated to store gene name or gene function. This association can be provided in the INI file during the annotation loading:


[AnnotationSearches]
; Add qualifier name-value to search term {GeneName, GeneFunction}
; Some qualifiers can have a special meaning: they represent gene name and gene function. 
; This will help narrow down the text search specifically for gene name or function in Persephone.
; This section will establish the distinction. The keyword GeneName tells which qualifier is designated as the gene name.
; Important: use qualifier names here, which can be different from the GFF attribute names. For example, if you have introduced a qualifier "transcriptName" by
; renaming the GFF attribute mRNA:Name, then type GeneName=transcriptName.
;SEARCH_TERM=QUALIFIER_NAME
GeneName="Name"
GeneFunction=Description

If needed, the AnnotationSearch values can be added at a later time interactively, from the command prompt - no control file is necessary:

add annotation_search {mapSetId | path}

As usual, reference the map set by MapSetId or MapSetPath:


PS> add annotation_search 16
Map set: /Arabidopsis thaliana/TAIR10
Qualifiers with example values:

Track 'Ensembl':
[0]    db_xref ( 48,315 records) : KEGG_Enzyme:00230+2.7.7.7, KEGG_Enzyme:00240+2.7.7.7, UniParc:UPI0008486B56
[1]       gene ( 48,315 records) : AT1G01010
[2]  locus_tag ( 23,064 records) : 1MMP
[3]       note ( 47,781 records) : (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase-like protein [Source:UniProtKB/TrEMBL;Acc:Q9LX13]
[4] protein_id ( 48,315 records) : AT1G01010.1

What will the qualifier store: gene Name or Function? (N/F): GeneName
Existing qualifier(s) currently used for GeneName: gene

Which qualifier will provide value for GeneName? Type the line [number] from the list above: 4

Nominate 'protein_id' as a qualifier that stores GeneName for map set /Arabidopsis thaliana/TAIR10? (Y/N)Y
Record inserted
DATA_VERSION updated

The list command will confirm the changes:


PS> list annotation_search 16
Qualifiers with special meaning for map set: /Arabidopsis thaliana/TAIR10
        GeneName        gene
        GeneName        protein_id
        GeneFunction    note