Issue 107: Add gene name property to proteins and UI to support it

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:3
Milestone:2.6
Opened:2011-11-09 by Brendan MacLean
Changed:2015-07-06 by Brendan MacLean
Resolved:2014-08-28 by Brendan MacLean
Resolution:Fixed
Closed:2015-07-06 by Brendan MacLean
2011-11-09 Brendan MacLean
Title»Add gene name property to proteins and UI to support it
Assigned To»vsharma@u.washington.edu
Type»Defect
Area»Skyline
Priority»3
At some point we should add a gene name property to proteins, both in the document tree and in the background proteome table. We would need some way to extract gene names from FASTA headers based on regular expressions. This might be done individually for each FASTA file when it is:
- Added to a background proteome
- Imported through File / Import / FASTA
- Pasted into the document

Or we could add a Settings / Options form, with a tab for a list of regular expressions to try on every FASTA header, e.g.
" GN=([^ ]+) "
" GENE_SYMBOL=([A-Z][a-z]+) "

We could pre-populate this list with expressions we know of, and the user could add any formats specific to their work.

When we have gene symbols we could use them in the Edit / Unique Peptides form. People have asked for this to help look for peptides that are unique to a gene when that gene may have multiple isoforms.

We can also add links in some places to allow getting gene information on the web.

2014-01-08 Brendan MacLean
Assigned ToVagisha»bspratt
This is your area now. Not sure when you will get to it, but it has been of interest for a long time.

2014-02-04 Brendan MacLean
TypeDefect»Todo

2014-02-04 Brendan MacLean
Milestone»2.6

2014-04-14 Brian Pratt
Not setting this to resolved quite yet due to these details:

When we have gene symbols we could use them in the Edit / Unique Peptides form. People have asked for this to help look for peptides that are unique to a gene when that gene may have multiple isoforms.

We can also add links in some places to allow getting gene information on the web.

2014-08-28 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned Tobspratt»Brendan MacLean
This is done. Add new issues for anything left that needs to be done relating to this.

2015-07-06 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest