Question: File Format For Storing Annotations For Both Organism And Sequence?
0
gravatar for hansyuhans
6.3 years ago by
hansyuhans0
hansyuhans0 wrote:

Hello,

Is there a file format that allows me to store properties of an organism and its sequence annotations (namely SNPs)?

Can I do it with GFF3? Or is GFF3 only for sequence annotations?

So for example (hypothetically), the file would contain information about the organism's color, average size, and planet of origin, and also its SNPs and other sequence annotations.

Thanks!

format • 1.2k views
ADD COMMENTlink modified 9 days ago by Biostar ♦♦ 20 • written 6.3 years ago by hansyuhans0
1
gravatar for Alex Reynolds
6.3 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

You might look at an example SNP GFF3 file from SNPedia as a starting point, using lowercase attributes to store custom data.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Alex Reynolds28k

Thanks for answering! I would have no problem storing SNPs in GFF3 file but is there an accepted method for storing organism information in GFF3 as well? I understand that each line in GFF3 identifies a chromosome (or another form of sequence) for which the annotation is for, but properties of an organism do not belong to any sequences so it does not seem legitimate.

ADD REPLYlink written 6.3 years ago by hansyuhans0
1
gravatar for Zev.Kronenberg
6.3 years ago by
United States
Zev.Kronenberg11k wrote:

GFF3 uses vocabulary from the sequence ontology.

http://www.sequenceontology.org/browser/obob.cgi

Check to see if there are terms that describe what you want. Also GVF annotates and stores variants, and it also uses sequence ontology vocabulary.

ADD COMMENTlink written 6.3 years ago by Zev.Kronenberg11k
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