[Bioperl-l] GO annotatinos in BioPerl. A tentative proposal...

Mark Wilkinson mwilkinson@gene.pbi.nrc.ca
Thu, 05 Apr 2001 11:55:19 -0600

Notice from my subject line that I am discussing Annotatinos, rather than
actual annotations...  "Annotatino" is Spanish for "small annotated thing".


w.r.t. the question of whether GO will become a standard... I may be biased,
but I think the winds are blowing strongly in this direction!

I would tend to side with Ewan on the <prejudice/> against Bio::Annotation.  It
seems quite shallow and unstructured.  This is one thing that I have quickly
come to appreciate about GO - that it does ~impose a hierarchy for its
annotation format (at a minimum:Evidence_type/ref/ref...,
Evidence_type/ref/ref).  This makes it much easier to extract the information
back out of teh Annotation object and properly slot it into a local database.
Currently my GO_Annotation object doesn't hold the full extent of this
hierarchy or the different types of evidence/annotation data; it is in its
infancy (I just noticed that Chris has written a message to the group and I
just bet that he is saying the same thing...), but it can be easily expanded
from here.  I just wanted some additional input on the idea before I take it
too far in any direction.

I like Ewans container idea, personally...


Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK