[Bioperl-l] Annotation proposal

Mark Wilkinson mwilkinson@gene.pbi.nrc.ca
Fri, 06 Apr 2001 15:38:46 -0600

Ewan Birney wrote:

> I will need help designing Evidence interface. Here is a stab
>     Bio::Annotation::EvidenceI
>     $evidence->type # string, one of "EVI_SIMILARITY,EVI_CURATOR,EVI_EXPERIMENT"
>     @dblink = $evidence->referrals # array of dblinks. Can be assummed that
>           SIMILARITY --- give database link
>           EXPERIMENT --- give pubmed link or pseudo-pubmed link
>           CURATOR    --- People object, which implements Bio::DBLinkI,
>                          with email == primary_id and name == optional_id
>           UNKNOWN    --- Means unknown

Evidence is also a controlled vocab in GO (at my last count, 10 codes) so it might
be worth having that loaded "on the fly" based on the

@types = AnnotationContainer->all_types

rather than hard-coding it into our interface.   Something like:

@evi_codes = Annotation->all_evidence_codes($type);

My earlier question remains, however: within BioPerl are these vocabularies static
(i.e. cvs-commited) or dynamic (pulled from a server)?  There are plus's und
minus's to each option...  and somebody is going to be unhappy no matter what we
decide because we are forcing someone to do something:  Either we don't enforce
vocab, which defeats the purpose of making the tool in the first place, or we
"force" the various ontology groups to commit the current-state of their vocab into
BioPerl on a regular basis, or we "force" the various ontology groups to set up
vocab servers, or we "force" bioperl users to hunt down and discover for themselves
what vocabularies exist out there, and load them onto their local machines in a
correct format (also static).  No matter how you look at it, someone is going to be

My personal preference would be a DAS-like method of having the ontologies
advertise/serve their vocabs through a standard set of query terms... but we can't
"force" them to do so...

Again, we come back to the need for a meeting like the one Dave and I are proposing
to host here in September:  Bring these database developers/curators together to
discuss an organized method for distributing their 'wares' (of all types)...  Such
a meeting is (IMHO) desperately needed...  Lincoln/Sean/Robin & the DAS project are
making laudable progress w.r.t. distributing sequence & annotation, but I think the
scope of the annotation-distribution problem is growing to include some issues that
are not currently part of DAS's "problem-space" (I may be completely wrong on
this!  If so, DAS-developers please set me straight!).  I worry about designing the
set of modules we are discussing in this thread without having a clear idea of
where we are going to get the controlled vocabularies from...


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