[Bioperl-l] Bio::Ontology additions
allenday at ucla.edu
Wed Jul 2 12:35:13 EDT 2003
using this file:
primary relationships are parsed correctly, but secondary relationships
are sometimes not. for instance, for entry CL:0000441 follicle_stem_cell
"follicle stem cell @ISA@ animal_cell" is not correctly parsed, while
"follicle stem cell @ISA@ epithelial_fate_stem_cell" is.
Upon closer inspection i see that the problem might be that
"follicle_stem_cell" is in the incorrectly parsed relationship is referred
to as "follicle stem cell", a synonym of CL:0000441.
This is also a problem with "blastoderm_cell" sometimes being referred to
in relationships as its synonym "blastomere".
So... it really looks like this is a bug with creation relationships
between entities where one or more of the entities is referred to by its
synonym rather than primary name.
On Wed, 2 Jul 2003, Hilmar Lapp wrote:
> Allen could you add a test case (possibly with sample data?) that
> reveals the bug so that we can start fixing it.
> On Sunday, June 22, 2003, at 03:28 PM, Allen Day wrote:
> > done. btw, i've introduced a bug in the parsing of secondary term
> > relationships when they use custom predicates. from what i've seen
> > this
> > doesn't affect the graph structure as the secondary relationships are
> > redundant, but it still needs fixin'...
> > -allen
> > On Sat, 21 Jun 2003, Hilmar Lapp wrote:
> >> On Friday, June 20, 2003, at 11:37 AM, Allen Day wrote:
> >>> So... I have added two new methods to SimpleGOEngine to accomodate
> >>> this:
> >>> add_relationship_type( $type_name, $ontology)
> >>> - adds new relationship types that don't already exist in the
> >>> ontology. creates Bio::Ontology::RelationshipTypeI objects.
> >>> returns 1 on successful creation, undef on failure.
> >>> get_relationship_type( $type_name)
> >>> - returns the previously created Bio::Ontology::RelationshipTypeI
> >>> object, or undef if there isn't one.
> >> It sounds like these could be generally useful (or even required). If
> >> so you may want to consider adding them to OntologyEngineI; generally
> >> speaking the parser may be supplied with an engine implementation
> >> different from SimpleGOEngine (although I believe right now the parser
> >> will throw up for other reasons if you do that ...).
> >> -hilmar
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