[Bioperl-l] Bio::Ontology

[Hilmar Lapp]

It appears that ideally and as one of the first steps of reconciling 
the two designs we should be able to merge ChrisM's VocabTermI and 
ChrisZ's TermI.

The following lists the differences and my votes.

1) Interface naming. My vote goes for the more general TermI, and 
VocabTermI can add vocabulary-specific properties if there are any.

2) Inheritance. My vote goes for largely if not completely 
decoupling Ontologies and Graphs, disregarding that of course in 
many practical cases you will want to execute graph-operations on 
ontologies. I think this can be easily and more flexibly achieved by 
composition rather than inheritance, which would mandate it. Hence, 
my vote is TermI should not inherit from Graph::NodeI or any similar 
interface.

3) identifier() vs ontology_id(). As I posted before, my vote is 
identifier().

4) label(). I'm not sure what this would be and whether it is 
crucial for a Term. ChrisM as the expert, could you comment?

5) definition()'s return value as an object or a string. ChrisM's 
proposal suggests that if you're serious about ontologies, a 
definition is much more than just a string. Adds to the complexity 
though. Nonetheless, I tend to go with the ChrisM's call.

6) each_synonym() vs each_alias(). Synonym sounds more like the 
language of the field, so I'd vote for that. (Actually ChrisM named 
it synonyms(), which is inconsistent with the each_XXX tradition 
Ewan introduced.)

7) each_dblink() vs each_reference. I vote for dblink because 
reference is used in bioperl for literature references.

8) timestamp(). ChrisM, is this crucial to a Term, or does it only 
pertain to those who created the ontology? Is it rather a version()?

9) category(). Isn't this in fact a relationship of the Term? Should 
there or should there not be an each_relationship() method on Term?

These are all the differences as far as I see.

RelationshipI makes a lot of sense to me, except that I think it 
should not inherit from Graph::ArcI, and I'm also not sure why 
Relationships shall have stable identifiers.

Comments/thoughts/votes more than welcome.

	-hilmar

On Thursday, September 19, 2002, at 08:11 AM, Chris Mungall wrote:

> namespace Bio::Ontology
>
> typedef string Identifier
>
> interface VocabTermI extends Bio::Graph::NodeI
>   attribute Identifier identifier
>   attribute string label
>   attribute VocabDefinition definition
>   attribute string[] synonyms
>   add_synonym(string synonym):
>   attribute DBLink[] dblinks
>   add_dblink(DBLink dblink):
>   timestamp(): timestamp
>   category(): VocabTerm
>   is_obsolete(): boolean
>
> interface RelationshipI extends Bio::Graph::ArcI
>   attribute Identifier identifier
>   attribute TermI parent_term
>   attribute TermI child_term
>   attribute TermI relationship_type
>
> interface VocabDefinitionI extends Bio::Root::RootI
>   attribute string definition
>   attribute DBLink reference
>   timestamp(): timestamp
>
>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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