[BioSQL-l] synonyms for ontology terms

[Matthew Pocock]

I'm not currently writing a BioSQL implementation, so I guess that makes 
my view partialy moot. My position is that relationships between terms 
shold be held in the ontology. There's nothing to stop us annotating the 
synonym relation with info itself e.g. synonym _isa_ identity_relation. 
At that point, a lot of the special case code will go away. You could 
ask for the transient closure of a,b over (union _isa_, 
identity_relation) to search if a _isa_ b taking into account all synonyms.

Re anonymous classes: I think some ontologies that are used as glorified 
dictionaries/lexicons/thesauruses flag all terms as to wether they are 
human-consumable or not - so you can add in as many 'plumbing' concepts 
as you need to make the ontology reasonable (all puns intended) without 
a user needing to see things that are inherently not for human 
consumption. By anonymous classes, do you mean terms that have no sane 
name (e.g. union isa, identity), or something else?

M

Chris Mungall wrote:
> Currently in GO, we do not use 'synonym' in the sense of truly synonymous
> - eg you cannot insert a synonym of term X into a sentence and have the
> sentence mean exactly the same thing.
> 
> At some point we will distinguish between aliases, exact-synonyms,
> more-specific-synonyms and more-general-synonyms. There is a good case for
> putting these in the term table with the above new relationship types.
> 
> I'm neutral as to how it's done - one way you have a schema that is more
> stable but punt more to the code layer - also more consistent with OWL,
> Cyc, whatever; the other way everything is explicit in the schema.
> 
> regarding identifiers - most ontology languages allow anonymous classes, I
> think we'll have to bite the bullet eventually.
> 
> the dbxref of a synonym can always be regarded as
> 
> dbname = english_language
> accession = synonym
> 
> you can't have two seperate synonyms with the same textual string by
> definition


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