ids and URLs (was Re: [DAS2] Ontologies in DAS/2)

[Andrew Dalke]

[Top-posting summary]

I agree with Chris that the DAS "type"s aren't really types.

Chris Mungall:
> I'm mostly skim the messages here, so I may be missing something, but 
> I'm a little confused by this:
>
> On Feb 8, 2006, at 8:36 AM, Andrew Dalke wrote:
>
>>
>>     http://das.server/../types?ontology=SO:exon
>
> I don't understand this - SO:exon isn't an ontology

I made it up; I mean "whatever the SO term is for an exon".
I think it's SO:0005845 ("single_exon") or SO:0000147 ("exon")


>> PROPOSAL:  Add a "source=" (case-insensitive substring search)
>> field to the types query.  (I don't think there is any contention
>> here so I'll add it.)
>>
>>     http://das.server/../types?ontology=SO:exon;source=Vega
>
> What does 'types' return? A type from an ontology (eg SO:exon) or 
> something else? Why would source be recorded here? Surely source would 
> be a valid constraint on a feature query, but not a type query.

A DAS type is a somewhat strange thing, in the type sense.  It
stores:
   - the link to the ontology
   - a list of the formats available for features of that type
   - this "source" field
   - potentially some per-source data used for depiction, or
      perhaps not

Thomas Down here has this use case.

He has a program which searches for exons.  All of the annotations
it makes for a month are from that program.  He wants them to be
the same type - conceptually "the exons predicted by the program".

Some of that data could be moved into the feature. The feature
can point directly to the ontology, and have a "source".

> Perhaps it's the case that in DAS a 'type' means some kind of 
> arbitrary grouping (eg features of type X and source Y), and 
> 'ontology' means a
> term/type from an ontology. If it isn't too late I'd suggest changing
> these conventions.

That is more like the case.  Got a better name.  "class"?  ROFL.  Or 
not.

It is not a type system.  It is closer to a group than
anything else.  I agree that "type" has connotations which are
not true for this case.

					Andrew
					dalke at dalkescientific.com