[BioSQL-l] Re: [Open-bio-l] Re: Ontology names

[Michael L. Heuer]

Rather than overload ontology_term, why not create new entities in the
datamodel to support ontology names?  I'd also propose an authority
entity:

authority --* domain (or namespace, or ontology_name) --* ontology_term

Authority should also be used for ontology_relationships

authority --* ontology_relationship


Note this provides legal LSIDs for instances of ontology_term:

<lsid> := <authority>:<namespace>:<value>:<version>
       := <authority>:<namespace>:<ontology_term>:<version>

   michael


On Fri, 27 Sep 2002, David Block wrote:

> The obvious ones should be enumerated as well:
> Sequence Ontology
> Relationship Ontology (coming soon)
> Molecular Function
> Cellular Component
> Biological Process
>
> any more?
>
> On Friday, September 27, 2002, at 11:52  AM, Hilmar Lapp wrote:
>
> > As may have been anticipated (at least I did), ontology_term is going
> > to be used quite heavily and in important places. Essentially we're
> > going to use several ontologies, and they'll all be in ontology_term.
> > The way to constrain a term to a certain ontology is by its FK to
> > itself (category_id), which should point to the name of the ontology
> > the term belongs to. There is a UK on (term_name,category_id).
> >
> > Ontology names will likely (but are not required to) have NULL in
> > category_id.
> >
> > Is everyone OK with this so far?
> >
> > In order to get things out by a Bio* package other than the one that
> > put it in, we need to agree on ontology names in the first place (but
> > also on terms).
> >
> > I am right now using the following ontology names:
> >
> > - 'Annotation Tags': the keys (tags, qualifier names) for simple
> > annotation values (qualifier values)
> > - 'SeqFeature Keys': the keys of seqfeatures ($feat->primary_tag() slot
> > in bioperl; e.g., the genbank feature key, or swissprot feature key,
> > like 'CDS', 'mRNA', ...)
> > - 'SeqFeature Sources': the source names of seqfeatures
> > ($feat->source_tag() slot in bioperl; like 'swissprot', 'genscan', etc).
> >
> > There is already a pre-defined number of terms for location properties
> > (min_start, etc), but without an ontology. I'd like to put them into an
> > ontology and suggest the name 'Location Tags' for it.
> >
> > Any ideas, comments, etc. more than welcome.
> >
> > 	-hilmar
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> >
> --
> David Block                                  dblock@gnf.org
> GNF - San Diego, CA             http://www.gnf.org
> Genome Informatics / Enterprise Programming
> Weblog:      http://radio.weblogs.com/0104507/
>
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