[BioSQL-l] Ontology names

[Hilmar Lapp]

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
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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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