[BioSQL-l] Seqfeature_Source

[Thomas Down]

On Thu, Sep 19, 2002 at 04:17:40PM -0700, Hilmar Lapp wrote:
> 
> Of course <eye opener> -- I overlooked that the association already 
> exists. So what about putting seqfeature_source there as well (i.e., 
> as a qualifier?)

How do you plan to do this?  I can think of three possibilities:

  - Have a standard tag for seqfeature_source, and then put
    the source value (as a string) in the current
    seqfeature_qualifier_value table.  I don't have any particular
    objections to this, but it's got the same problem as putting
    the source as a text attribute in the main seqfeature
    table: it leaves the source as an opaque string.

  - Add a second qualifier_value table, for associations
    in which the value part is a second ontology_term.  This
    might have uses beyond storing the source.

  - Just tag each seqfeature with a particular ontology_term which
    defines its source.  This could go in seqfeature_qualifier_value
    will a NULL value.  Quite elegant, but really requires some
    `proper' ontology support (rather than just the current stuff,
    which is just controlled vocab).  At least enough to be
    able to specify which ontology_terms are valid as sources.

All of these are potentially workable.  None are simpler than the
current setup, though :-(.

      Thomas.