[BioSQL-l] Bug in loading duplicate but non-identical swissprot
elia at tll.org.sg
Thu Apr 17 17:56:35 EDT 2003
> Once it's been located you can just say $reference->store(), and the
> medline ID would be updated.
> The problem is in locating
Not sure I follow... as I say right now I inverted the logic in the
get_unique_key_query and it stores the medline fine as well as not
duplicating the reference...
> , and I'd be happy to hear how the 'old' bioperl-db would have solved
> this, given that it did not employ the solution strategy outlined in
> the aforementioned thread under 3)
;) Sorry, I was talking about the veeeery old bioperl-db back in the
days when we wrote it, of course it was nothing comparable and nothing
robust, but what I meant is I could have easily put in special case
code... don't worry I guess I am just too lost as yet and am trying to
find my way around BioSQL.
> The problem is that one and the same reference isn't always given with
> the same literal title/author/journal or medline ID. I.e., you do not
> know a-priori which search is going to locate the reference at hand in
> the database. Sometimes (in fact, very often) it is going to be the
> medline ID, *not* the CRC (due to slight variations in authors or
> journal between say Swissprot and genbank). It could, however, also be
> the pubmed ID. Or indeed the CRC.
Yep, got that...
> What needs to be done is overriding find_by_unique_key() in
> Bio::DB::BioSQL::ReferenceAdaptor and calling the inherited method
> with the three searches until it is found. I can do this tomorrow
> (today that is). It shouldn't be that hard.
Ok, that's much clearer, it's end of day here and beginning of
long-weekend, but if you don't find the time to do it I'll be happy to
give it a shot after the week-end.
> That's not really such a different angle. More or less, this is what I
> have been using it for. The problem you've encountered is just one we
> didn't have before Singapore (not because of the schema changes, but
> because swissprot changed).
Ok, understood, as I said above, I am just exposing my ignorance,
should be back on top of things as I get into it, I already am starting
to make some sense of it.
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