[Biopython-dev] [Bug 2833] Features insertion on previous bioentry_id

[Cymon Cox]

2009/6/10 Hilmar Lapp <hlapp at gmx.net>

>
> On Jun 9, 2009, at 6:57 PM, Peter wrote:
>
>  You're not saying in BioSQL bioentry.identifier should for an NCBI GI
>> number *only*, are you?
>>
>
>
> No, absolutely not. It is the "internal database identifier" from where the
> record came from, if that database assigns - and publishes - such
> identifiers. For example, it might be the primary key in some database.
>
> Just keep in mind that accession is required, whereas identifier is not,
> and they are not synonymous. So if you only have one identifier for a
> record, unless you know that it's the GI# and what you have is a GenBank
> record, the identifier would likely be called the accession, and the
> identifier column would remain null.


Thanks Hilmar.

If I'm interpreting you correctly, by implication, the only time a value
that is not a NCBI GI number gets added to the bioentry.identifier, is when
a database (other than NCBI) implements two unique 'identifiers' such that
one would be assigned to the accession and one to the identifier fields.
What are these databases? It would be useful to check that they are being
dealt with correctly.

In which case biopython should not be assigning bioentry.identifier to
record.id when the record.annotations['gi'] is missing.

Cheers, C.




>
>
>        -hilmar
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>


-- 
____________________________________________________________________

Cymon J. Cox

Centro de Ciencias do Mar
Faculdade de Ciencias do Mar e Ambiente (FCMA)
Universidade do Algarve
Campus de Gambelas
8005-139 Faro
Portugal

Phone: +0351 289800909 ext 7909
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Email: cy at cymon.org, cymon at ualg.pt, cymon.cox at gmail.com
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