[BioSQL-l] error loading uniprot release 49.6 into mysql

[s.rayner at att.net]

I found where the script is hiccuping....

The Uniprot release contains lines with identical annotation for the RL keyword for two different sequences.

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First occurence...  
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ID   1433T_PONPY    STANDARD;      PRT;   245 AA.
AC   Q5RFJ2; Q5RDK2;
DT   05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2005, sequence version 2.
DT   18-APR-2006, entry version 13.
DE   14-3-3 protein theta.
GN   Name=YWHAQ;
OS   Pongo pygmaeus (Orangutan).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Pongo.
OX   NCBI_TaxID=9600;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Brain cortex, and Kidney;
RG   The German cDNA consortium;
RL   Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.  <======  Not Unique


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Second occurence...  
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ID   1433G_PONPY    STANDARD;      PRT;   246 AA.
AC   Q5RC20;
DT   05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2005, sequence version 2.
DT   18-APR-2006, entry version 13.
DE   14-3-3 protein gamma.
GN   Name=YWHAG;
OS   Pongo pygmaeus (Orangutan).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Pongo.
OX   NCBI_TaxID=9600;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Heart;
RG   The German cDNA consortium;
RL   Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.   <======  Not Unique



in these two cases the generated CRC key is identical and so MySQL throws a wobbly.

if i look at the MySQL entry in the REFERENCE table for the first sequence
------+-------+---------+----------------------+
|          139 |      NULL | Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases. | NULL  | NULL    | CRC-E7973FEA4B5611DC |
+--------------+-----------+----------------------------------------------------

and the error when the script choked was 

 MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were 
 ("","","Submitted (NOV-2004) to the EMBL/GenBank/DDBJ 
 databases.","CRC-E7973FEA4B5611DC","","","") FKs (<NULL)
 Duplicate entry 'CRC-E7973FEA4B5611DC' for key 3

hence the problem.

I'm guessing i'm not the first person to encounter this, but dont see any hints for an easy way around this.  

any suggestions....?

ta