[InterMine Dev] uniprot and go-annotation failing?

Julie Sullivan julie at flymine.org
Thu Aug 27 16:22:35 BST 2009



Sierra Moxon wrote:
>> Gene is a subclass of BioEntity, and you can't set the priority for 
>> primaryIdentifier twice.  Remove the priority entry for 
>> "BioEntity.primaryIdentifier" and check for any other duplicate 
>> entries, eg. Gene/Protein/BioEntity.name.
>>
> Thanks Julie,
> I don't think I added this in the first place?  Is it possible to remove
> the duplication from the file in SVN, or would that break other things?
> 
> I commented out the entries for BioEntity in genomic_priorities.properties
> and got this error when running uniprot again:
> 
> Caused by: java.lang.IllegalArgumentException: Conflicting values for 
> field org.intermine.model.bio.GeneShadow.symbol between zfin-identifiers 
> (value thrap6) and uniprot-zebrafish (value med30) while comparing: Gene

Gene.symbol seems to be the problem here.  What is your priority config for that 
field?  eg:

Gene.symbol = \
   zfin-identifiers, \
   uniprot, \
   *

> Here is my priority for genes in zfinmine:
> Gene=zfin-identifiers,zfin_genotypes,zfin_expression,go-annotation,uniprot-zebrafish 
> 
> 
> and I loaded zfin-identifiers before uniprot-zebrafish.
> 
> Also, the doc indicates that I should be removing the sub-entity's (I
> think) priority: the Gene primary identifier in this case, or is this a
> different issue?

Different issue.  I think.

> "Note - there is currently a 'bug' with the priority system, the priority
> needs to be defined for the class in which the field is defined, it cannot
> be defined in a class that inherits that field. For example length is
> defined in LocatedSequenceFeature and inherited by Gene and Exon, to
> configure a priority for Gene lengths it must be set for
> LocatedSequenceFeature. It isn't possible to set different priorities for
> each subclass. "
> 
> Thanks and talk to you soon,
> Sierra :)
> 



More information about the dev mailing list