[InterMine Dev] Interesting problem

Daniela Butano daniela at intermine.org
Wed Jan 29 11:14:57 GMT 2020


Hi Paulo,

I noticed that the Allele class doesn't extend BioEntity.....is it 
intentional?

It might be possible that wormine loads other bio-sources which contain 
in their addionals.xml files a different definition of Allele (which 
extend BioEntity)?

Daniela

On 29/01/2020 03:37, Paulo Nuin wrote:
> Hi everyone
>
> We are stuck with a really interesting problem, that came back 2 or 3 
> releases ago. We have a class in WormMine, Allele, that is getting 
> duplicated and showing up in the singular Allele and plural Allele, 
> with mostly identical items on the output. I grepped my whole code and 
> I don’t see anywhere the class/word Alleles showing up (we have 
> affectedByAlleles).
>
> An example of the result is attached (3 screen caps).
>
> The class Allele is below.
>
>
>         <class name="Allele" is-interface="true">
>           <attribute name="naturalVariant" type="java.lang.String" />
>           <attribute name="method" type="java.lang.String" />
>           <attribute name="type" type="java.lang.String" />
>           <attribute name="publicName" type="java.lang.String" />
>           <attribute name="otherName" type="java.lang.String" />
>           <attribute name="KOAllele" type="java.lang.String" />
>           <attribute name="NBPAllele" type="java.lang.String" />
>           <attribute name="nemaAllele" type="java.lang.String" />
>           <attribute name="amber_UAG" type="java.lang.String" />
>           <attribute name="ochre_UAA" type="java.lang.String" />
>           <attribute name="opal_UGA" type="java.lang.String" />
>           <attribute name="donorSpliceSite" type="java.lang.String" />
>           <attribute name="acceptorSpliceSite" type="java.lang.String" />
>           <attribute name="productionMethod" type="java.lang.String" />
> <!--      <attribute name="sequenceDetails" type="java.lang.String" /> -->
>           <attribute name="status" type="java.lang.String" />
> <!--      <attribute name="affects" type="java.lang.String" /> -->
>           <attribute name="NemaGENETAGConsortiumAllele" 
> type="java.lang.String" />
> <!--      <attribute name="missense" type="java.lang.String" /> -->
>           <attribute name="detectionMethod" type="java.lang.String" />
>           <attribute name="positiveClone" type="java.lang.String" />
>           <attribute name="typeOfMutation" type="java.lang.String" />
>           <attribute name="sequenceStatus" type="java.lang.String" />
>           <attribute name="KOConsortiumAllele" type="java.lang.String" />
>           <attribute name="missenseChange" type="java.lang.String" />
>           <attribute name="mutagen" type="java.lang.String" />
>           <attribute name="natureOfVariation" type="java.lang.String" />
>           <attribute name="interpolatedMapPosition" 
> type="java.lang.String" />
>           <attribute name="species" type="java.lang.String" />
>           <attribute name="rearrangement" type="java.lang.String" />
>           <attribute name="linkedTo" type="java.lang.String" />
>           <collection name="phenotype" referenced-type="Phenotype" 
> reverse-reference="phenotypeAllele" />
>           <collection name="phenotypeNotObserved" 
> referenced-type="Phenotype" 
> reverse-reference="phenotypeAlleleNotObserved" />
>           <collection name="affectsGenes" referenced-type="Gene" 
> reverse-reference="affectedByAlleles" />
>           <collection name="affectsCDSs" referenced-type="CDS" 
> reverse-reference="affectedByAlleles" />
>           <collection name="affectsTranscripts" 
> referenced-type="Transcript" reverse-reference="affectedByAlleles" />
>           <!--<collection name="strains" referenced-type="Strain" 
> reverse-reference="variations" /> -->
>           <collection name="fromLabs" referenced-type="Laboratory" 
> reverse-reference="variations" />
>           <collection name="geneClass" referenced-type="GeneClass" 
> reverse-reference="variations" />
>           <collection name="genes" referenced-type="Gene" 
> reverse-reference="allele" />
>         </class>
>
>
> I am at loss here. We have tried most things in our tool belt to 
> define why this is happening to no success. Any help appreciated.
>
> Thanks
>
> Paulo
>
>
>
>
>
>
> \
>
> _______________________________________________
> dev mailing list
> dev at lists.intermine.org
> https://lists.intermine.org/mailman/listinfo/dev
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200129/5e5761e4/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 20.32.45.png
Type: image/png
Size: 91170 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200129/5e5761e4/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 19.42.02.png
Type: image/png
Size: 149420 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200129/5e5761e4/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 19.42.08.png
Type: image/png
Size: 156047 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200129/5e5761e4/attachment-0005.png>


More information about the dev mailing list