[InterMine Dev] gene ontology display problem

Julie Sullivan julie at flymine.org
Tue Aug 4 09:38:23 BST 2015


All evidence codes should work.

This is the query that displayer runs:

<query name="" model="genomic" 
view="Gene.goAnnotation.ontologyTerm.parents.name 
Gene.goAnnotation.ontologyTerm.name 
Gene.goAnnotation.evidence.code.code" longDescription="" 
sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc" 
constraintLogic="(A or B or C) and D">
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name" 
code="A" op="=" value="biological_process"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name" 
code="B" op="=" value="molecular_function"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name" 
code="C" op="=" value="cellular_component"/>
   <constraint path="Gene" code="D" op="LOOKUP" value="eve" extraValue=""/>
</query>


Run that query in your own mine. Do you get results?

To run that query, go to the QueryBuilder tab, click on "import query 
from xml. Copy and paste the above and click on submit. This query is 
looking for the fruit fly gene "eve". You'll want to replace "eve" with 
the identifier for your gene. Let me know if you need help.





On 04/08/15 09:19, Pengcheng Yang wrote:
> Hi,
>
> I have loaded go-annotation, and "select   * from genegoannotation;"
> return two columns of gene and goannotation. However, when I checked the
> gene report page, the gene ontology display always nothing although
> there indeed GO annotation for that gene. I have searched mail archive
> and found a similar questions has been asked:
> http://gmod.827538.n3.nabble.com/GO-evidence-td4026625.html. The
> evidences in my go-annotation file all are "IEA". Is this the reason?
>
> The gene ontology displayer part in the
> mymine/webapp/resources/webapp/WEB-INF/webconfig-model.xml is:
>
>     <reportdisplayer
> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>                       jspName="model/geneOntologyDisplayer.jsp"
> replacesFields="goAnnotation,ontologyAnnotations"
>                       placement="Genomics"
>                       types="Gene"/>
>
> Thanks a lot!
>
> Any suggestions are appreciated.
>
> Best,
> Pengcheng Yang
>
>
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