[InterMine Dev] gene ontology display problem

Pengcheng Yang yangpc at biols.ac.cn
Tue Aug 4 10:13:20 BST 2015


Hi Julie Sullivan,

I have created the query using "import query from xml", changed the 
"eve" to the gene id in mymine. But nothing returned.

I have the following information to share:
1) I haven't load the go data because the long time need and I just want 
to test the go-annotation data.
2) I have loaded go-annnotation data, which can be valided by "select * 
from genegoannotation", and the gene report page give a link to the Data 
Set of GOannotation page. When I click to the latter page, there will 
display all the genes with GO annotation. When I click "Showl all in a 
table", and then add the columns "Manage Columns" and add "Ontology 
Name", "Ontology Term Identifier" and "Ontology Term Name", nothing 
returned.
3) I want to display the gene ontology information on the gene report 
webpage.

Many thanks!

Best,
Pengcheng Yang

On 2015/8/4 16:38, Julie Sullivan wrote:
> 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
>>
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>





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