[InterMine Dev] gene ontology display problem

Julie Sullivan julie at flymine.org
Tue Aug 4 10:17:35 BST 2015


You will have to load GO data source to use the GO data displayer on the 
report page.

You can still query for the data. You could also remove the displayer 
from the XML file and it might show the raw data on the report page 
instead. Try that?

On 04/08/15 10:13, Pengcheng Yang wrote:
> 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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