[InterMine Dev] gene ontology display problem

Chen, Yian chenyian at nibiohn.go.jp
Wed Aug 5 02:42:44 BST 2015


Hi,

The content is not empty, your screen shot shows that there are 4 GO 
annotations associated with the gene.
Try to add the following settings in your webconfig-model.xml to display 
the ontology term info.

   <class className="org.intermine.model.bio.OntologyAnnotation">
     <fields>
       <fieldconfig fieldExpr="subject.primaryIdentifier"/>
       <fieldconfig fieldExpr="ontologyTerm.identifier"/>
       <fieldconfig fieldExpr="ontologyTerm.name"/>
       <fieldconfig fieldExpr="ontologyTerm.namespace"/>
     </fields>
   </class>

Chen

On 2015/08/05 8:52, Pengcheng Yang wrote:
> Hi Julie Sullivan,
>
> Thank you for your help.
>
> Following your suggestion, I have 1) loaded the GO data source, and 
> then found the Gene ontology still can not be displayed on the gene 
> report page. then I 2) removed the displayer from webconfig-model.xml 
> file, indeed, as you said, there appeared two section in the Other 
> group. But the content is empty as listed below. Is there any other 
> thing I have missed and any other information I can provide to resolve 
> this problem?
>
> Thank you very much!
>
> Best,
> Pengcheng Yang
>
>
>       4 GO Annotation
>
> //Annotation Extension 	//Qualifier
> 	0
> 	0
> 	0
> 	0
>
>
>       4 Ontology Annotations
>
> //Annotation Extension 	//Qualifier
> 	0
> 	0
> 	0
> 	0
>
>
>
> On 2015/8/4 17:17, Julie Sullivan wrote:
>> 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
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.intermine.org/pipermail/dev/attachments/20150805/d5a3fe69/attachment-0001.html>


More information about the dev mailing list