[InterMine Dev] gene ontology display problem

Pengcheng Yang yangpc at biols.ac.cn
Wed Aug 5 04:33:53 BST 2015


Ok, I just want to set in the file on the server and forgot it can be 
configured through website.

Best,
Pengcheng Yang


On 2015/8/5 11:20, Chen, Yian wrote:
> Hi Pengcheng Yang,
>
> To hide "Ontology Annotations" is quite easy.
> 1. Login as administrator.
> 2. Visit any gene report page and find the "Ontology Annotations" section.
> 3. Click on the "Add tags" and add a tag "im:hidden".
>
> See the InterMine document:
> http://intermine.readthedocs.org/en/latest/webapp/report-page/report-page/
> It is described at the last line.
>
> Best,
>
> Chen
>
> On 2015/08/05 12:09, Pengcheng Yang wrote:
>> Hi Chen Yian,
>>
>> Thank you for your help information. The output displayed as 
>> expected. Thank you. And another question is there exists two part 
>> "GO Annotation" and "Ontology Annotations" with the same content [1]. 
>> How can I remain "GO Annotation" only and remove "Ontology Annotations".
>>
>> Thank you.
>>
>> Best,
>> Pengcheng Yang
>>
>> [1] the same content of the two part. (the content has been hided)
>>
>>
>>       4 GO Annotation
>>
>>
>>       4 Ontology Annotations
>>
>>
>>
>> On 2015/8/5 9:42, Chen, Yian wrote:
>>> 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
>>>
>>
>

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