[InterMine Dev] sources for load expression data

Pengcheng Yang pengchy at gmail.com
Tue Jul 21 09:54:18 BST 2015


Dear Sergio,

Thanks for your reply and the helpful information. I will carefully 
check this file to load my own data. This site is great that I haven't 
found before.

Thanks again for your help on my questions.

Best,
Pengcheng Yang

On 2015/7/21 16:42, sergio contrino wrote:
> dear Pengcheng,
> in modmine the model addition were all collected in this file
>
> https://github.com/modENCODE-DCC/modmine/blob/dev/modmine/dbmodel/resources/modencode-metadata_additions.xml 
>
>
> the ones you are looking for should be at the bottom.
> please let us know if this does not help
> thanks!
> sergio
>
>
>
> On 21/07/15 02:02, Pengcheng Yang wrote:
>> Dear Sergio,
>>
>> Thank you for your reply. I want to construct our Mine data warehouse.
>> InterMine is a flexible and powerful database framework. Thank you for
>> your work on this project.
>>
>> A question for the <model>_additions.xml, the content of the two files
>> from modmine/worm-expression-score and modmine/fly-expression-score both
>> do not define any models in the InterMine release. Could you please send
>> these two files to me as a reference?
>>
>> Thank you and best wishes,
>>
>> Pengcheng Yang
>>
>> On 2015/7/20 18:08, sergio contrino wrote:
>>> dear Pengcheng,
>>> thank you for your suggestion. we could try to provide a
>>> (configurable) default loader. for the moment it should be feasible to
>>> adapt one of the example you mentioned for your needs. the 2 modmine
>>> ones are using data from a tab separated file, which i think is what
>>> you describe as table format.
>>> best
>>> sergio
>>>
>>>
>>> On 20/07/15 09:56, Pengcheng Yang wrote:
>>>> Hi,
>>>>
>>>> I have searched the mail list archive, the issues in github/intermine
>>>> and the related Mines sources file. Existed sources for expression 
>>>> data
>>>> are fly/flybase-expression, modmine/fly-expression-score,
>>>> modmine/worm-expression-score and ratmine_bio_sources/geo*. Is it
>>>> possible for InterMine provide a general source to load gene 
>>>> expression
>>>> data in table format. Related questions is to group samples, such as
>>>> tissues, developmental stages and other treatments.
>>>>
>>>> Best,
>>>> Pengcheng Yang
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> dev at intermine.org
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>
>>>
>>
>>
>




More information about the dev mailing list