[InterMine Dev] sources for load expression data

sergio contrino sergio at modencode.org
Tue Jul 21 09:42:40 BST 2015


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
>>>
>>
>
>

-- 
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org



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