[InterMine Dev] protein2ipr loader

Pengcheng Yang yangpc at biols.ac.cn
Wed Jul 22 15:21:08 BST 2015


Dear Sergio,

Thank you for your reply and the information.

I have write a perl script to convert the protein2ipr table into xml 
file following the model defined at 
https://github.com/chenyian-nibio/targetmine/blob/targetmine/bio/sources/targetmine/protein2ipr. 
The data has been successfully loaded. Any problem will be posted to 
this thread in the future.

Thank you!

Best,
Pengcheng Yang


On 2015/7/22 17:47, sergio contrino wrote:
> hi Pengcheng,
> the source will be integrated in intermine 1.6, due in the autumn.
> see ticket
> https://github.com/intermine/intermine/issues/169
>
> you could use the implementation in araport,
> https://github.com/Arabidopsis-Information-Portal/intermine/tree/stable/bio/sources/protein2ipr 
>
>
> or refer directly to the original one in targetmine
> https://github.com/chenyian-nibio/intermine/tree/chenyian/bio/sources/targetmine/protein2ipr 
>
>
> thanks!
> sergio
>
>
>
> On 22/07/15 04:37, Pengcheng Yang wrote:
>> Hi InterMiners,
>>
>> Following the InterMine documentation, I want to load the protein2ipr
>> data, but the protein2ipr sources directory not exist.
>>
>> So I searched the intermine issues and found this thread
>> https://github.com/intermine/intermine/issues/169, then redirected to
>> the protein2ipr sources
>> https://github.com/chenyian-nibio/targetmine/blob/targetmine/bio/sources/targetmine/protein2ipr. 
>>
>> I have put the protein2ipr to the intermine/bio/sources directory and
>> test with ant and found that the "package org.intermine.model.bio does
>> not exist". It seems that this converter used not existed package
>> org.intermine.model.bio. I also do not found this package in
>> http://www.flymine.org/api/ and the intermine latest release.
>>
>> Just for your information and is there possible to integrate this
>> sources into intermine in the future?
>>
>> Best,
>> Pengcheng Yang
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>





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