[InterMine Dev] orthologues in InterMine -

Julie Sullivan julie at flymine.org
Tue Oct 23 13:24:13 BST 2012


Hi Intikhab!

We don't have a tree, just a homologue pair. The model is this:

  1. A Gene has a collection of Homologues
  2. A Homologue has a:
	- gene (the homologue for gene in #1)
	- evidence code (eg. Amino acid sequence comparison - AA)
	- type (eg. paralogue, orthologue or homologue)

<query name="" model="genomic" view="Gene.primaryIdentifier 
Gene.homologues.homologue.primaryIdentifier" longDescription="" 
sortOrder="Gene.primaryIdentifier asc">
</query>

We have many sources to load homologues available in InterMine:

	treefam
	ensembl compara
	panther*
	orthodb*
	homologene*
	inparanoid
	kegg

* - new, so they may not be in your InterMine release

To use one of these sources, download the data file and put in project XML as 
usual. Here's the docs:

	http://intermine.org/wiki/BioSources

Cheers
Julie



On 23/10/12 08:16, Dr Intikhab Alam wrote:
> Dear Julie,
>
> Thanks, it helped.
>
> Can I ask about orthologues, what is the format in which these are loaded
> and what loader is used. I see that in flymine can generates a tree for
> orthologues, I want to try this out for my mines.
>
> Many Thanks,
>
> Intikhab
>
> --
> --
> Intikhab Alam, PhD
>
> Research Scientist
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4332
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, KSA
> W: http://www.kaust.edu.sa
> T +966 (0) 2 808-2423  F +966 (2) 802 0127
>
>
>
>
>
>
> On 10/22/12 10:55 AM, "Julie Sullivan"<julie at flymine.org>  wrote:
>
>> Hi Intikhab!
>>
>> Your mine gets the list of mines to query from global.web.properties:
>>
>>     ./intermine/webapp/main/resources/webapp/WEB-INF/global.web.properties
>>
>> Maybe you could remove the `intermines` properties and see if that helps?
>>
>> Cheers
>> Julie
>>
>> On 20/10/12 15:30, Dr Intikhab Alam wrote:
>>> Dear Dev at intermine,
>>>
>>> I hope you are doing well,
>>>
>>> I had a question regarding link to other mines.
>>>
>>> How can we enable/disable searching in other mines?, e.g. Yeastmine,
>>> Flymine, modMine search seem to automatically appear on the Gene report
>>> page.
>>>
>>> Many Thanks,
>>>
>>> Intikhab
>>>
>>> Link to other Mines
>>> YeastMine
>>>
>>> No results found.
>>>
>>> FlyMine
>>>
>>> No results found.
>>>
>>> modMine
>>>
>>> No results found.
>>>
>>> metabolicMine
>>>
>>> No results found.
>>>
>>> RatMine
>>>
>>> No results found.
>>>
>>>
>>>
>>> --
>>> --
>>> Intikhab Alam, PhD
>>>
>>> Research Scientist
>>> Computational Bioscience Research Centre (CBRC), Building #2, Office
>>> #4336
>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>> Thuwal 23955-6900, KSA
>>> W: http://www.kaust.edu.sa
>>> T +966 (0) 2 808-2423  F +966 (2) 802 0127
>>>
>>> ________________________________
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>>>
>>>
>>>
>>>
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>
>
> This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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