[InterMine Dev] orthologues in InterMine -

Dr Intikhab Alam intikhab.alam at kaust.edu.sa
Wed Oct 24 08:58:13 BST 2012


Dear Julie,

Thank you so much for your response. I will definitely get the new release of intermine and give it a go. 

I have obtained my orthologues using OrthoMCL software that reports one line per orthologous group as the following line:

ORTHOMCL6227(2 genes,2 taxa):    AAA831C14_00243(AAA831C14) AAA831J21_00092(AAA831J21)

where the first column is orthologous cluster id with information on number of genes and taxa followed by a tab and then gene names (orgranism) delimeted by a space. Is there any source which can handle this type of data format? or can you tell me the format in which I should transform my data and one of your sources are able to load my data?


Organisms and all annotations are already loaded using large xml for each of the organism. If I load the orthologous data using any of the sources you have mentioned, do you expect any conflict for e.g. organism being loaded a second time or I need to do anything in priorities file? 

Many Thanks,

IA.
________________________________________
From: Julie Sullivan [julie at flymine.org]
Sent: Tuesday, October 23, 2012 3:24 PM
To: Dr Intikhab Alam
Cc: dev at intermine.org
Subject: orthologues in InterMine -

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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>>> printing this email.
>>>
>>>
>>>
>>>
>>> _______________________________________________
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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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