null primary ids for C.elegans in HomoloGene

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

null primary ids for C.elegans in HomoloGene

Howie Motenko
For interoperability, when attempting to load homologue data from HomoloGene into MouseMine the gene primary identifier is null for all genes. I noticed RatMine has the same results/problem.

Here's the query for RatMine:
<query name="" model="genomic" view="Homologue.gene.primaryIdentifier Homologue.gene.symbol Homologue.gene.name Homologue.gene.sequenceOntologyTerm.name Homologue.gene.organism.name Homologue.gene.dataSets.name Homologue.gene.dataSets.url" longDescription="" sortOrder="Homologue.gene.primaryIdentifier asc" constraintLogic="A and B">
  <constraint path="Homologue.gene.primaryIdentifier" code="A" op="IS NULL"/>
  <constraint path="Homologue.gene.organism.taxonId" code="B" op="=" value="6239"/>
</query>

Any idea of why this is happening?



Gratefully,
Howie

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: null primary ids for C.elegans in HomoloGene

Julie Sullivan
I've made a ticket:

https://github.com/intermine/intermine/issues/469

I think it stems from the problem that homologene uses a mix of symbols,
names and aliases (for yeast anyway).



On 15/11/13 16:48, Howie Motenko wrote:

> For interoperability, when attempting to load homologue data from
> HomoloGene into MouseMine the gene primary identifier is null for all
> genes. I noticed RatMine has the same results/problem.
>
> Here's the query for RatMine:
>
> <query name="" model="genomic" view="Homologue.gene.primaryIdentifier Homologue.gene.symbol Homologue.gene.name Homologue.gene.sequenceOntologyTerm.name Homologue.gene.organism.name Homologue.gene.dataSets.name Homologue.gene.dataSets.url" longDescription="" sortOrder="Homologue.gene.primaryIdentifier asc" constraintLogic="A and B">
>    <constraint path="Homologue.gene.primaryIdentifier" code="A" op="IS NULL"/>
>    <constraint path="Homologue.gene.organism.taxonId" code="B" op="=" value="6239"/>
> </query>
>
>
> Any idea of why this is happening?
>
>
>
> Gratefully,
> Howie
>
> The information in this email, including attachments, may be
> confidential and is intended solely for the addressee(s). If you believe
> you received this email by mistake, please notify the sender by return
> email as soon as possible.
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: null primary ids for C.elegans in HomoloGene

Jayaraman, Pushkala
Yeah as I said to Julie,
We need to know exactly what we need to use in the hommologene loader config.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Julie Sullivan
Sent: Friday, November 15, 2013 10:59 AM
To: Howie Motenko; [hidden email]
Subject: Re: [InterMine Dev] null primary ids for C.elegans in HomoloGene

I've made a ticket:

https://github.com/intermine/intermine/issues/469

I think it stems from the problem that homologene uses a mix of symbols, names and aliases (for yeast anyway).



On 15/11/13 16:48, Howie Motenko wrote:

> For interoperability, when attempting to load homologue data from
> HomoloGene into MouseMine the gene primary identifier is null for all
> genes. I noticed RatMine has the same results/problem.
>
> Here's the query for RatMine:
>
> <query name="" model="genomic" view="Homologue.gene.primaryIdentifier Homologue.gene.symbol Homologue.gene.name Homologue.gene.sequenceOntologyTerm.name Homologue.gene.organism.name Homologue.gene.dataSets.name Homologue.gene.dataSets.url" longDescription="" sortOrder="Homologue.gene.primaryIdentifier asc" constraintLogic="A and B">
>    <constraint path="Homologue.gene.primaryIdentifier" code="A" op="IS NULL"/>
>    <constraint path="Homologue.gene.organism.taxonId" code="B" op="=" value="6239"/>
> </query>
>
>
> Any idea of why this is happening?
>
>
>
> Gratefully,
> Howie
>
> The information in this email, including attachments, may be
> confidential and is intended solely for the addressee(s). If you believe
> you received this email by mistake, please notify the sender by return
> email as soon as possible.
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev