[BioMart Users] accessing the ensemble mart archives using the API

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[BioMart Users] accessing the ensemble mart archives using the API

Christophe Klopp
Hi,

Which host and port have I to use to query the Ensembl archive mart
databases using the API?

Cheers

Christophe

--
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
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Re: [BioMart Users] accessing the ensemble mart archives using the API

Syed Haider-2
Hi Christophe,

Follow this link below and then choose the version you prefer, then go
to Biomart link and you will see the URL:port

http://www.ensembl.org/Help/ArchiveList

Best,
Syed

On 12/10/2011 13:03, Christophe Klopp wrote:
> Hi,
>
> Which host and port have I to use to query the Ensembl archive mart
> databases using the API?
>
> Cheers
>
> Christophe
>
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Re: [BioMart Users] accessing the ensemble mart archives using the API

Christophe Klopp
Hi Syed,

If I choose lets' say Ensembl 62: Apr 2011 and go to the corresponding biomart http://apr2011.archive.ensembl.org/biomart/martview where do I find the URL:port ?

Cheers

Christophe


Le 12/10/2011 14:07, Syed Haider a écrit :
Hi Christophe,

Follow this link below and then choose the version you prefer, then go to Biomart link and you will see the URL:port

http://www.ensembl.org/Help/ArchiveList

Best,
Syed

On 12/10/2011 13:03, Christophe Klopp wrote:
Hi,

Which host and port have I to use to query the Ensembl archive mart
databases using the API?

Cheers

Christophe


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

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Re: [BioMart Users] accessing the ensemble mart archives using the API

Rhoda Kinsella
Hi Christophe
You can access the archived marts at martdb.ensembl.org. Connection details are here:


Regards
Rhoda



On 12 Oct 2011, at 13:58, Christophe Klopp wrote:

Hi Syed,

If I choose lets' say Ensembl 62: Apr 2011 and go to the corresponding biomart http://apr2011.archive.ensembl.org/biomart/martview where do I find the URL:port ?

Cheers

Christophe


Le 12/10/2011 14:07, Syed Haider a écrit :
Hi Christophe,

Follow this link below and then choose the version you prefer, then go to Biomart link and you will see the URL:port

http://www.ensembl.org/Help/ArchiveList

Best,
Syed

On 12/10/2011 13:03, Christophe Klopp wrote:
Hi,

Which host and port have I to use to query the Ensembl archive mart
databases using the API?

Cheers

Christophe


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


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Re: [BioMart Users] accessing the ensemble mart archives using the API

Syed Haider-2
Correct, thats what you need for RDBMS access, i thought (incorrectly)
that you meant webservice access to archive dbs.

On 12/10/2011 14:12, Rhoda Kinsella wrote:

> Hi Christophe
> You can access the archived marts at martdb.ensembl.org. Connection details are here:
>
> http://www.ensembl.org/info/data/mysql.html
>
> Regards
> Rhoda
>
>
>
> On 12 Oct 2011, at 13:58, Christophe Klopp wrote:
>
> Hi Syed,
>
> If I choose lets' say Ensembl 62: Apr 2011<http://Apr2011.archive.ensembl.org/>  and go to the corresponding biomart http://apr2011.archive.ensembl.org/biomart/martview where do I find the URL:port ?
>
> Cheers
>
> Christophe
>
>
> Le 12/10/2011 14:07, Syed Haider a écrit :
> Hi Christophe,
>
> Follow this link below and then choose the version you prefer, then go to Biomart link and you will see the URL:port
>
> http://www.ensembl.org/Help/ArchiveList
>
> Best,
> Syed
>
> On 12/10/2011 13:03, Christophe Klopp wrote:
> Hi,
>
> Which host and port have I to use to query the Ensembl archive mart
> databases using the API?
>
> Cheers
>
> Christophe
>
>
>
> --
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email: [hidden email]<mailto:[hidden email]>  =
> = http://www.sigenae.org/                                          =
> = http://bioinfo.genotoul.fr/                                      =
> ====================================================================
>
>
> _______________________________________________
> Users mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.biomart.org/mailman/listinfo/users
>
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
>
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Re: [BioMart Users] accessing the ensemble mart archives using the API

Christophe Klopp
In reply to this post by Rhoda Kinsella
Hi Rhoda and thank you,

When I put these elements in my registry file and use the standard perl code given by martview, I get the following error  :
Dataset default.btaurus_gene_ensembl not found in registry

I try to extract gene names from given regions.
What should I replace default with?

Cheers

Christophe




Le 12/10/2011 15:12, Rhoda Kinsella a écrit :
Hi Christophe
You can access the archived marts at martdb.ensembl.org. Connection details are here:


Regards
Rhoda



On 12 Oct 2011, at 13:58, Christophe Klopp wrote:

Hi Syed,

If I choose lets' say Ensembl 62: Apr 2011 and go to the corresponding biomart http://apr2011.archive.ensembl.org/biomart/martview where do I find the URL:port ?

Cheers

Christophe


Le 12/10/2011 14:07, Syed Haider a écrit :
Hi Christophe,

Follow this link below and then choose the version you prefer, then go to Biomart link and you will see the URL:port

http://www.ensembl.org/Help/ArchiveList

Best,
Syed

On 12/10/2011 13:03, Christophe Klopp wrote:
Hi,

Which host and port have I to use to query the Ensembl archive mart
databases using the API?

Cheers

Christophe


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

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Re: [BioMart Users] accessing the ensemble mart archives using the API

Rhoda Kinsella
Hi Christophe
Can you send me a personal email with your registry file and some more details about the query you wish to do so that I can try to reproduce your error?
Regards
Rhoda

On 12 Oct 2011, at 14:47, Christophe Klopp wrote:

Hi Rhoda and thank you,

When I put these elements in my registry file and use the standard perl code given by martview, I get the following error  :
Dataset default.btaurus_gene_ensembl not found in registry

I try to extract gene names from given regions.
What should I replace default with?

Cheers

Christophe




Le 12/10/2011 15:12, Rhoda Kinsella a écrit :
Hi Christophe
You can access the archived marts at martdb.ensembl.org. Connection details are here:


Regards
Rhoda



On 12 Oct 2011, at 13:58, Christophe Klopp wrote:

Hi Syed,

If I choose lets' say Ensembl 62: Apr 2011 and go to the corresponding biomart http://apr2011.archive.ensembl.org/biomart/martview where do I find the URL:port ?

Cheers

Christophe


Le 12/10/2011 14:07, Syed Haider a écrit :
Hi Christophe,

Follow this link below and then choose the version you prefer, then go to Biomart link and you will see the URL:port

http://www.ensembl.org/Help/ArchiveList

Best,
Syed

On 12/10/2011 13:03, Christophe Klopp wrote:
Hi,

Which host and port have I to use to query the Ensembl archive mart
databases using the API?

Cheers

Christophe


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


-- 
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     = 
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users