[BioMart Users] About connection to ICGC data portal

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[BioMart Users] About connection to ICGC data portal

Wang, Zhining (NIH/NCI) [C]

Hi,

 

I am playing with the R package, BiomaRt. I tried

 

library("biomaRt");

listMarts();

 

 

It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help?

 

Thanks,

 

Zhining

 

 

 

Zhining Wang, Ph. D.

Senior Scientist, Bioinformatics

SRA International, Inc.

Contractor, TCGA program office, NCI/NIH

Bethesda, Maryland

Building31A, room 3A20

Tel: 301-435-0680

Email: [hidden email]

 


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Re: [BioMart Users] About connection to ICGC data portal

Junjun Zhang
Hi Zhining,

biomaRt may only list marts available from www.biomart.org, ICGC marts are not included in there.

Junjun


From: "Wang, Zhining (NIH/NCI) [C]" <[hidden email]>
Date: Mon, 1 Aug 2011 09:05:14 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] About connection to ICGC data portal

Hi,

 

I am playing with the R package, BiomaRt. I tried

 

library("biomaRt");

listMarts();

 

 

It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help?

 

Thanks,

 

Zhining

 

 

 

Zhining Wang, Ph. D.

Senior Scientist, Bioinformatics

SRA International, Inc.

Contractor, TCGA program office, NCI/NIH

Bethesda, Maryland

Building31A, room 3A20

Tel: 301-435-0680

Email: [hidden email]

 


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Re: [BioMart Users] About connection to ICGC data portal

Steffen Durinck-2
In reply to this post by Wang, Zhining (NIH/NCI) [C]
Hi Zhining,


By default, biomaRt queries the central BioMart server.  ICGC is not hosted there.
If you know the host of the ICGC web service URL you could use that directy to establish your connection through biomaRt.

e.g. Ensembl can be queried through the central BioMart service but also by doing:

listMarts(host="may2009.archive.ensembl.org")
mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org")


Cheers,
Steffen

On Mon, Aug 1, 2011 at 6:05 AM, Wang, Zhining (NIH/NCI) [C] <[hidden email]> wrote:

Hi,

 

I am playing with the R package, BiomaRt. I tried

 

library("biomaRt");

listMarts();

 

 

It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help?

 

Thanks,

 

Zhining

 

 

 

Zhining Wang, Ph. D.

Senior Scientist, Bioinformatics

SRA International, Inc.

Contractor, TCGA program office, NCI/NIH

Bethesda, Maryland

Building31A, room 3A20

Tel: <a href="tel:301-435-0680" value="+13014350680" target="_blank">301-435-0680

Email: [hidden email]

 


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Users mailing list
[hidden email]
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Re: [BioMart Users] About connection to ICGC data portal

Junjun Zhang
In reply to this post by Wang, Zhining (NIH/NCI) [C]
Hi Zhining,

biomaRt package relies on BioMart REST API, it works with the current BioMart central portal and others that run BioMart release 0.7. ICGC Data Portal runs off BioMart 0.8 release candidate 6 which does not provide 0.7 compatible REST API at this time, so it will not work even you specify ICGC's URL while using biomaRt.

This is actually a good timing, we are planning to standardize REST API in 0.8. I hope biomaRt will work with data sources that run BioMart 0.8 software in the near future.

Cheers,
Junjun


From: "Wang, Zhining (NIH/NCI) [C]" <[hidden email]>
Date: Mon, 1 Aug 2011 12:38:50 -0400
To: jzhang <[hidden email]>
Subject: FW: [BioMart Users] About connection to ICGC data portal

Hi Junjun,

 

Sorry to bother you again. What is the URL for the ICGC web service that biomaRt can connect to?  Steffen told me that I could use the URL directly to establish connection through biomaRt.

 

e.g. Ensembl can be queried by doing:

listMarts(host="may2009.archive.ensembl.org")

mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org")

 

Thanks,

 

Zhining

 

From: Steffen Durinck [[hidden email]]
Sent: Monday, August 01, 2011 12:23 PM
To: Wang, Zhining (NIH/NCI) [C]
Cc: [hidden email]
Subject: Re: [BioMart Users] About connection to ICGC data portal

 

Hi Zhining,

 

 

By default, biomaRt queries the central BioMart server.  ICGC is not hosted there.

If you know the host of the ICGC web service URL you could use that directy to establish your connection through biomaRt.

 

e.g. Ensembl can be queried through the central BioMart service but also by doing:

 

listMarts(host="may2009.archive.ensembl.org")

mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org")

 

 

Cheers,

Steffen

On Mon, Aug 1, 2011 at 6:05 AM, Wang, Zhining (NIH/NCI) [C] <[hidden email]> wrote:

Hi,

 

I am playing with the R package, BiomaRt. I tried

 

library("biomaRt");

listMarts();

 

 

It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help?

 

Thanks,

 

Zhining

 

 

 

Zhining Wang, Ph. D.

Senior Scientist, Bioinformatics

SRA International, Inc.

Contractor, TCGA program office, NCI/NIH

Bethesda, Maryland

Building31A, room 3A20

Tel: <a href="tel:301-435-0680" target="_blank">301-435-0680

Email: [hidden email]

 


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

 


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Re: [BioMart Users] About connection to ICGC data portal

Wang, Zhining (NIH/NCI) [C]

Wonderful. Cannot wait. Thanks, Junjun.

 

Zhining

 

 

From: Junjun Zhang [mailto:[hidden email]]
Sent: Monday, August 01, 2011 1:26 PM
To: Wang, Zhining (NIH/NCI) [C]
Cc: [hidden email]
Subject: Re: [BioMart Users] About connection to ICGC data portal

 

Hi Zhining,

 

biomaRt package relies on BioMart REST API, it works with the current BioMart central portal and others that run BioMart release 0.7. ICGC Data Portal runs off BioMart 0.8 release candidate 6 which does not provide 0.7 compatible REST API at this time, so it will not work even you specify ICGC's URL while using biomaRt.

 

This is actually a good timing, we are planning to standardize REST API in 0.8. I hope biomaRt will work with data sources that run BioMart 0.8 software in the near future.

 

Cheers,

Junjun

 

 

From: "Wang, Zhining (NIH/NCI) [C]" <[hidden email]>
Date: Mon, 1 Aug 2011 12:38:50 -0400
To: jzhang <[hidden email]>
Subject: FW: [BioMart Users] About connection to ICGC data portal

 

Hi Junjun,

 

Sorry to bother you again. What is the URL for the ICGC web service that biomaRt can connect to?  Steffen told me that I could use the URL directly to establish connection through biomaRt.

 

e.g. Ensembl can be queried by doing:

listMarts(host="may2009.archive.ensembl.org")

mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org")

 

Thanks,

 

Zhining

 

From: Steffen Durinck [[hidden email]]
Sent: Monday, August 01, 2011 12:23 PM
To: Wang, Zhining (NIH/NCI) [C]
Cc: [hidden email]
Subject: Re: [BioMart Users] About connection to ICGC data portal

 

Hi Zhining,

 

 

By default, biomaRt queries the central BioMart server.  ICGC is not hosted there.

If you know the host of the ICGC web service URL you could use that directy to establish your connection through biomaRt.

 

e.g. Ensembl can be queried through the central BioMart service but also by doing:

 

listMarts(host="may2009.archive.ensembl.org")

mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org")

 

 

Cheers,

Steffen

On Mon, Aug 1, 2011 at 6:05 AM, Wang, Zhining (NIH/NCI) [C] <[hidden email]> wrote:

Hi,

 

I am playing with the R package, BiomaRt. I tried

 

library("biomaRt");

listMarts();

 

 

It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help?

 

Thanks,

 

Zhining

 

 

 

Zhining Wang, Ph. D.

Senior Scientist, Bioinformatics

SRA International, Inc.

Contractor, TCGA program office, NCI/NIH

Bethesda, Maryland

Building31A, room 3A20

Tel: <a href="tel:301-435-0680" target="_blank">301-435-0680

Email: [hidden email]

 


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

 


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Re: [BioMart Users] About connection to ICGC data portal

Arek Kasprzyk
In reply to this post by Steffen Durinck-2
Hi everyone,
In the longer term all publically available sources, including ICGC
portal will be available through the central service.

a



On Mon, Aug 1, 2011 at 12:22 PM, Steffen Durinck <[hidden email]> wrote:

> Hi Zhining,
>
> By default, biomaRt queries the central BioMart server.  ICGC is not hosted
> there.
> If you know the host of the ICGC web service URL you could use that directy
> to establish your connection through biomaRt.
> e.g. Ensembl can be queried through the central BioMart service but also by
> doing:
> listMarts(host="may2009.archive.ensembl.org")
> mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl',
> host="may2009.archive.ensembl.org")
>
> Cheers,
> Steffen
>
> On Mon, Aug 1, 2011 at 6:05 AM, Wang, Zhining (NIH/NCI) [C]
> <[hidden email]> wrote:
>>
>> Hi,
>>
>>
>>
>> I am playing with the R package, BiomaRt. I tried
>>
>>
>>
>> library("biomaRt");
>>
>> listMarts();
>>
>>
>>
>>
>>
>> It returned 66 Mart, but I can not find the Mart for ICGC which is powered
>> by BioMart (http://dcc.icgc.org/). Can you help?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Zhining
>>
>>
>>
>>
>>
>>
>>
>> Zhining Wang, Ph. D.
>>
>> Senior Scientist, Bioinformatics
>>
>> SRA International, Inc.
>>
>> Contractor, TCGA program office, NCI/NIH
>>
>> Bethesda, Maryland
>>
>> Building31A, room 3A20
>>
>> Tel: 301-435-0680
>>
>> Email: [hidden email]
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>
>
_______________________________________________
Users mailing list
[hidden email]
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