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Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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Arek Kasprzyk

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan,

this looks like misconfiguration on the Reactome side. I am forwarding your email to the Reactome mart administrators who will be able to help with that

On Thu, Jun 21, 2012 at 3:08 PM, Stanley Wai-Kwong Ng <[hidden email]> wrote:

Hi Arek,

I am a PhD student at the University of Toronto and am using biomart in R to get a list of entrez gene Ids for some reactome pathways in humans.

I ran the following query last month and it worked with no problems:

library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")

pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)
However, I tried to run the commands again last night and today and I get the following error:

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

  Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:
<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>
<Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">

        <Dataset name = "pathway" interface = "default" >
                                <Attribute name = "referencedatabase_entrez_gene" />
                <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
          </Dataset>
</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.
Error message from remote server as below:
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'

</pre>

Can you advise on what might be wrong?

Thanks,
Stan

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for looking into this for me.

Regards,

Stan

From: Arek Kasprzyk [mailto:[hidden email]]
Sent: June-21-12 10:44 AM
To: Stanley Wai-Kwong Ng
Cc: [hidden email]; Robin Haw
Subject: Re: Stanley Ng - R Biomart Reactome Query Error

Hi Stan,

this looks like misconfiguration on the Reactome side. I am forwarding your email to the Reactome mart administrators who will be able to help with that

On Thu, Jun 21, 2012 at 3:08 PM, Stanley Wai-Kwong Ng <[hidden email]> wrote:

Hi Arek,

I am a PhD student at the University of Toronto and am using biomart in R to get a list of entrez gene Ids for some reactome pathways in humans.

I ran the following query last month and it worked with no problems:

library("biomaRt")

mart = useMart("REACTOME", dataset="pathway")

pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

pathwayids = c(do.call("cbind",pathwayids))

entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)

However, I tried to run the commands again last night and today and I get the following error:

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'

</pre>

Can you advise on what might be wrong?

Thanks,

Stan

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

In reply to this post by Arek Kasprzyk

Hi All,

I tried using biomart in R again today and got a different error than before.

When trying to return a list of ENTREZ GENE IDs for some REACTOME pathways , either the attribute name for entrez gene ids have changed or is missing as per the below error.

Any advice is appreciated.

Thanks,

Stan

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Hi Stan,

this looks like misconfiguration on the Reactome side. I am forwarding your email to the Reactome mart administrators who will be able to help with that

On Thu, Jun 21, 2012 at 3:08 PM, Stanley Wai-Kwong Ng <[hidden email]> wrote:

Hi Arek,

I am a PhD student at the University of Toronto and am using biomart in R to get a list of entrez gene Ids for some reactome pathways in humans.

I ran the following query last month and it worked with no problems:

library("biomaRt")

mart = useMart("REACTOME", dataset="pathway")

pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

pathwayids = c(do.call("cbind",pathwayids))

entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)

However, I tried to run the commands again last night and today and I get the following error:

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'

</pre>

Can you advise on what might be wrong?

Thanks,

Stan

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Arek Kasprzyk

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

In reply to this post by Arek Kasprzyk

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

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

Robin Haw

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.

> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.

Robin Haw

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 18:23
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.

Arek Kasprzyk

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:

Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

In reply to this post by Robin Haw

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the
email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave
me the following error message. Please let me know if I need a certain
version of biomaRt for my query to work or if there is another name for the
attribute (the output of listAttributes(mart) still lists
"referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:
> entrezids =
getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_list",
values=c(pathwayids[1]), mart=mart)
Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters =
"pathway_id_list", :
Invalid attribute(s): referencedatabase_ncbi_gene
Please use the function 'listAttributes' to get valid attribute names

Thanks,
Stan

-----Original Message-----
From: Robin Haw [mailto:[hidden email]]
Sent: June-25-12 10:02 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be
"referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with
the sending and receiving some emails with the utoronto mail system. So,
this might explain why you did not receive the email earlier because it was
definitely sent by our mail server and received at a number of different
locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 18:23
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing
in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for
each specified pathway.

Do you know what is the new attribute name I should be using to get lists of
NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it
doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway") pathwayids =
getBM(attributes=c("stableidentifier_identifier"),filters="species_selection
",values=c("Homo sapiens"), mart=mart) pathwayids =
c(do.call("cbind",pathwayids)) entrezids =
getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list
",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute
referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue,
last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email]
[[hidden email]] on behalf of David Croft
[[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer
working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to reflect
this, so if you run the query on our website, it should work. I do not have
any experience with R-BioMart, you may need to experiment a little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of
entrez gene ids for the pathways that I was interested in.

>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids =
> getBM(attributes=c("stableidentifier_identifier"),filters="species_sel
> ection",values=c("Homo sapiens"), mart=mart)
>
> entrezids =

getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list
",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no
longer works. I see the following error and was wondering if the query
requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters =
"pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at
web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200"
count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name =
"referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value =
"REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain
illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Unknown column
'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entr
ez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l
will be able to help you

Sent from my BlackBerryR smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

In reply to this post by Arek Kasprzyk

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:

thank you

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Robin Haw

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

Robin and David:

thank you

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

Robin and David:

thank you

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Steffen Durinck-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

The error is thrown by the biomaRt package as there is no attribute named 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see 'referencedatabase_entrez_gene' does exists, and think that is the attribute that the user is querying for, that should work.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:
Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

a

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Steffen,

Thanks for your input.

I had originally been querying for the attribute "referencedatabase_entrez_gene" and it was working one month ago but I tried that query since last week and it gives the below error message so I'm not sure if the attribute name may be changed to something else or if I need to update to a newer biomaRt package in R?

> library("biomaRt")

> mart = useMart("REACTOME", dataset="pathway")

> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

> pathwayids = c(do.call("cbind",pathwayids))

> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

From: Steffen Durinck [[hidden email]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:
Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

a

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

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

Arek Kasprzyk

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan,

I agree with Steffen. The attribute that you are looking for seems to be missing in the pathway dataset. I just checked on the Reactome Mart site and only can see the following atts for gene refs:

	<Attribute name = "stableidentifier_identifier" />
		<Attribute name = "referencedatabase_ncbi_gene" />
		<Attribute name = "referencedatabase_ensembl" />
		<Attribute name = "referencedatabase_kegg_gene" />
		<Attribute name = "referencedatabase_omim" />
		<Attribute name = "referencednasequence__dm_db_id" />
		<Attribute name = "referencednasequence__dm__displayname" />
		<Attribute name = "referencednasequence__dm_species__displayname" />

Perhaps David would like to comment here?

On Tue, Jun 26, 2012 at 6:08 PM, Stanley Ng <[hidden email]> wrote:

Hi Steffen,

Thanks for your input.

I had originally been querying for the attribute "referencedatabase_entrez_gene" and it was working one month ago but I tried that query since last week and it gives the below error message so I'm not sure if the attribute name may be changed to something else or if I need to update to a newer biomaRt package in R?

> library("biomaRt")

> mart = useMart("REACTOME", dataset="pathway")

> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

> pathwayids = c(do.call("cbind",pathwayids))

> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

<Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">

<Dataset name = "pathway" interface = "default" >

<Attribute name = "referencedatabase_entrez_gene" />

<ValueFilter name = "pathway_id_list" value = "REACT_1698"/>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

From: Steffen Durinck [[hidden email]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [hidden email]

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

The error is thrown by the biomaRt package as there is no attribute named 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see 'referencedatabase_entrez_gene' does exists, and think that is the attribute that the user is querying for, that should work.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:
Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

a

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Steffen Durinck-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Just want to add that as no host is specified in the biomaRt query, by default, the R package will send the query to the central BioMart repository and will get the list of valid attributes from here:

http://www.biomart.org/biomart/martservice?type=attributes&dataset=pathway&mart=REACTOME

which lists:

referencedatabase_entrez_gene	Gene Entrez ID		naive_attributes	html,txt,tsv,xls	pathway__referencednasequence__dm

So it indicates referencedatabase_entrez_gene is a valid attribute but if the user actually uses it and sends the XML query:

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name = 'pathway'><Attribute name = 'referencedatabase_entrez_gene'/><Filter name = 'pathway_id_list' value = 'test' /></Dataset></Query>

To the central repository, the central repository returns the error that says this attribute does not exists....:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Is the central repository forwarding this query to the actual Reactome BioMart at http://www.reactome.org:5555/biomart/martservice?

and might this BioMart be out of sync with the central repository?

Steffen

On Tue, Jun 26, 2012 at 10:25 AM, Arek Kasprzyk <[hidden email]> wrote:

Hi Stan,
I agree with Steffen. The attribute that you are looking for seems to be missing in the pathway dataset. I just checked on the Reactome Mart site and only can see the following atts for gene refs:
	<Attribute name = "stableidentifier_identifier" />
		<Attribute name = "referencedatabase_ncbi_gene" />
		<Attribute name = "referencedatabase_ensembl" />
		<Attribute name = "referencedatabase_kegg_gene" />
		<Attribute name = "referencedatabase_omim" />
		<Attribute name = "referencednasequence__dm_db_id" />
		<Attribute name = "referencednasequence__dm__displayname" />
		<Attribute name = "referencednasequence__dm_species__displayname" />
Perhaps David would like to comment here?

a

On Tue, Jun 26, 2012 at 6:08 PM, Stanley Ng <[hidden email]> wrote:

Hi Steffen,

Thanks for your input.

I had originally been querying for the attribute "referencedatabase_entrez_gene" and it was working one month ago but I tried that query since last week and it gives the below error message so I'm not sure if the attribute name may be changed to something else or if I need to update to a newer biomaRt package in R?

> library("biomaRt")

> mart = useMart("REACTOME", dataset="pathway")

> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

> pathwayids = c(do.call("cbind",pathwayids))

> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

<Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">

<Dataset name = "pathway" interface = "default" >

<Attribute name = "referencedatabase_entrez_gene" />

<ValueFilter name = "pathway_id_list" value = "REACT_1698"/>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

From: Steffen Durinck [[hidden email]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [hidden email]

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

The error is thrown by the biomaRt package as there is no attribute named 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see 'referencedatabase_entrez_gene' does exists, and think that is the attribute that the user is querying for, that should work.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:
Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

a

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Arek Kasprzyk

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Very likely. If the Reactome guys made a configuration change without letting us know this would be the likely problem.

I will coordinate BioPortal update so this will hopefully fix it

a

Sent from my BlackBerry® smartphone on O2

From: Steffen Durinck <[hidden email]>

Date: Tue, 26 Jun 2012 10:45:51 -0700

To: Arek Kasprzyk<[hidden email]>

Cc: Stanley Ng<[hidden email]>; Francis Ouellette<[hidden email]>; [hidden email]<[hidden email]>; <[hidden email]>

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

http://www.biomart.org/biomart/martservice?type=attributes&dataset=pathway&mart=REACTOME

which lists:

referencedatabase_entrez_gene	Gene Entrez ID		naive_attributes	html,txt,tsv,xls	pathway__referencednasequence__dm

So it indicates referencedatabase_entrez_gene is a valid attribute but if the user actually uses it and sends the XML query:

To the central repository, the central repository returns the error that says this attribute does not exists....:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Is the central repository forwarding this query to the actual Reactome BioMart at http://www.reactome.org:5555/biomart/martservice?

and might this BioMart be out of sync with the central repository?

Steffen

On Tue, Jun 26, 2012 at 10:25 AM, Arek Kasprzyk <[hidden email]> wrote:

Hi Stan,
I agree with Steffen. The attribute that you are looking for seems to be missing in the pathway dataset. I just checked on the Reactome Mart site and only can see the following atts for gene refs:
	<Attribute name = "stableidentifier_identifier" />
		<Attribute name = "referencedatabase_ncbi_gene" />
		<Attribute name = "referencedatabase_ensembl" />
		<Attribute name = "referencedatabase_kegg_gene" />
		<Attribute name = "referencedatabase_omim" />
		<Attribute name = "referencednasequence__dm_db_id" />
		<Attribute name = "referencednasequence__dm__displayname" />
		<Attribute name = "referencednasequence__dm_species__displayname" />
Perhaps David would like to comment here?

a

On Tue, Jun 26, 2012 at 6:08 PM, Stanley Ng <[hidden email]> wrote:

Hi Steffen,

Thanks for your input.

I had originally been querying for the attribute "referencedatabase_entrez_gene" and it was working one month ago but I tried that query since last week and it gives the below error message so I'm not sure if the attribute name may be changed to something else or if I need to update to a newer biomaRt package in R?

> library("biomaRt")

> mart = useMart("REACTOME", dataset="pathway")

> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

> pathwayids = c(do.call("cbind",pathwayids))

> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

<Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">

<Dataset name = "pathway" interface = "default" >

<Attribute name = "referencedatabase_entrez_gene" />

<ValueFilter name = "pathway_id_list" value = "REACT_1698"/>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

From: Steffen Durinck [[hidden email]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [hidden email]

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

The error is thrown by the biomaRt package as there is no attribute named 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see 'referencedatabase_entrez_gene' does exists, and think that is the attribute that the user is querying for, that should work.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

From: Arek Kasprzyk [[hidden email]]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [hidden email]; Francis Ouellette; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Robin and David:
Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community

thank you

a

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

Hi Stan,

I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".

Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations.

If you have any other questions, please let me know.

Robin

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
>
> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no longer works. I see the following error and was wondering if the query requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name = "referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [hidden email]
> https://lists.reactome.org/mailman/listinfo/reactome-help

_______________________________________________
Reactome-help mailing list
[hidden email]
https://lists.reactome.org/mailman/listinfo/reactome-help

________________________________________
From: Stanley Ng [[hidden email]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

When do you think this can be fixed?

Thanks,
Stan

________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [hidden email]
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Thanks for clarifying. I had thought it may have been a new issue.

Stan
________________________________________
From: arek kasprzyk [[hidden email]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [hidden email]; Robin Haw; Francis Ouellette ([hidden email])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan

This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you

Sent from my BlackBerry® smartphone on O2

-----Original Message-----
From: Stanley Wai-Kwong Ng <[hidden email]>
Sender: [hidden email]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[hidden email]>
Cc: <[hidden email]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

Stanley Wai-Kwong Ng-2

Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Arek,

Please let me know when the update is complete and I can help verify if the queries work.

Thanks,

Stan

From: arek kasprzyk [mailto:[hidden email]]
Sent: June-26-12 1:52 PM
To: Steffen Durinck
Cc: Stanley Ng; Francis Ouellette ([hidden email]); [hidden email]; [hidden email]
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Very likely. If the Reactome guys made a configuration change without letting us know this would be the likely problem.

I will coordinate BioPortal update so this will hopefully fix it

a

Sent from my BlackBerry® smartphone on O2

From: Steffen Durinck <[hidden email]>

Date: Tue, 26 Jun 2012 10:45:51 -0700

To: Arek Kasprzyk<[hidden email]>

Cc: Stanley Ng<[hidden email]>; Francis Ouellette<[hidden email]>; [hidden email]>; <[hidden email]>

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

http://www.biomart.org/biomart/martservice?type=attributes&dataset=pathway&mart=REACTOME

which lists:

referencedatabase_entrez_gene  Gene Entrez ID         naive_attributes       html,txt,tsv,xls        pathway__referencednasequence__dm

So it indicates referencedatabase_entrez_gene is a valid attribute but if the user actually uses it and sends the XML query:

To the central repository, the central repository returns the error that says this attribute does not exists....:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Is the central repository forwarding this query to the actual Reactome BioMart at http://www.reactome.org:5555/biomart/martservice?

and might this BioMart be out of sync with the central repository?

Steffen

On Tue, Jun 26, 2012 at 10:25 AM, Arek Kasprzyk <[hidden email]> wrote:

Hi Stan,

I agree with Steffen. The attribute that you are looking for seems to be missing in the pathway dataset. I just checked on the Reactome Mart site and only can see the following atts for gene refs:

        <Attribute name = "stableidentifier_identifier" />

               <Attribute name = "referencedatabase_ncbi_gene" />

               <Attribute name = "referencedatabase_ensembl" />

               <Attribute name = "referencedatabase_kegg_gene" />

               <Attribute name = "referencedatabase_omim" />

               <Attribute name = "referencednasequence__dm_db_id" />

               <Attribute name = "referencednasequence__dm__displayname" />

               <Attribute name = "referencednasequence__dm_species__displayname" />

Perhaps David would like to comment here?

On Tue, Jun 26, 2012 at 6:08 PM, Stanley Ng <[hidden email]> wrote:

Hi Steffen,

Thanks for your input.

> library("biomaRt")

> mart = useMart("REACTOME", dataset="pathway")

> pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)

> pathwayids = c(do.call("cbind",pathwayids))

> entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", :

Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source!

Remote data source: http://www.reactome.org:5555/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

</Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

From: Steffen Durinck [[hidden email]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [hidden email]

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stan, Robin,

I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is.

Cheers,

Steffen

On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[hidden email]> wrote:

Hi Robin and David,

Thanks for looking into this issue for me.

Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.

Thanks,

Stan

From: Robin Haw [[hidden email]]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]; Arek Kasprzyk

Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Stanley,

I might defer to my colleague David Croft for some additional input here.

Robin

From: Stanley Ng <[hidden email]>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, Francis Ouellette <[hidden email]>, David Croft <[hidden email]>, Arek Kasprzyk <[hidden email]>
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

I am using the new email system here at UofT but thanks for forwarding the email to me.

I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).

Command and Error:

> entrezids =

> getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_

> list",values=c(pathwayids[1]), mart=mart)

Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", :

Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names

Thanks,

Stan

Robin and David:

thank you

On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[hidden email]> wrote:

________________________________________
From: Stanley Ng [[hidden email]]

Sent: 25 June 2012 18:23

To: Robin Haw
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Hi Robin,

Thanks for your email.

I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders)

I have written some small R scripts to help me collect entrez gene IDs for each specified pathway.

Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now?

Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway")
pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo sapiens"), mart=mart)
pathwayids = c(do.call("cbind",pathwayids))
entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), mart=mart)

Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre>

Thanks,
Stan

________________________________________
From: Robin Haw [[hidden email]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [hidden email]; Francis Ouellette; [hidden email]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error

Dear Stanley,

Is this still a problem? I thought we'd been able to address this issue, last week?

If not, can you please let us know?

Thanks,
Robin

________________________________________
From: [hidden email] [[hidden email]] on behalf of David Croft [[hidden email]]
Sent: 22 June 2012 10:42
To: [hidden email]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working?

Hi Stanley,

Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to
reflect this, so if you run the query on our website, it should work. I
do not have any experience with R-BioMart, you may need to experiment a
little.

Cheers,

David Croft.

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

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