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 [[email protected]]
Sent: June 26, 2012 12:58 PM
To: Stanley Ng
Cc: Robin Haw; Francis Ouellette; Arek Kasprzyk; [email protected]
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
<[email protected]<mailto:[email protected]>> 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 [[email protected]<mailto:[email protected]>]
Sent: June 26, 2012 12:47 PM
To: Stanley Ng
Cc: [email protected]<mailto:[email protected]>; Francis Ouellette;
[email protected]<mailto:[email protected]>; 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
<[email protected]<mailto:[email protected]>>
Date: Tuesday, 26 June, 2012 12:42 PM
To: Robin Haw <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>, Francis Ouellette
<[email protected]<mailto:[email protected]>>, David Croft
<[email protected]<mailto:[email protected]>>, Arek Kasprzyk
<[email protected]<mailto:[email protected]>>
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 [[email protected]<mailto:[email protected]>]
Sent: June 26, 2012 4:38 AM
To: Robin Haw
Cc: Stanley Ng; [email protected]<mailto:[email protected]>; Francis Ouellette;
[email protected]<mailto:[email protected]>
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
<[email protected]<mailto:[email protected]>> 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
[[email protected]<mailto:[email protected]>]
Sent: 25 June 2012 18:23
To: Robin Haw
Cc: [email protected]<mailto:[email protected]>; Francis Ouellette;
[email protected]<mailto:[email protected]>
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 [[email protected]<mailto:[email protected]>]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [email protected]<mailto:[email protected]>; Francis Ouellette;
[email protected]<mailto:[email protected]>
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:
[email protected]<mailto:[email protected]>
[[email protected]<mailto:[email protected]>]
on behalf of David Croft [[email protected]<mailto:[email protected]>]
Sent: 22 June 2012 10:42
To: [email protected]<mailto:[email protected]>
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
> [email protected]<mailto:[email protected]>
> https://lists.reactome.org/mailman/listinfo/reactome-help
_______________________________________________
Reactome-help mailing list
[email protected]<mailto:[email protected]>
https://lists.reactome.org/mailman/listinfo/reactome-help
________________________________________
From: Stanley Ng
[[email protected]<mailto:[email protected]>]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [email protected]<mailto:[email protected]>; Francis Ouellette;
[email protected]<mailto:[email protected]>
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: [email protected]<mailto:[email protected]>
Cc: [email protected]<mailto:[email protected]>; Robin Haw; Francis Ouellette
([email protected]<mailto:[email protected]>)
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 [[email protected]<mailto:[email protected]>]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [email protected]<mailto:[email protected]>; Robin Haw; Francis Ouellette
([email protected]<mailto:[email protected]>)
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
<[email protected]<mailto:[email protected]>>
Sender: [email protected]<mailto:[email protected]>
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[email protected]<mailto:[email protected]>>
Cc: <[email protected]<mailto:[email protected]>>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
_______________________________________________
Users mailing list
[email protected]<mailto:[email protected]>
https://lists.biomart.org/mailman/listinfo/users
--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org<http://www.biomart.org>
_______________________________________________
Users mailing list
[email protected]<mailto:[email protected]>
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
