[BioMart Users] PRIDE and BioMart: Filtering Problems

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[BioMart Users] PRIDE and BioMart: Filtering Problems

Greenman, Ronald (NIH/CIT) [C]
I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at <http://sourceforge.net/projects/pride-proteome/files/>. Although I can get basic queries to work, some of the filters don't seem to be working. In particular, under the Sample Details filter collection, I seem to only be able to filter by species: the BRENDA, Cell Type, GO, and Disease filters aren't displayed in martview. They also don't seem to function: they don't throw any errors if I attempt to use them, but they also don't appear to have any effect on the result set.

What sorts of things could cause these filters to not show up, even though they're configured?
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Joachim Baran-3
Hi!

On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
<[hidden email]> wrote:
> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at <http://sourceforge.net/projects/pride-proteome/files/>.
  The files on SourceForge seem to be outdated by a couple of years
now. You can access a current version of the PRIDE BioMart via
http://www.ebi.ac.uk/pride/prideMart.do

  Whilst you can run your own BioMart locally, I suggest that you also
have a look at querying the PRIDE BioMart at EBI. You can submit
queries manually via the web-interface or you can submit queries
programmatically via the XML/RESTful-interface or via the Perl API.

  Hope that helps.

Joachim
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Joachim Baran-2
In reply to this post by Greenman, Ronald (NIH/CIT) [C]
Hi!

On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C] <[hidden email]> wrote:
> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at <http://sourceforge.net/projects/pride-proteome/files/>.
 The files on SourceForge seem to be outdated by a couple of years now. You can access a current version of the PRIDE BioMart via http://www.ebi.ac.uk/pride/prideMart.do

 Whilst you can run your own BioMart locally, I suggest that you also have a look at querying the PRIDE BioMart at EBI. You can submit queries manually via the web-interface or you can submit queries programmatically via the XML/RESTful-interface or via the Perl API.

 Hope that helps. 

Joachim


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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Arek Kasprzyk-2
In reply to this post by Joachim Baran-3




________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Joachim Baran [[hidden email]]
Sent: Tuesday, February 01, 2011 3:20 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Hi!

On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
<[hidden email]> wrote:
> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at <http://sourceforge.net/projects/pride-proteome/files/>.
  The files on SourceForge seem to be outdated by a couple of years
now. You can access a current version of the PRIDE BioMart via
http://www.ebi.ac.uk/pride/prideMart.do

  Whilst you can run your own BioMart locally, I suggest that you also
have a look at querying the PRIDE BioMart at EBI. You can submit
queries manually via the web-interface or you can submit queries
programmatically via the XML/RESTful-interface or via the Perl API.

  Hope that helps.

Joachim



just to add to Joachim message:
probably the best starting point is www.biomart.org. It contains all the publicly available marts (that we know of) :)

a


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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Greenman, Ronald (NIH/CIT) [C]
In reply to this post by Joachim Baran-3
I'm sorry that I haven't been able to reply sooner. I was pulled off to other tasks at work, and I'm only now able to get back to this.

Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm now using the config files from PRIDE's Google Code repository, so those should in theory be up to date, though I notice that they haven't been updated in a long time either.

However, the problem remains. In particular, the only Sample Attribute I can filter on is Species, even though the configuration seems to also offer filters on Tissue, Cell Type, GO, and Disease. The attributes appear to work normally when displayed in query results; I just can't filter on them.

What would cause an attribute to be viewable, but not filterable?

-----Original Message-----
From: Joachim Baran [mailto:[hidden email]]
Sent: Tuesday, February 01, 2011 3:21 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Hi!

On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
<[hidden email]> wrote:
> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at <http://sourceforge.net/projects/pride-proteome/files/>.
  The files on SourceForge seem to be outdated by a couple of years
now. You can access a current version of the PRIDE BioMart via
http://www.ebi.ac.uk/pride/prideMart.do

  Whilst you can run your own BioMart locally, I suggest that you also
have a look at querying the PRIDE BioMart at EBI. You can submit
queries manually via the web-interface or you can submit queries
programmatically via the XML/RESTful-interface or via the Perl API.

  Hope that helps.

Joachim
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Joachim Baran-2
Hi!

On 11-02-15 2:10 PM, "Greenman, Ronald (NIH/CIT) [C]"
<[hidden email]> wrote:
>Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm
>now using the config files from PRIDE's Google Code repository, so those
>should in theory be up to date, though I notice that they haven't been
>updated in a long time either.
  I am not familiar with PRIDE's Google Code repository, but you can get
the latest BioMart configuration from their mart by connecting to it via
MartEditor, then saving it, and then you open your local mart and load the
previously saved configuration into your local installation. If the
configurations are the same, then the marts will behave the same.

  Perhaps this blog-post will give you a rough idea on how to do that
(check the section on "Meta-Data Transfer"):
http://bergmanlab.smith.man.ac.uk/?p=35

Joachim

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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Syed Haider
In reply to this post by Greenman, Ronald (NIH/CIT) [C]
Ronald,

does your project require you to run the:
- BioMart server locally
  OR
- BioMart server + PRIDE database as well ?

Best,
Syed

On 15/02/2011 19:10, Greenman, Ronald (NIH/CIT) [C] wrote:

> I'm sorry that I haven't been able to reply sooner. I was pulled off to other tasks at work, and I'm only now able to get back to this.
>
> Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm now using the config files from PRIDE's Google Code repository, so those should in theory be up to date, though I notice that they haven't been updated in a long time either.
>
> However, the problem remains. In particular, the only Sample Attribute I can filter on is Species, even though the configuration seems to also offer filters on Tissue, Cell Type, GO, and Disease. The attributes appear to work normally when displayed in query results; I just can't filter on them.
>
> What would cause an attribute to be viewable, but not filterable?
>
> -----Original Message-----
> From: Joachim Baran [mailto:[hidden email]]
> Sent: Tuesday, February 01, 2011 3:21 PM
> To: Greenman, Ronald (NIH/CIT) [C]
> Cc: [hidden email]; [hidden email]
> Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems
>
> Hi!
>
> On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
> <[hidden email]>  wrote:
>> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at<http://sourceforge.net/projects/pride-proteome/files/>.
>    The files on SourceForge seem to be outdated by a couple of years
> now. You can access a current version of the PRIDE BioMart via
> http://www.ebi.ac.uk/pride/prideMart.do
>
>    Whilst you can run your own BioMart locally, I suggest that you also
> have a look at querying the PRIDE BioMart at EBI. You can submit
> queries manually via the web-interface or you can submit queries
> programmatically via the XML/RESTful-interface or via the Perl API.
>
>    Hope that helps.
>
> Joachim
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Greenman, Ronald (NIH/CIT) [C]
I need to run both BioMart and PRIDE locally.

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Tuesday, February 15, 2011 2:26 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: Joachim Baran; [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Ronald,

does your project require you to run the:
- BioMart server locally
  OR
- BioMart server + PRIDE database as well ?

Best,
Syed

On 15/02/2011 19:10, Greenman, Ronald (NIH/CIT) [C] wrote:

> I'm sorry that I haven't been able to reply sooner. I was pulled off to other tasks at work, and I'm only now able to get back to this.
>
> Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm now using the config files from PRIDE's Google Code repository, so those should in theory be up to date, though I notice that they haven't been updated in a long time either.
>
> However, the problem remains. In particular, the only Sample Attribute I can filter on is Species, even though the configuration seems to also offer filters on Tissue, Cell Type, GO, and Disease. The attributes appear to work normally when displayed in query results; I just can't filter on them.
>
> What would cause an attribute to be viewable, but not filterable?
>
> -----Original Message-----
> From: Joachim Baran [mailto:[hidden email]]
> Sent: Tuesday, February 01, 2011 3:21 PM
> To: Greenman, Ronald (NIH/CIT) [C]
> Cc: [hidden email]; [hidden email]
> Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems
>
> Hi!
>
> On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
> <[hidden email]>  wrote:
>> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at<http://sourceforge.net/projects/pride-proteome/files/>.
>    The files on SourceForge seem to be outdated by a couple of years
> now. You can access a current version of the PRIDE BioMart via
> http://www.ebi.ac.uk/pride/prideMart.do
>
>    Whilst you can run your own BioMart locally, I suggest that you also
> have a look at querying the PRIDE BioMart at EBI. You can submit
> queries manually via the web-interface or you can submit queries
> programmatically via the XML/RESTful-interface or via the Perl API.
>
>    Hope that helps.
>
> Joachim
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Greenman, Ronald (NIH/CIT) [C]
In reply to this post by Joachim Baran-2
I'll try that. Thanks!

-----Original Message-----
From: Joachim Baran [mailto:[hidden email]]
Sent: Tuesday, February 15, 2011 2:23 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Hi!

On 11-02-15 2:10 PM, "Greenman, Ronald (NIH/CIT) [C]"
<[hidden email]> wrote:
>Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm
>now using the config files from PRIDE's Google Code repository, so those
>should in theory be up to date, though I notice that they haven't been
>updated in a long time either.
  I am not familiar with PRIDE's Google Code repository, but you can get
the latest BioMart configuration from their mart by connecting to it via
MartEditor, then saving it, and then you open your local mart and load the
previously saved configuration into your local installation. If the
configurations are the same, then the marts will behave the same.

  Perhaps this blog-post will give you a rough idea on how to do that
(check the section on "Meta-Data Transfer"):
http://bergmanlab.smith.man.ac.uk/?p=35

Joachim

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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Syed Haider
In reply to this post by Greenman, Ronald (NIH/CIT) [C]
well in this case, the simplest solution is to ask Pride guys to give
you their database dump including metadata tables. Over to
pride-helpdesk guys.

Best,
Syed



On 15/02/2011 19:27, Greenman, Ronald (NIH/CIT) [C] wrote:

> I need to run both BioMart and PRIDE locally.
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Tuesday, February 15, 2011 2:26 PM
> To: Greenman, Ronald (NIH/CIT) [C]
> Cc: Joachim Baran; [hidden email]; [hidden email]
> Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems
>
> Ronald,
>
> does your project require you to run the:
> - BioMart server locally
>    OR
> - BioMart server + PRIDE database as well ?
>
> Best,
> Syed
>
> On 15/02/2011 19:10, Greenman, Ronald (NIH/CIT) [C] wrote:
>> I'm sorry that I haven't been able to reply sooner. I was pulled off to other tasks at work, and I'm only now able to get back to this.
>>
>> Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm now using the config files from PRIDE's Google Code repository, so those should in theory be up to date, though I notice that they haven't been updated in a long time either.
>>
>> However, the problem remains. In particular, the only Sample Attribute I can filter on is Species, even though the configuration seems to also offer filters on Tissue, Cell Type, GO, and Disease. The attributes appear to work normally when displayed in query results; I just can't filter on them.
>>
>> What would cause an attribute to be viewable, but not filterable?
>>
>> -----Original Message-----
>> From: Joachim Baran [mailto:[hidden email]]
>> Sent: Tuesday, February 01, 2011 3:21 PM
>> To: Greenman, Ronald (NIH/CIT) [C]
>> Cc: [hidden email]; [hidden email]
>> Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems
>>
>> Hi!
>>
>> On 28 January 2011 10:05, Greenman, Ronald (NIH/CIT) [C]
>> <[hidden email]>   wrote:
>>> I'm running a locally installed PRIDE/BioMart combination, using the configuration offered by PRIDE at<http://sourceforge.net/projects/pride-proteome/files/>.
>>     The files on SourceForge seem to be outdated by a couple of years
>> now. You can access a current version of the PRIDE BioMart via
>> http://www.ebi.ac.uk/pride/prideMart.do
>>
>>     Whilst you can run your own BioMart locally, I suggest that you also
>> have a look at querying the PRIDE BioMart at EBI. You can submit
>> queries manually via the web-interface or you can submit queries
>> programmatically via the XML/RESTful-interface or via the Perl API.
>>
>>     Hope that helps.
>>
>> Joachim
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Richard Cote
In reply to this post by Greenman, Ronald (NIH/CIT) [C]
Hi all

Unfortunately, our mart server is behind a firewall and marteditor will not be able to connect to it from an external ip. Having said that, the mart config files in Google code should be up to date as the mart structure has been stable for a while now. I'll look into this tomorrow.

In the interim, could you please not cc the pride-support email in each reply as this opens a new support ticket in our tracker and makes it difficult to track the progress of this issue.

Cheers,
Rc

---
Sent from my mobile. Apologies for brevity and typos.

----- Reply message -----
From: "Greenman, Ronald (NIH/CIT) [C]" <[hidden email]>
Date: Tue, Feb 15, 2011 19:28
Subject: [BioMart Users] PRIDE and BioMart: Filtering Problems
To: "Joachim Baran" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>


I'll try that. Thanks!

-----Original Message-----
From: Joachim Baran [mailto:[hidden email]]
Sent: Tuesday, February 15, 2011 2:23 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Hi!

On 11-02-15 2:10 PM, "Greenman, Ronald (NIH/CIT) [C]"
<[hidden email]> wrote:
>Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm
>now using the config files from PRIDE's Google Code repository, so those
>should in theory be up to date, though I notice that they haven't been
>updated in a long time either.
 I am not familiar with PRIDE's Google Code repository, but you can get
the latest BioMart configuration from their mart by connecting to it via
MartEditor, then saving it, and then you open your local mart and load the
previously saved configuration into your local installation. If the
configurations are the same, then the marts will behave the same.

 Perhaps this blog-post will give you a rough idea on how to do that
(check the section on "Meta-Data Transfer"):
http://bergmanlab.smith.man.ac.uk/?p=35

Joachim

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Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Greenman, Ronald (NIH/CIT) [C]

I apologize for the cc problem. Thanks for looking into this.

 

From: [hidden email] [mailto:[hidden email]]
Sent: Tuesday, February 15, 2011 2:57 PM
To: Greenman, Ronald (NIH/CIT) [C]; Joachim Baran
Cc: [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

 

Hi all

Unfortunately, our mart server is behind a firewall and marteditor will not be able to connect to it from an external ip. Having said that, the mart config files in Google code should be up to date as the mart structure has been stable for a while now. I'll look into this tomorrow.

In the interim, could you please not cc the pride-support email in each reply as this opens a new support ticket in our tracker and makes it difficult to track the progress of this issue.

Cheers,
Rc

---
Sent from my mobile. Apologies for brevity and typos.

----- Reply message -----
From: "Greenman, Ronald (NIH/CIT) [C]" <[hidden email]>
Date: Tue, Feb 15, 2011 19:28
Subject: [BioMart Users] PRIDE and BioMart: Filtering Problems
To: "Joachim Baran" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>


I'll try that. Thanks!

-----Original Message-----
From: Joachim Baran [mailto:[hidden email]]
Sent: Tuesday, February 15, 2011 2:23 PM
To: Greenman, Ronald (NIH/CIT) [C]
Cc: [hidden email]; [hidden email]
Subject: Re: [BioMart Users] PRIDE and BioMart: Filtering Problems

Hi!

On 11-02-15 2:10 PM, "Greenman, Ronald (NIH/CIT) [C]"
<[hidden email]> wrote:
>Unfortunately, my project requires me to run PRIDE/BioMart locally. I'm
>now using the config files from PRIDE's Google Code repository, so those
>should in theory be up to date, though I notice that they haven't been
>updated in a long time either.
 I am not familiar with PRIDE's Google Code repository, but you can get
the latest BioMart configuration from their mart by connecting to it via
MartEditor, then saving it, and then you open your local mart and load the
previously saved configuration into your local installation. If the
configurations are the same, then the marts will behave the same.

 Perhaps this blog-post will give you a rough idea on how to do that
(check the section on "Meta-Data Transfer"):
http://bergmanlab.smith.man.ac.uk/?p=35

Joachim

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