[BioMart Users] MultiSelect operation

classic Classic list List threaded Threaded
11 messages Options
Reply | Threaded
Open this post in threaded view
|

[BioMart Users] MultiSelect operation

nqueralt

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Arek Kasprzyk
Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

nqueralt

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Arek Kasprzyk
Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

nqueralt

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Arek Kasprzyk
Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a


On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

nqueralt

Dear Arek,

 

I tried to configure the filter type in the configuration with the ‘multiSelectBoolean’ option, but it seems not to work quite well. Is this the way to configure the multiselect operation as you described me on the below email?

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 28 de septiembre de 2011 19:18
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a

On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Arek Kasprzyk
Hi Nuria,

Please look at the example from central.biomart.org (under protein domains)

http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+64+%28WTSI%2C+UK%29&step=2


'transmemebrane domains'

'signal domains'.


I believe that this XML is committed to the source code of biomart under 'registry' or something similar.
You can use this example if  this is what you are after.

If you can't find the XML please drop an email to Junjun Zang. I am sure he would not mind pointing you to it
or he may even have better example in a smaller XML file (this one is quite big)


a




On Wed, Oct 19, 2011 at 6:40 AM, <[hidden email]> wrote:

Dear Arek,

 

I tried to configure the filter type in the configuration with the ‘multiSelectBoolean’ option, but it seems not to work quite well. Is this the way to configure the multiselect operation as you described me on the below email?

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 28 de septiembre de 2011 19:18


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a

On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 

 


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



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Junjun Zhang
Hi Nuria,

You do not need to use multiSelectBoolean filter type for your use case, you just need two (or more) separate boolean filters, as such:

filter1: 'expressed in tissue 1', type=boolean
filter2: 'expressed in tissue 2', type=boolean

Then you will be able to get something similar to what Arek presented be below.

Hope this helps!

Best,
Junjun


From: Arek Kasprzyk <[hidden email]>
Date: Wed, 19 Oct 2011 10:11:29 -0400
To: "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] MultiSelect operation

Hi Nuria,

Please look at the example from central.biomart.org (under protein domains)

<a href="http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl&#43;Genes&#43;64&#43;%28WTSI%2C&#43;UK%29&amp;step=2">http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+64+%28WTSI%2C+UK%29&step=2


'transmemebrane domains'

'signal domains'.


I believe that this XML is committed to the source code of biomart under 'registry' or something similar.
You can use this example if  this is what you are after.

If you can't find the XML please drop an email to Junjun Zang. I am sure he would not mind pointing you to it
or he may even have better example in a smaller XML file (this one is quite big)


a




On Wed, Oct 19, 2011 at 6:40 AM, <[hidden email]> wrote:

Dear Arek,

 

I tried to configure the filter type in the configuration with the ‘multiSelectBoolean’ option, but it seems not to work quite well. Is this the way to configure the multiselect operation as you described me on the below email?

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 28 de septiembre de 2011 19:18


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a

On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 

 


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



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

nqueralt
In reply to this post by Arek Kasprzyk

Dear all,

 

We have a table in our relational database with a column where we write down the information related to the specimen type used in an experiment. In our biomart web interface we want that this item looks like the example below:

 

http://central.biomart.org/martwizard/#!/Gene_expression?mart=Pancreatic+Expression+Database+(Barts+Cancer+Institute%2C+UK)&step=2

 

where in ‘Pancreatic Specimen/Cell Type’ each Specimen/cell type is a different line with two different radio buttons. How can I configure this in our biomart access point? Many thanks in advance.

 

Best,

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 19 de octubre de 2011 16:11
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,

Please look at the example from central.biomart.org (under protein domains)

http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+64+%28WTSI%2C+UK%29&step=2


'transmemebrane domains'

'signal domains'.


I believe that this XML is committed to the source code of biomart under 'registry' or something similar.
You can use this example if  this is what you are after.

If you can't find the XML please drop an email to Junjun Zang. I am sure he would not mind pointing you to it
or he may even have better example in a smaller XML file (this one is quite big)


a



On Wed, Oct 19, 2011 at 6:40 AM, <[hidden email]> wrote:

Dear Arek,

 

I tried to configure the filter type in the configuration with the ‘multiSelectBoolean’ option, but it seems not to work quite well. Is this the way to configure the multiselect operation as you described me on the below email?

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 28 de septiembre de 2011 19:18


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a

On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 

 


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

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] MultiSelect operation

Arek Kasprzyk
Hi Nuria,
do you have access to the BioMart central configuration? You can just open it in the Mconfigurator and follow this very example.

a

On Thu, Dec 15, 2011 at 7:23 AM, <[hidden email]> wrote:

Dear all,

 

We have a table in our relational database with a column where we write down the information related to the specimen type used in an experiment. In our biomart web interface we want that this item looks like the example below:

 

http://central.biomart.org/martwizard/#!/Gene_expression?mart=Pancreatic+Expression+Database+(Barts+Cancer+Institute%2C+UK)&step=2

 

where in ‘Pancreatic Specimen/Cell Type’ each Specimen/cell type is a different line with two different radio buttons. How can I configure this in our biomart access point? Many thanks in advance.

 

Best,

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 19 de octubre de 2011 16:11


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,

Please look at the example from central.biomart.org (under protein domains)

http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+64+%28WTSI%2C+UK%29&step=2


'transmemebrane domains'

'signal domains'.


I believe that this XML is committed to the source code of biomart under 'registry' or something similar.
You can use this example if  this is what you are after.

If you can't find the XML please drop an email to Junjun Zang. I am sure he would not mind pointing you to it
or he may even have better example in a smaller XML file (this one is quite big)


a



On Wed, Oct 19, 2011 at 6:40 AM, <[hidden email]> wrote:

Dear Arek,

 

I tried to configure the filter type in the configuration with the ‘multiSelectBoolean’ option, but it seems not to work quite well. Is this the way to configure the multiselect operation as you described me on the below email?

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: miércoles, 28 de septiembre de 2011 19:18


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
you just need a simple combination of boolean filters ei

'expressed in tissue 1' yes no
'expressed in tissue 2' yes no

the user is supposed to click 'yes' twice

this is supported and easy to configure. We usually use boolean columns in the main table that have precomputed values based on the content of dimension tables. the existing mart implementations have plenty of examples like that.

please let me know if you need more pointers
a

On Wed, Sep 28, 2011 at 3:36 AM, <[hidden email]> wrote:

Hi Arek,

 

You are right, this select i also think would not work. But, let me explain what kind of information I want to retrieve from my database. We store information of probesets ID and in which tissues are expressed. If we want to query which probesets are expressed in tissue 1 and tissue 2 (but not to retrieve probesets expressed only in one of these two tissues), how could it be the best way to do it? Maybe, the multiselect operation type of setting for the tissue filter is not suitable for this kind of queries? Maybe is it not possible to query this?

 

Thank you!

 

Regards,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 18:13


Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
i am not sure if this would logically work. Your query multiselct with intersection would be equivallent to:

select bla, bla ... where id ="ABL" and id="BCR".

this would not really work, would it? I would always return an empty set.

or am i missing something?

a

On Tue, Sep 27, 2011 at 11:22 AM, <[hidden email]> wrote:

Thanks for your fast reply!

 

Ok, understood. Then, how could we configure martservice in order to query the intersection among several options related to a same filter? Thanks again!!

 

Cheers,

 

Núria


De: Arek Kasprzyk [mailto:[hidden email]]
Enviado el: martes, 27 de septiembre de 2011 17:04
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] MultiSelect operation

 

Hi Nuria,
'multiselect' is a logical 'OR' (union).

For multi-datasets multiselect this is implemented as paralel querying and software 'unionizes' it for you, for intra dataset query e.g filter box, this is translated to SQL 'in list' which is an equivalent of 'OR' (union).

give us a shout if you need more info

a

On Tue, Sep 27, 2011 at 10:56 AM, <[hidden email]> wrote:

Dear all,

 

I was wondering when a filter is configured as a multiselect operation type, if the end-user is marking more than one option at the same query in the multiselection box in the martexplorer, then how is done the filtering, taking into account interaction (AND) among multi-selected options or union (OR)?

 

On the other hand, is it available the Human Metabolome DataBase as a mart? Many thanks in advance.

 

Kind regards,

 

Núria

 

 


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

 

 

 


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

 


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



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