[BioMart Users] Biomart query: Filters

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[BioMart Users] Biomart query: Filters

Parul Kudtarkar
Dear Biomart users,

I want to filter my results based on functional category which has class
and corresponding sub class. If I select a particular class, I want the
system to auto pull corresponding sub classes related to that class. For
example if I select class: Adhesion , I want the system to pull only the
corresponding sub classes present in the database such as
Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR,
Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc.

Is this possible in biomart, if yes how?

Thanks,
Parul Kudtarkar


--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology







--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org




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Re: [BioMart Users] Biomart query: Filters

Junjun Zhang
Dear Parul,

If I understand your question correctly, then yes, this is support in BioMart 0.7. Your use case is similar to the ontology filters in Ensembl gene data mart. See the query below (please copy and paste the whole URL into your web browser):

http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term."endocrine"|hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000198712"&VISIBLEPANEL=resultspanel

In this example, user specify a anatomical term: endocrine, the system returns sub-terms that are under it, such as: thyroid, adrenal gland etc.

Briefly, here is how it works: in addition to a usual data mart, we need to create a hidden helper mart which does the conversion of user-specified term into sub-terms. More specifically, the helper mart has a filter that takes the term as input, it also has an exportable that gives output of sub-terms. The sub-terms will be fed to the main mart to retrieve corresponding records.

Below is how the table in the helper mart looks like for the example I gave:

mysql> select * from hsap_evoc_AnatomicalSystem__Vocabulary__main where term_108 = "endocrine";
+----------------------+-----------------+-----------+-------------+
| unrolled_name        | Node_id_108_key | Term_108  | unrolled_id |
+----------------------+-----------------+-----------+-------------+
| endocrine            |             144 | endocrine |         144 | 
| endocrine pancreas   |             144 | endocrine |         145 | 
| pineal gland         |             144 | endocrine |         147 | 
| pituitary gland      |             144 | endocrine |         148 | 
| thyroid              |             144 | endocrine |         149 | 
| parathyroid          |             144 | endocrine |         150 | 
| adrenal gland        |             144 | endocrine |         151 | 
| thymus               |             144 | endocrine |         154 | 
| islets of Langerhans |             144 | endocrine |         146 | 
| adrenal cortex       |             144 | endocrine |         152 | 
| adrenal medulla      |             144 | endocrine |         153 | 
+----------------------+-----------------+-----------+-------------+
11 rows in set (0.00 sec)

If you confirm this is what you are looking for, we will provide more details on how to create and configure necessary marts.

Cheers,
Junjun


On 11-08-22 1:02 PM, "Parul Kudtarkar" <[hidden email]> wrote:

Dear Biomart users,

I want to filter my results based on functional category which has class
and corresponding sub class. If I select a particular class, I want the
system to auto pull corresponding sub classes related to that class. For
example if I select class: Adhesion , I want the system to pull only the
corresponding sub classes present in the database such as
Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR,
Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc.

Is this possible in biomart, if yes how?

Thanks,
Parul Kudtarkar


--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology







--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology




_______________________________________________
Users mailing list


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Re: [BioMart Users] Biomart query: Filters

Parul Kudtarkar
Dear Junjun,

This is indeed what I am looking for, however I have installed and created
mart for Biomart 0.8 candidate 6 instead of Biomart 0.7. Is it possible to
do the same with this latest Biomart release?

Could you please provide further details and configuration on creating
hidden helper mart?

Also with regards to GUI; biomart 0.8 offers MartForm, MartWizard,
MartAnalysis and MartExplorer, is it possible to use MartView GUI used by
Biomart 0.7? If yes could you please provide the details.

Thanks and I do appreciate all the guidance provided by the Biomart team.

Thanks and regards,
Parul Kudtarkar

> Dear Parul,
>
> If I understand your question correctly, then yes, this is support in
> BioMart 0.7. Your use case is similar to the ontology filters in Ensembl
> gene data mart. See the query below (please copy and paste the whole URL
> into your web browser):
>
> http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term."endocrine"|hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000198712"&VISIBLEPANEL=resultspanel
>
> In this example, user specify a anatomical term: endocrine, the system
> returns sub-terms that are under it, such as: thyroid, adrenal gland etc.
>
> Briefly, here is how it works: in addition to a usual data mart, we need
> to create a hidden helper mart which does the conversion of user-specified
> term into sub-terms. More specifically, the helper mart has a filter that
> takes the term as input, it also has an exportable that gives output of
> sub-terms. The sub-terms will be fed to the main mart to retrieve
> corresponding records.
>
> Below is how the table in the helper mart looks like for the example I
> gave:
>
> mysql> select * from hsap_evoc_AnatomicalSystem__Vocabulary__main where
> term_108 = "endocrine";
> +----------------------+-----------------+-----------+-------------+
> | unrolled_name        | Node_id_108_key | Term_108  | unrolled_id |
> +----------------------+-----------------+-----------+-------------+
> | endocrine            |             144 | endocrine |         144 |
> | endocrine pancreas   |             144 | endocrine |         145 |
> | pineal gland         |             144 | endocrine |         147 |
> | pituitary gland      |             144 | endocrine |         148 |
> | thyroid              |             144 | endocrine |         149 |
> | parathyroid          |             144 | endocrine |         150 |
> | adrenal gland        |             144 | endocrine |         151 |
> | thymus               |             144 | endocrine |         154 |
> | islets of Langerhans |             144 | endocrine |         146 |
> | adrenal cortex       |             144 | endocrine |         152 |
> | adrenal medulla      |             144 | endocrine |         153 |
> +----------------------+-----------------+-----------+-------------+
> 11 rows in set (0.00 sec)
>
> If you confirm this is what you are looking for, we will provide more
> details on how to create and configure necessary marts.
>
> Cheers,
> Junjun
>
>
> On 11-08-22 1:02 PM, "Parul Kudtarkar"
> <[hidden email]<mailto:[hidden email]>> wrote:
>
> Dear Biomart users,
>
> I want to filter my results based on functional category which has class
> and corresponding sub class. If I select a particular class, I want the
> system to auto pull corresponding sub classes related to that class. For
> example if I select class: Adhesion , I want the system to pull only the
> corresponding sub classes present in the database such as
> Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR,
> Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc.
>
> Is this possible in biomart, if yes how?
>
> Thanks,
> Parul Kudtarkar
>
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
>
>
>
>
>
>
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
> http://www.spbase.org
>
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.biomart.org/mailman/listinfo/users
>
>


--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] Biomart query: Filters

Junjun Zhang
Dear Parul,

Just to clarify that BioMart 0.8 rc6 does support the query we were discussing. It does not support creation of the unrolled dataset, this can be done using MartBuilder in 0.7, Or you can prepare it yourself, you just need to create a table with two columns, one for parent terms, the other for child terms under given parent term. See the example below.

If you are running BioMart 0.8 rc6, you can open one of the registry XML file under 'registry' folder called icgc6.xml in MartConfigurator. This is the registry for the ICGC DCC data portal (dcc.icgc.org). In the data portal, there is a similar filter as well, the 'Pathway name' filter under: http://dcc.icgc.org/martanalysis/#!/Quick/gene_ensembl_config_quick?ds=hsapiens_gene_ensembl_QCMGPancreas&_displayname=Acetylation. Here, user specifies a 'pathway name' for the filter, it converts the pathway to Ensembl Genes that are involved in the specified pathway. 

The following screenshot shows how this filter is configured in Gene quick search.




I understand is not possible to provide all the information in this email for you to set it up yourself. If you need further assistance, maybe we should set up a Skype session to walk you through all of the steps.

For your question about MartView, the answer is no, we do not have similar GUI in 0.8 as it is in 0.7.

Cheers,
Junjun


On 11-08-22 6:31 PM, "Parul Kudtarkar" <[hidden email]> wrote:

Dear Junjun,

This is indeed what I am looking for, however I have installed and created
mart for Biomart 0.8 candidate 6 instead of Biomart 0.7. Is it possible to
do the same with this latest Biomart release?

Could you please provide further details and configuration on creating
hidden helper mart?

Also with regards to GUI; biomart 0.8 offers MartForm, MartWizard,
MartAnalysis and MartExplorer, is it possible to use MartView GUI used by
Biomart 0.7? If yes could you please provide the details.

Thanks and I do appreciate all the guidance provided by the Biomart team.

Thanks and regards,
Parul Kudtarkar

Dear Parul,

If I understand your question correctly, then yes, this is support in
BioMart 0.7. Your use case is similar to the ontology filters in Ensembl
gene data mart. See the query below (please copy and paste the whole URL
into your web browser):

<a href="http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&amp;ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&amp;FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term.&quot;endocrine&quot;|hsapiens_gene_ensembl.default.filters.ensembl_gene_id.&quot;ENSG00000198712&quot;&amp;VISIBLEPANEL=resultspanel">http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term."endocrine"|hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000198712"&VISIBLEPANEL=resultspanel

In this example, user specify a anatomical term: endocrine, the system
returns sub-terms that are under it, such as: thyroid, adrenal gland etc.

Briefly, here is how it works: in addition to a usual data mart, we need
to create a hidden helper mart which does the conversion of user-specified
term into sub-terms. More specifically, the helper mart has a filter that
takes the term as input, it also has an exportable that gives output of
sub-terms. The sub-terms will be fed to the main mart to retrieve
corresponding records.

Below is how the table in the helper mart looks like for the example I
gave:

mysql> select * from hsap_evoc_AnatomicalSystem__Vocabulary__main where
term_108 = "endocrine";
+----------------------+-----------------+-----------+-------------+
| unrolled_name        | Node_id_108_key | Term_108  | unrolled_id |
+----------------------+-----------------+-----------+-------------+
| endocrine            |             144 | endocrine |         144 |
| endocrine pancreas   |             144 | endocrine |         145 |
| pineal gland         |             144 | endocrine |         147 |
| pituitary gland      |             144 | endocrine |         148 |
| thyroid              |             144 | endocrine |         149 |
| parathyroid          |             144 | endocrine |         150 |
| adrenal gland        |             144 | endocrine |         151 |
| thymus               |             144 | endocrine |         154 |
| islets of Langerhans |             144 | endocrine |         146 |
| adrenal cortex       |             144 | endocrine |         152 |
| adrenal medulla      |             144 | endocrine |         153 |
+----------------------+-----------------+-----------+-------------+
11 rows in set (0.00 sec)

If you confirm this is what you are looking for, we will provide more
details on how to create and configure necessary marts.

Cheers,
Junjun


On 11-08-22 1:02 PM, "Parul Kudtarkar"

Dear Biomart users,

I want to filter my results based on functional category which has class
and corresponding sub class. If I select a particular class, I want the
system to auto pull corresponding sub classes related to that class. For
example if I select class: Adhesion , I want the system to pull only the
corresponding sub classes present in the database such as
Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR,
Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc.

Is this possible in biomart, if yes how?

Thanks,
Parul Kudtarkar


--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology







--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology




_______________________________________________
Users mailing list




--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
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Re: [BioMart Users] Biomart query: Filters

Parul Kudtarkar
Dear Junjun,

Thanks for a very prompt response. I shall try this query first with ICGC
as a model and if it is not working we should definitely have a skype
session as per your convenience.

Now that I am navigating through ICGC website I like the latest web
interface that comes with release 0.8 and the many options it offers to
query the mart!

Thanks and regards,
Parul Kudtarkar

> Dear Parul,
>
> Just to clarify that BioMart 0.8 rc6 does support the query we were
> discussing. It does not support creation of the unrolled dataset, this can
> be done using MartBuilder in 0.7, Or you can prepare it yourself, you just
> need to create a table with two columns, one for parent terms, the other
> for child terms under given parent term. See the example below.
>
> If you are running BioMart 0.8 rc6, you can open one of the registry XML
> file under 'registry' folder called icgc6.xml in MartConfigurator. This is
> the registry for the ICGC DCC data portal (dcc.icgc.org). In the data
> portal, there is a similar filter as well, the 'Pathway name' filter
> under:
> http://dcc.icgc.org/martanalysis/#!/Quick/gene_ensembl_config_quick?ds=hsapiens_gene_ensembl_QCMGPancreas&_displayname=Acetylation.
> Here, user specifies a 'pathway name' for the filter, it converts the
> pathway to Ensembl Genes that are involved in the specified pathway.
>
> The following screenshot shows how this filter is configured in Gene quick
> search.
>
>
> [cid:7B21EE9F-0561-49E8-A447-D5B181D7E429]
>
>
> I understand is not possible to provide all the information in this email
> for you to set it up yourself. If you need further assistance, maybe we
> should set up a Skype session to walk you through all of the steps.
>
> For your question about MartView, the answer is no, we do not have similar
> GUI in 0.8 as it is in 0.7.
>
> Cheers,
> Junjun
>
>
> On 11-08-22 6:31 PM, "Parul Kudtarkar"
> <[hidden email]<mailto:[hidden email]>> wrote:
>
> Dear Junjun,
>
> This is indeed what I am looking for, however I have installed and created
> mart for Biomart 0.8 candidate 6 instead of Biomart 0.7. Is it possible to
> do the same with this latest Biomart release?
>
> Could you please provide further details and configuration on creating
> hidden helper mart?
>
> Also with regards to GUI; biomart 0.8 offers MartForm, MartWizard,
> MartAnalysis and MartExplorer, is it possible to use MartView GUI used by
> Biomart 0.7? If yes could you please provide the details.
>
> Thanks and I do appreciate all the guidance provided by the Biomart team.
>
> Thanks and regards,
> Parul Kudtarkar
>
> Dear Parul,
>
> If I understand your question correctly, then yes, this is support in
> BioMart 0.7. Your use case is similar to the ontology filters in Ensembl
> gene data mart. See the query below (please copy and paste the whole URL
> into your web browser):
>
> http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term."endocrine"|hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000198712"&VISIBLEPANEL=resultspanel
>
> In this example, user specify a anatomical term: endocrine, the system
> returns sub-terms that are under it, such as: thyroid, adrenal gland etc.
>
> Briefly, here is how it works: in addition to a usual data mart, we need
> to create a hidden helper mart which does the conversion of user-specified
> term into sub-terms. More specifically, the helper mart has a filter that
> takes the term as input, it also has an exportable that gives output of
> sub-terms. The sub-terms will be fed to the main mart to retrieve
> corresponding records.
>
> Below is how the table in the helper mart looks like for the example I
> gave:
>
> mysql> select * from hsap_evoc_AnatomicalSystem__Vocabulary__main where
> term_108 = "endocrine";
> +----------------------+-----------------+-----------+-------------+
> | unrolled_name        | Node_id_108_key | Term_108  | unrolled_id |
> +----------------------+-----------------+-----------+-------------+
> | endocrine            |             144 | endocrine |         144 |
> | endocrine pancreas   |             144 | endocrine |         145 |
> | pineal gland         |             144 | endocrine |         147 |
> | pituitary gland      |             144 | endocrine |         148 |
> | thyroid              |             144 | endocrine |         149 |
> | parathyroid          |             144 | endocrine |         150 |
> | adrenal gland        |             144 | endocrine |         151 |
> | thymus               |             144 | endocrine |         154 |
> | islets of Langerhans |             144 | endocrine |         146 |
> | adrenal cortex       |             144 | endocrine |         152 |
> | adrenal medulla      |             144 | endocrine |         153 |
> +----------------------+-----------------+-----------+-------------+
> 11 rows in set (0.00 sec)
>
> If you confirm this is what you are looking for, we will provide more
> details on how to create and configure necessary marts.
>
> Cheers,
> Junjun
>
>
> On 11-08-22 1:02 PM, "Parul Kudtarkar"
> <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>>
> wrote:
>
> Dear Biomart users,
>
> I want to filter my results based on functional category which has class
> and corresponding sub class. If I select a particular class, I want the
> system to auto pull corresponding sub classes related to that class. For
> example if I select class: Adhesion , I want the system to pull only the
> corresponding sub classes present in the database such as
> Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR,
> Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc.
>
> Is this possible in biomart, if yes how?
>
> Thanks,
> Parul Kudtarkar
>
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
>
>
>
>
>
>
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
> http://www.spbase.org
>
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
> https://lists.biomart.org/mailman/listinfo/users
>
>
>
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
> http://www.spbase.org
>
>
>


--
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org

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