[BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

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[BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Jorge Zamora-2
Dear Biomart team,

We have a local ICGC biomart where we need to update the 'Dataset Summary' and the 'Mutation Summary' since both show an incorrect number of samples corresponding to our previous release. Also in the 'Dataset Summary' we would to add an extra pubmed id.

Could you please point me to the place in the documentation to check how do the update?


Thanks
Jorge  



Jorge Zamora Berna. PhD.
Structural Biology and Biocomputing Programme
Spanish National Cancer Research Centre (CNIO)
Melchor Fdez. Almagro, 3 E-28029 Madrid, Spain
+34 91 7328000 ext. 3015
[hidden email]


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Junjun Zhang
Hi Jorge,


ICGC DCC Support (cc'd) is the best place for this question. Some of the
features were not officially advertised in BioMart as they were under
development and subjected to changes.

Junjun


On 11-11-21 3:19 AM, "Zamora.Jorge_Aurelio" <[hidden email]> wrote:

>Dear Biomart team,
>
>We have a local ICGC biomart where we need to update the 'Dataset
>Summary' and the 'Mutation Summary' since both show an incorrect number
>of samples corresponding to our previous release. Also in the 'Dataset
>Summary' we would to add an extra pubmed id.
>
>Could you please point me to the place in the documentation to check how
>do the update?
>
>
>Thanks
>Jorge  
>
>
>
>Jorge Zamora Berna. PhD.
>Structural Biology and Biocomputing Programme
>Spanish National Cancer Research Centre (CNIO)
>Melchor Fdez. Almagro, 3 E-28029 Madrid, Spain
>+34 91 7328000 ext. 3015
>[hidden email]
>
>
>**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
>ficheros adjuntos, pueden contener información protegida para el uso
>exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
>cualquier otro tipo de transmisión por parte de otra persona que no sea
>el destinatario. Si usted recibe por error este correo, se ruega
>comunicarlo al remitente y borrar el mensaje recibido.
>**CONFIDENTIALITY NOTICE** This email communication and any attachments
>may contain confidential and privileged information for the sole use of
>the designated recipient named above. Distribution, reproduction or any
>other use of this transmission by any party other than the intended
>recipient is prohibited. If you are not the intended recipient please
>contact the sender and delete all copies.
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Arek Kasprzyk
Junjun:
I want to make sure that everyone on this list receives an answer to questions related to BioMart configuration and software because they maybe of interest to a wider audience. Please keep them on this list. I'll make sure that your support is cc'ed on anything related to ICGC

a


On Mon, Nov 21, 2011 at 9:55 AM, Junjun Zhang <[hidden email]> wrote:
Hi Jorge,


ICGC DCC Support (cc'd) is the best place for this question. Some of the
features were not officially advertised in BioMart as they were under
development and subjected to changes.

Junjun


On 11-11-21 3:19 AM, "Zamora.Jorge_Aurelio" <[hidden email]> wrote:

>Dear Biomart team,
>
>We have a local ICGC biomart where we need to update the 'Dataset
>Summary' and the 'Mutation Summary' since both show an incorrect number
>of samples corresponding to our previous release. Also in the 'Dataset
>Summary' we would to add an extra pubmed id.
>
>Could you please point me to the place in the documentation to check how
>do the update?
>
>
>Thanks
>Jorge
>
>
>
>Jorge Zamora Berna. PhD.
>Structural Biology and Biocomputing Programme
>Spanish National Cancer Research Centre (CNIO)
>Melchor Fdez. Almagro, 3 E-28029 Madrid, Spain
><a href="tel:%2B34%2091%207328000%20ext.%203015" value="+34917328000">+34 91 7328000 ext. 3015
>[hidden email]
>
>
>**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
>ficheros adjuntos, pueden contener información protegida para el uso
>exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
>cualquier otro tipo de transmisión por parte de otra persona que no sea
>el destinatario. Si usted recibe por error este correo, se ruega
>comunicarlo al remitente y borrar el mensaje recibido.
>**CONFIDENTIALITY NOTICE** This email communication and any attachments
>may contain confidential and privileged information for the sole use of
>the designated recipient named above. Distribution, reproduction or any
>other use of this transmission by any party other than the intended
>recipient is prohibited. If you are not the intended recipient please
>contact the sender and delete all copies.
>
>_______________________________________________
>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
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Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Junjun Zhang
Hi Jorge,

For update the number of total donor in the 'Mutation summary' section in the report, as there is no details about how the gene report is configured in the BioMart documentation, I show you how it was done in the following screenshots.

As you can see in 'Gene Report' access point, under 'Mutation Summary' there are three AttributeLists. In the screenshot below, I highlighted the Simple somatic mutation, this attribute list contains a pseudo attribute named snp_donor_count (as highlighted to the bottom of the screenshot):



The following screenshot shows you how the snp_donor_count is configured. A pseudo attribute is a special attribute that does not dependent on any table column as any normal attribute would. In the 'value' field of an attribute, you can put any string as you like, the string becomes the value of that pseudo attribute. In such case, the value will be a constant. There is a special case where the value is a partition index, denoted as (pxcy), x and y are integers. In the example below, the value is (p0c30), this means the actual value for this pseudo attribute is kept in partition table 0 column 30. I will show you partition table in the next screenshot.



Double-click 'Genes' source to the left main panel, this will bring you the data source management window. At the bottom of this window there is a button: View Partition Table. Click that will show you the partition table, column 30 is highlighted as below, it records all the snp_donor_count value for each different cancer types. As you can see the value for esCLL is 4. This is the value you'd need to update to the new number.



Hope this helps.

Let me know if there is anything unclear to you.

Junjun


From: Arek Kasprzyk <[hidden email]>
Date: Mon, 21 Nov 2011 12:30:58 -0500
To: jzhang <[hidden email]>
Cc: "Zamora.Jorge_Aurelio" <[hidden email]>, "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Junjun:
I want to make sure that everyone on this list receives an answer to questions related to BioMart configuration and software because they maybe of interest to a wider audience. Please keep them on this list. I'll make sure that your support is cc'ed on anything related to ICGC

a


On Mon, Nov 21, 2011 at 9:55 AM, Junjun Zhang <[hidden email]> wrote:
Hi Jorge,


ICGC DCC Support (cc'd) is the best place for this question. Some of the
features were not officially advertised in BioMart as they were under
development and subjected to changes.

Junjun


On 11-11-21 3:19 AM, "Zamora.Jorge_Aurelio" <[hidden email]> wrote:

>Dear Biomart team,
>
>We have a local ICGC biomart where we need to update the 'Dataset
>Summary' and the 'Mutation Summary' since both show an incorrect number
>of samples corresponding to our previous release. Also in the 'Dataset
>Summary' we would to add an extra pubmed id.
>
>Could you please point me to the place in the documentation to check how
>do the update?
>
>
>Thanks
>Jorge
>
>
>
>Jorge Zamora Berna. PhD.
>Structural Biology and Biocomputing Programme
>Spanish National Cancer Research Centre (CNIO)
>Melchor Fdez. Almagro, 3 E-28029 Madrid, Spain
><a href="tel:%2B34%2091%207328000%20ext.%203015" value="+34917328000">+34 91 7328000 ext. 3015
>[hidden email]
>
>
>**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
>ficheros adjuntos, pueden contener información protegida para el uso
>exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
>cualquier otro tipo de transmisión por parte de otra persona que no sea
>el destinatario. Si usted recibe por error este correo, se ruega
>comunicarlo al remitente y borrar el mensaje recibido.
>**CONFIDENTIALITY NOTICE** This email communication and any attachments
>may contain confidential and privileged information for the sole use of
>the designated recipient named above. Distribution, reproduction or any
>other use of this transmission by any party other than the intended
>recipient is prohibited. If you are not the intended recipient please
>contact the sender and delete all copies.
>
>_______________________________________________
>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
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Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Jorge Zamora-2
Thanks for the screen-shots Junjun,

it's all clear now.

Jorge


On 11/22/2011 06:47 AM, Junjun Zhang wrote:
Hi Jorge,

For update the number of total donor in the 'Mutation summary' section in the report, as there is no details about how the gene report is configured in the BioMart documentation, I show you how it was done in the following screenshots.

As you can see in 'Gene Report' access point, under 'Mutation Summary' there are three AttributeLists. In the screenshot below, I highlighted the Simple somatic mutation, this attribute list contains a pseudo attribute named snp_donor_count (as highlighted to the bottom of the screenshot):



The following screenshot shows you how the snp_donor_count is configured. A pseudo attribute is a special attribute that does not dependent on any table column as any normal attribute would. In the 'value' field of an attribute, you can put any string as you like, the string becomes the value of that pseudo attribute. In such case, the value will be a constant. There is a special case where the value is a partition index, denoted as (pxcy), x and y are integers. In the example below, the value is (p0c30), this means the actual value for this pseudo attribute is kept in partition table 0 column 30. I will show you partition table in the next screenshot.



Double-click 'Genes' source to the left main panel, this will bring you the data source management window. At the bottom of this window there is a button: View Partition Table. Click that will show you the partition table, column 30 is highlighted as below, it records all the snp_donor_count value for each different cancer types. As you can see the value for esCLL is 4. This is the value you'd need to update to the new number.



Hope this helps.

Let me know if there is anything unclear to you.

Junjun


From: Arek Kasprzyk <[hidden email]>
Date: Mon, 21 Nov 2011 12:30:58 -0500
To: jzhang <[hidden email]>
Cc: "Zamora.Jorge_Aurelio" <[hidden email]>, "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] updating 'Dataset Summary' and 'Mutation Summary'

Junjun:
I want to make sure that everyone on this list receives an answer to questions related to BioMart configuration and software because they maybe of interest to a wider audience. Please keep them on this list. I'll make sure that your support is cc'ed on anything related to ICGC

a


On Mon, Nov 21, 2011 at 9:55 AM, Junjun Zhang <[hidden email]> wrote:
Hi Jorge,


ICGC DCC Support (cc'd) is the best place for this question. Some of the
features were not officially advertised in BioMart as they were under
development and subjected to changes.

Junjun


On 11-11-21 3:19 AM, "Zamora.Jorge_Aurelio" <[hidden email]> wrote:

>Dear Biomart team,
>
>We have a local ICGC biomart where we need to update the 'Dataset
>Summary' and the 'Mutation Summary' since both show an incorrect number
>of samples corresponding to our previous release. Also in the 'Dataset
>Summary' we would to add an extra pubmed id.
>
>Could you please point me to the place in the documentation to check how
>do the update?
>
>
>Thanks
>Jorge
>
>
>
>Jorge Zamora Berna. PhD.
>Structural Biology and Biocomputing Programme
>Spanish National Cancer Research Centre (CNIO)
>Melchor Fdez. Almagro, 3 E-28029 Madrid, Spain
><a moz-do-not-send="true" href="tel:%2B34%2091%207328000%20ext.%203015" value="+34917328000">+34 91 7328000 ext. 3015
>[hidden email]
>
>
>**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
>ficheros adjuntos, pueden contener información protegida para el uso
>exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
>cualquier otro tipo de transmisión por parte de otra persona que no sea
>el destinatario. Si usted recibe por error este correo, se ruega
>comunicarlo al remitente y borrar el mensaje recibido.
>**CONFIDENTIALITY NOTICE** This email communication and any attachments
>may contain confidential and privileged information for the sole use of
>the designated recipient named above. Distribution, reproduction or any
>other use of this transmission by any party other than the intended
>recipient is prohibited. If you are not the intended recipient please
>contact the sender and delete all copies.
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

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



**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.

**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.


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