[biomart-users] Obtaining gene summary through biomaRt

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[biomart-users] Obtaining gene summary through biomaRt

Kristoffer Vitting-Seerup
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

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Re: [biomart-users] Obtaining gene summary through biomaRt

Arek Kasprzyk
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

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Re: [biomart-users] Obtaining gene summary through biomaRt

Kristoffer Vitting-Seerup
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

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That means you've stood up for something, sometime in your life.”

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Re: [biomart-users] Obtaining gene summary through biomaRt

Arek Kasprzyk
Hi Kristoffer,

there is a description attribute if this is I correctly understand what you are after:

e.g 


Inline images 1




On 26 November 2013 13:14, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

--
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That means you've stood up for something, sometime in your life.”

― Winston Churchill






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― Winston Churchill


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Re: [biomart-users] Obtaining gene summary through biomaRt

Kristoffer Vitting-Seerup
Unfortunatly not - it is the full gene summary.

Example from the link in the first mail for the KRAS gene (http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 ):

This is what i'm after:
" This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008] "

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer,

there is a description attribute if this is I correctly understand what you are after:

e.g 


Inline images 1




On 26 November 2013 13:14, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

--
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That means you've stood up for something, sometime in your life.”

― Winston Churchill






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That means you've stood up for something, sometime in your life.”

― Winston Churchill



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Re: [biomart-users] Obtaining gene summary through biomaRt

Arek Kasprzyk

ok. I understand.  We'll need help from Ensembl experts :)

Rhoda: Does Ensembl provide any other type of gene description from the one that I already included in my previous example?


a





On 26 November 2013 15:36, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Unfortunatly not - it is the full gene summary.

Example from the link in the first mail for the KRAS gene (http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 ):

This is what i'm after:
" This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008] "

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer,

there is a description attribute if this is I correctly understand what you are after:

e.g 


Inline images 1




On 26 November 2013 13:14, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

--
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--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill


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Re: [biomart-users] Obtaining gene summary through biomaRt

Rhoda Kinsella
Hi Kristoffer
Please email the Ensembl helpdesk with your question and someone will be able to give you advice ([hidden email])
Cheers
Rhoda



On 26 Nov 2013, at 14:44, Arek Kasprzyk <[hidden email]> wrote:


ok. I understand.  We'll need help from Ensembl experts :)

Rhoda: Does Ensembl provide any other type of gene description from the one that I already included in my previous example?


a





On 26 November 2013 15:36, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Unfortunatly not - it is the full gene summary.

Example from the link in the first mail for the KRAS gene (http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 ):

This is what i'm after:
" This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008] "

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer,

there is a description attribute if this is I correctly understand what you are after:

e.g 


<image.png>




On 26 November 2013 13:14, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <[hidden email]>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <[hidden email]> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

--
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--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






--


“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill



Rhoda Kinsella Ph.D.
Ensembl Production Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,
Cambridge
CB10 1SD




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Re: [biomart-users] Obtaining gene summary through biomaRt

Xulong Wang
R package mygene can do this.
http://www.bioconductor.org/packages/release/bioc/html/mygene.html

Highly recommend biomart to incorporate the gene summary information.

On Tuesday, November 26, 2013 at 9:55:48 AM UTC-5, Rhoda Kinsella wrote:
Hi Kristoffer
Please email the Ensembl helpdesk with your question and someone will be able to give you advice (<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">help...@...)
Cheers
Rhoda



On 26 Nov 2013, at 14:44, Arek Kasprzyk <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">arek.k...@...> wrote:


ok. I understand.  We'll need help from Ensembl experts :)

Rhoda: Does Ensembl provide any other type of gene description from the one that I already included in my previous example?


a





On 26 November 2013 15:36, Kristoffer Vitting-Seerup <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">tall...@...> wrote:
Unfortunatly not - it is the full gene summary.

Example from the link in the first mail for the KRAS gene (<a href="http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=3845" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%3Fcmd%3DRetrieve%26dopt%3Dfull_report%26list_uids%3D3845\46sa\75D\46sntz\0751\46usg\75AFQjCNGlw3t-mSCpnsQTsg_JcMRPTgOofA';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%3Fcmd%3DRetrieve%26dopt%3Dfull_report%26list_uids%3D3845\46sa\75D\46sntz\0751\46usg\75AFQjCNGlw3t-mSCpnsQTsg_JcMRPTgOofA';return true;">http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 ):

This is what i'm after:
" This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008] "

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">arek.k...@...>
Hi Kristoffer,

there is a description attribute if this is I correctly understand what you are after:

e.g 


<image.png>




On 26 November 2013 13:14, Kristoffer Vitting-Seerup <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">tall...@...> wrote:
Hi Arek

I think you misunderstood me, I was referring to all the information, just the gene summary (meaning the sort text written on the pages (This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family..."))

M.v.h.
Kristoffer Vitting-Seerup


2013/11/26 Arek Kasprzyk <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">arek.k...@...>
Hi Kristoffer
There is a large number of gene attributes that could be used to build such page. (For instance please have a look at the <a href="http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartview%2Feda3f22766b5735a0b78e0737b334b18\46sa\75D\46sntz\0751\46usg\75AFQjCNHyq8cFebl3na7nG-tr7u89UqEPFQ';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartview%2Feda3f22766b5735a0b78e0737b334b18\46sa\75D\46sntz\0751\46usg\75AFQjCNHyq8cFebl3na7nG-tr7u89UqEPFQ';return true;">http://www.biomart.org/biomart/martview/eda3f22766b5735a0b78e0737b334b18 and click 'attributes' on the left hand side and browse them in the right panel).   I am assuming  (Steffen to correct me here) that all these attributes are available from the biomaRt packege?


a


On 20 November 2013 10:41, Kristoffer Vitting-Seerup <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="SBAtc5xbzfEJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">tall...@...> wrote:
Hi All

To help my collaborators dig through long lists of significantly differentially expressed genes I would like to supply each gene not only with the full length gene name (for example obtained though ensembl's attributed mgi_description) but also a summary of each gene. Such gene summaries are out there ( <a href="http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=3845" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%3Fcmd%3DRetrieve%26dopt%3Dfull_report%26list_uids%3D3845\46sa\75D\46sntz\0751\46usg\75AFQjCNGlw3t-mSCpnsQTsg_JcMRPTgOofA';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%3Fcmd%3DRetrieve%26dopt%3Dfull_report%26list_uids%3D3845\46sa\75D\46sntz\0751\46usg\75AFQjCNGlw3t-mSCpnsQTsg_JcMRPTgOofA';return true;">http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=3845 , <a href="http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&amp;search=ras" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.genecards.org%2Fcgi-bin%2Fcarddisp.pl%3Fgene%3DKRAS%26search%3Dras\46sa\75D\46sntz\0751\46usg\75AFQjCNFuRMQTVZMm8oeiB7NbIiUxQTLhoA';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.genecards.org%2Fcgi-bin%2Fcarddisp.pl%3Fgene%3DKRAS%26search%3Dras\46sa\75D\46sntz\0751\46usg\75AFQjCNFuRMQTVZMm8oeiB7NbIiUxQTLhoA';return true;">http://www.genecards.org/cgi-bin/carddisp.pl?gene=KRAS&search=ras )

But I cannot figure out to obtain them through biomart!

Can anybody help me?

Kindest Regards
Kristoffer Vitting-Seerup

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“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






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“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill






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“You have enemies? Good. 
That means you've stood up for something, sometime in your life.”

― Winston Churchill



Rhoda Kinsella Ph.D.
Ensembl Production Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,
Cambridge
CB10 1SD




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