[BioMart Users] General query

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[BioMart Users] General query

Morgan Mouchka
Hello,

I'm currently using the ID converter to convert UniPort/SwissProt Accessions to GO and then GO slim identifiers.  I'm wondering if there is a way to also obtain the GO term names (e.g. transport, RNA metabolic process, etc.) using Biomart?  Of if you have any other suggestions as to the best approach to match the GO IDs with their names.  I can't seem to find method for doing this with multiple sequences. 

Thanks,
Morgan


Morgan Mouchka
PhD Candidate 
E231 Corson Hall
Dept. Ecology and Evolutionary Biology
Cornell University 
[hidden email] 
http://www.eeb.cornell.edu/mouchka



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Re: [BioMart Users] General query

Arek Kasprzyk
Hi Kathleen,
I am forwarding your question to the users mailing list to seek help from Ensembl experts.

Rhoda: are you planning to make the attribute that Kathleen is after available at some point?


cheers,
a



On 5 April 2013 17:41, kathleen askland <[hidden email]> wrote:
Hi Arek,
I'm using the regular biomart portal: http://central.biomart.org/
I choose: Database>Gene Annotation>Hugo Gene Nomenclature (HGNC) (EBI, UK), then choose Dataset: HGNC data.
Once HGNC data (dataset) is chosen, I click 'Next' which brings me to the filter selection screen. I don't want to filter, I want all symbols, so I make no filtering selection. I click 'Next' again,  which brings me to the Attributes selection screen. I can select 'Approved Name' and 'Previous Symbols,' but not 'Approved Symbol' (or any option for active symbols.) So, I make my selections and, regardless of what I choose (I tried several different times), I do not get output with the current, approved symbols.
(I will be on vacation from today through 4/15, so if I don't respond right away, that is why.)
Thanks for your help.
Kathleen


On Fri, Apr 5, 2013 at 4:54 AM, Arek Kasprzyk <[hidden email]> wrote:
Hi Kathleen,
which BioMart portal are you using? Could you describe it to me please and send me the URL?

cheers,
a


On 26 March 2013 18:24, kathleen askland <[hidden email]> wrote:
Hello,
I am attempting to download the full set of HGNC gene symbols (as well as some additional information such as HGNC id, locus type, status, etc...) through BioMart,Database: Hugo Gene Nomenclature (HGNC) (EBI, UK), Dataset: HGNC data. However, I'm puzzled by the fact that HGNC gene symbol does not appear to be one of the output features available for selection. I can choose the HGNC id and the 'Approved Name' (which is the full HGNC descriptive gene name), but not the symbol.
Any suggestions?
Kathleen

--
‘It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so.’ -Mark Twain
---
Kathleen Askland, MD
Assistant Professor
Department of Psychiatry & Human Behavior
Warren Alpert School of Medicine
Brown University/Butler Hospital




--
‘It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so.’ -Mark Twain
---
Kathleen Askland, MD
Assistant Professor
Department of Psychiatry & Human Behavior
Warren Alpert School of Medicine
Brown University/Butler Hospital


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Re: [BioMart Users] General query

Arek Kasprzyk
In reply to this post by Morgan Mouchka
Hi Morgan,
Please try our 'wizard interface' accessible under 'database search'.


This should give you what you need

a





On 5 April 2013 15:29, Morgan Mouchka <[hidden email]> wrote:
Hello,

I'm currently using the ID converter to convert UniPort/SwissProt Accessions to GO and then GO slim identifiers.  I'm wondering if there is a way to also obtain the GO term names (e.g. transport, RNA metabolic process, etc.) using Biomart?  Of if you have any other suggestions as to the best approach to match the GO IDs with their names.  I can't seem to find method for doing this with multiple sequences. 

Thanks,
Morgan


Morgan Mouchka
PhD Candidate 
E231 Corson Hall
Dept. Ecology and Evolutionary Biology
Cornell University 
[hidden email] 
http://www.eeb.cornell.edu/mouchka



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



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Re: [BioMart Users] General query

Rhoda Kinsella
In reply to this post by Arek Kasprzyk
Hi Arek and Kathleen,
As I do not create the HGNC BioMart databases, it would be best if you contacted the HGNC group directly. You can contact them using this email address: [hidden email]
Regards
Rhoda



On 8 Apr 2013, at 09:57, Arek Kasprzyk <[hidden email]> wrote:

Hi Kathleen,
I am forwarding your question to the users mailing list to seek help from Ensembl experts.

Rhoda: are you planning to make the attribute that Kathleen is after available at some point?


cheers,
a



On 5 April 2013 17:41, kathleen askland <[hidden email]> wrote:
Hi Arek,
I'm using the regular biomart portal: http://central.biomart.org/
I choose: Database>Gene Annotation>Hugo Gene Nomenclature (HGNC) (EBI, UK), then choose Dataset: HGNC data.
Once HGNC data (dataset) is chosen, I click 'Next' which brings me to the filter selection screen. I don't want to filter, I want all symbols, so I make no filtering selection. I click 'Next' again,  which brings me to the Attributes selection screen. I can select 'Approved Name' and 'Previous Symbols,' but not 'Approved Symbol' (or any option for active symbols.) So, I make my selections and, regardless of what I choose (I tried several different times), I do not get output with the current, approved symbols.
(I will be on vacation from today through 4/15, so if I don't respond right away, that is why.)
Thanks for your help.
Kathleen


On Fri, Apr 5, 2013 at 4:54 AM, Arek Kasprzyk <[hidden email]> wrote:
Hi Kathleen,
which BioMart portal are you using? Could you describe it to me please and send me the URL?

cheers,
a


On 26 March 2013 18:24, kathleen askland <[hidden email]> wrote:
Hello,
I am attempting to download the full set of HGNC gene symbols (as well as some additional information such as HGNC id, locus type, status, etc...) through BioMart,Database: Hugo Gene Nomenclature (HGNC) (EBI, UK), Dataset: HGNC data. However, I'm puzzled by the fact that HGNC gene symbol does not appear to be one of the output features available for selection. I can choose the HGNC id and the 'Approved Name' (which is the full HGNC descriptive gene name), but not the symbol.
Any suggestions?
Kathleen

--
‘It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so.’ -Mark Twain
---
Kathleen Askland, MD
Assistant Professor
Department of Psychiatry & Human Behavior
Warren Alpert School of Medicine
Brown University/Butler Hospital




--
‘It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so.’ -Mark Twain
---
Kathleen Askland, MD
Assistant Professor
Department of Psychiatry & Human Behavior
Warren Alpert School of Medicine
Brown University/Butler Hospital


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




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