[biomart-users] Custom Biomart on Chado database - creating new links?

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[biomart-users] Custom Biomart on Chado database - creating new links?

Colin
Hi all,
I am trying to create a Biomart using a Chado database, and it has gone fairly good, but I am stuck on a little problem.

I have BioMart centered on the Chado "feature" table, and it is linked to a "featureloc" (location) table, but I am having trouble using featureloc to tell me what chromosome my features are on. This is because the featureloc table has a "srcfeature_id" column that points back to the feature table to indicate the “chromosome level” features. Is it possible to get biomart to recognize this sort of problem with "two levels" of indirection?

I am currently using biomart-perl (0.7) and the martj MartBuilder currently.


Thanks
-Colin

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Re: [biomart-users] Custom Biomart on Chado database - creating new links?

Arek Kasprzyk
Hi Colin,
I do understand the recursive referencing in chado database quite well because did some BioMart prototyping work on this in the past. However, this was never implemented. So the short answer to you question: "No, it is not possible at present"

a


On 27 March 2014 19:54, Colin D <[hidden email]> wrote:
Hi all,
I am trying to create a Biomart using a Chado database, and it has gone fairly good, but I am stuck on a little problem.

I have BioMart centered on the Chado "feature" table, and it is linked to a "featureloc" (location) table, but I am having trouble using featureloc to tell me what chromosome my features are on. This is because the featureloc table has a "srcfeature_id" column that points back to the feature table to indicate the “chromosome level” features. Is it possible to get biomart to recognize this sort of problem with "two levels" of indirection?

I am currently using biomart-perl (0.7) and the martj MartBuilder currently.


Thanks
-Colin

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy


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Re: [biomart-users] Custom Biomart on Chado database - creating new links?

Colin
Alright, thanks for checking! I'll probably create a new featureloc type table that works better for this case.

-Colin


On Fri, Mar 28, 2014 at 4:51 AM, Arek Kasprzyk <[hidden email]> wrote:
Hi Colin,
I do understand the recursive referencing in chado database quite well because did some BioMart prototyping work on this in the past. However, this was never implemented. So the short answer to you question: "No, it is not possible at present"

a


On 27 March 2014 19:54, Colin D <[hidden email]> wrote:
Hi all,
I am trying to create a Biomart using a Chado database, and it has gone fairly good, but I am stuck on a little problem.

I have BioMart centered on the Chado "feature" table, and it is linked to a "featureloc" (location) table, but I am having trouble using featureloc to tell me what chromosome my features are on. This is because the featureloc table has a "srcfeature_id" column that points back to the feature table to indicate the “chromosome level” features. Is it possible to get biomart to recognize this sort of problem with "two levels" of indirection?

I am currently using biomart-perl (0.7) and the martj MartBuilder currently.


Thanks
-Colin

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy



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