Re: [BioMart Users] BioMart Question

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Re: [BioMart Users] BioMart Question

Youens-Clark, Ken
BioMart developers,

A user describes a problem with programmatic access to BioMart as follows:

> When  accessing the data sets for the mart ENSEMBL_MART_PLANT via the MartService at biomart.org, an error is being generated if the virtualschema=default parameter is not included.
>
> Example:
>
> this isn't working
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyrata_eg_gene
>
> and this is
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyrata_eg_gene&virtualschema=default
>
> The services are accessed via the MartService urls.  To access the mart in question we are using the url:
>
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyrata_eg_gene
>
> which currently responds:
> Dataset name conflict for alyrata_eg_gene. Need to further qualify with the virtualSchema param as well
>
> If I add the virtualschema parameter as default, the correct information is retrieved:
>
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyrata_eg_gene&virtualschema=default
>
> However, based upon the  documentation, the virtualschema is 'default' by default.  Do we have to  alter the client code to include the virtualschema=default parameter?  Based on our reading of the docs it shouldn't be required, e.g. accessing http://www.gramene.org/biomart/martservice?type=configuration&dataset=alyrata_eg_gene it is unnecessary.
>
> If this doesn't make sense, let me know.

I would appreciate any advice you could provide.

--
Ken Youens-Clark
[hidden email]
Gramene.org Project Manager
Ware Lab/CSHL/USDA-ARS



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Re: [BioMart Users] BioMart Question

Junjun Zhang
Hi Ken,


Yes, this is confusing.

Here is how it works. As the central portal, biomart.org federates
databases from different data providers. With more data sources to be
federated, it is unavoidable that datasets from different sources may have
the same name. In such case, we have to put these data sources in
different virtual schemas.

When a dataset name is globally uniquely in biomart server, you don't need
to specify which virtualSchema in order to access its configuration. This
is why
http://www.gramene.org/biomart/martservice?type=configuration&dataset=alyra
ta_eg_gene works without virtualSchema=default. But in the case of
biomart.org, since there are two datasets are named as alyrata_eg_gene,
when you access configuration you will have to specify the virtualSchema.
In biomart.org, alyrata_eg_gene exists in default and default2
virtualSchema:

http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyra
ta_eg_gene&virtualschema=default


http://www.biomart.org/biomart/martservice?type=configuration&dataset=alyra
ta_eg_gene&virtualschema=default2


BTW, it is the second one (default2) that is the same as
http://www.gramene.org/biomart/martservice?type=configuration&dataset=alyra
ta_eg_gen

One thing to note is that when a dataset name is globally unique, and can
be access without specifying the virtualSchema does not mean that dataset
is under virtaulSchema. Here is one example:

http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p
ancreas (this works)


http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p
ancreas&virtualSchema=default2 (this works)


http://www.biomart.org/biomart/martservice?type=configuration&dataset=cnv_p
ancreas&virtualSchema=default (this doesn't work)



Junjun



On 11-08-26 11:57 AM, "Youens-Clark, Ken" <[hidden email]> wrote:

>BioMart developers,
>
>A user describes a problem with programmatic access to BioMart as
>follows:
>
>> When  accessing the data sets for the mart ENSEMBL_MART_PLANT via the
>>MartService at biomart.org, an error is being generated if the
>>virtualschema=default parameter is not included.
>>
>> Example:
>>
>> this isn't working
>>
>>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly
>>rata_eg_gene
>>
>> and this is
>>
>>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly
>>rata_eg_gene&virtualschema=default
>>
>> The services are accessed via the MartService urls.  To access the mart
>>in question we are using the url:
>>
>>
>>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly
>>rata_eg_gene
>>
>> which currently responds:
>> Dataset name conflict for alyrata_eg_gene. Need to further qualify with
>>the virtualSchema param as well
>>
>> If I add the virtualschema parameter as default, the correct
>>information is retrieved:
>>
>>
>>http://www.biomart.org/biomart/martservice?type=configuration&dataset=aly
>>rata_eg_gene&virtualschema=default
>>
>> However, based upon the  documentation, the virtualschema is 'default'
>>by default.  Do we have to  alter the client code to include the
>>virtualschema=default parameter?  Based on our reading of the docs it
>>shouldn't be required, e.g. accessing
>>http://www.gramene.org/biomart/martservice?type=configuration&dataset=aly
>>rata_eg_gene it is unnecessary.
>>
>> If this doesn't make sense, let me know.
>
>I would appreciate any advice you could provide.
>
>--
>Ken Youens-Clark
>[hidden email]
>Gramene.org Project Manager
>Ware Lab/CSHL/USDA-ARS
>
>
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

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