[BioMart Users] Alerts for database migrations, attribute name changes and the like

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[BioMart Users] Alerts for database migrations, attribute name changes and the like

David Croft
Hi,

Is there any kind of centralized point of distribution for alerts on
changes to the various BioMarts?  We have been going to
http://www.biomart.org/biomart/martservice to get information about
ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
changed - as far as I can work out, we now need to get this data from
http://plants.ensembl.org/biomart/martservice.  We are also having
problems with Dictostelium and Plasmodium genomes, I guess they have
also moved to some more specialized location?

Cheers,

David Croft.
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

Jonathan Guberman
Hello David,

When biomart.org is updated we announce it on this mailing list. For specifics of changes made to individual datasets, you will need to contact the individual data providers.

Your specific problem with Ensembl Plant is a little bit more complicated: the issue is that within one registry dataset names must be unique. In Biomart.org, we have two marts that use the same dataset names for A. Thaliana and O. sativa: Ensembl Plant and Gramene 30 Ensembl Genes. In order to accommodate this, we have a concept of "virtualSchema"; each of these two marts is contained in a virtualSchema. If the dataset name is unique then the virtualSchema can be ignored; however, in this case, because it is not unique, the query must be qualified with the virtualSchema name.

To see this, you may use the XML button in the upper right corner of the query page. For example, for the same query against Ensembl Plant and Gramene 30 you will get the following XMLs:

ENSEMBL PLANT:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.7">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>

GRAMENE:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default2" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>

Notice that for Ensembl Plant, the property is set as virtualSchemaName="default", whereas for Gramene is is "default2".

I imagine that this is also the cause of your problem for Dictostelium and Plasmodium genomes, because they are also still contained at biomart.org.

I hope that helps!

Sincerely,


Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

On 2011-06-09, at 9:33 AM, David Croft wrote:

Hi,

Is there any kind of centralized point of distribution for alerts on
changes to the various BioMarts?  We have been going to
http://www.biomart.org/biomart/martservice to get information about
ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
changed - as far as I can work out, we now need to get this data from
http://plants.ensembl.org/biomart/martservice.  We are also having
problems with Dictostelium and Plasmodium genomes, I guess they have
also moved to some more specialized location?

Cheers,

David Croft.
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

Dan Staines
In reply to this post by David Croft


On 06/09/2011 02:33 PM, David Croft wrote:
>
> Is there any kind of centralized point of distribution for alerts on
> changes to the various BioMarts?  We have been going to
> http://www.biomart.org/biomart/martservice to get information about
> ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
> changed - as far as I can work out, we now need to get this data from
> http://plants.ensembl.org/biomart/martservice.  We are also having
> problems with Dictostelium and Plasmodium genomes, I guess they have
> also moved to some more specialized location?

David,

I suspect the problem with Dicty and Plasmodium is due to the underlying
dataset name changing in the last release of Ensembl Protists adopt the
xyyyy_eg_gene dataset naming convention that applies to other divisions
of Ensembl Genomes.

Apologies for the problems this has caused - let me know if it helps.

Best,

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

David Croft
In reply to this post by Jonathan Guberman
Hi Jonathan,

When biomart.org is updated we announce it on this mailing list. For specifics of changes made to individual datasets, you will need to contact the individual data providers.

OK.

Your specific problem with Ensembl Plant is a little bit more complicated: the issue is that within one registry dataset names must be unique. In Biomart.org, we have two marts that use the same dataset names for A. Thaliana and O. sativa: Ensembl Plant and Gramene 30 Ensembl Genes. In order to accommodate this, we have a concept of "virtualSchema"; each of these two marts is contained in a virtualSchema. If the dataset name is unique then the virtualSchema can be ignored; however, in this case, because it is not unique, the query must be qualified with the virtualSchema name.

To see this, you may use the XML button in the upper right corner of the query page. For example, for the same query against Ensembl Plant and Gramene 30 you will get the following XMLs:

ENSEMBL PLANT:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.7">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>

GRAMENE:
<!DOCTYPE Query SYSTEM "null">
<Query virtualSchemaName="default2" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">
<Dataset name="athaliana_eg_gene" interface="default">
<Attribute name="ensembl_gene_id"/>
<Attribute name="ensembl_transcript_id"/>
</Dataset>
</Query>

Notice that for Ensembl Plant, the property is set as virtualSchemaName="default", whereas for Gramene is is "default2".

I imagine that this is also the cause of your problem for Dictostelium and Plasmodium genomes, because they are also still contained at biomart.org.

This was indeed one of the problems.  I also found that (for rice) I needed to point the BioMart at http://plants.ensembl.org/biomart/martservice, rather than at http://www.biomart.org/biomart/martservice, as we had originally being doing.

One thing that I noticed was that the virtual schema we had to use was plant_mart_9.  Will this always remain the same, or is the "9" some kind of release or version number that could change with time?

Cheers,

David Croft.

Is there any kind of centralized point of distribution for alerts on
changes to the various BioMarts?  We have been going to
http://www.biomart.org/biomart/martservice to get information about
ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
changed - as far as I can work out, we now need to get this data from
http://plants.ensembl.org/biomart/martservice.  We are also having
problems with Dictostelium and Plasmodium genomes, I guess they have
also moved to some more specialized location?

Cheers,

David Croft.
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

David Croft
In reply to this post by Dan Staines
Hi Dan,

>
>> Is there any kind of centralized point of distribution for alerts on
>> changes to the various BioMarts?  We have been going to
>> http://www.biomart.org/biomart/martservice to get information about
>> ENSEMBL A.Thaliana and O.sativa genomes, but the location seems to have
>> changed - as far as I can work out, we now need to get this data from
>> http://plants.ensembl.org/biomart/martservice.  We are also having
>> problems with Dictostelium and Plasmodium genomes, I guess they have
>> also moved to some more specialized location?
>
> I suspect the problem with Dicty and Plasmodium is due to the
> underlying dataset name changing in the last release of Ensembl
> Protists adopt the xyyyy_eg_gene dataset naming convention that
> applies to other divisions of Ensembl Genomes.
>
> Apologies for the problems this has caused - let me know if it helps.
>
It did!  Thanks for letting me know, I can now access these databases.

Cheers,

David.
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

Jonathan Guberman
In reply to this post by David Croft
On 2011-06-10, at 4:54 AM, David Croft wrote:

This was indeed one of the problems.  I also found that (for rice) I needed to point the BioMart at http://plants.ensembl.org/biomart/martservice, rather than athttp://www.biomart.org/biomart/martservice, as we had originally being doing.

One thing that I noticed was that the virtual schema we had to use was plant_mart_9.  Will this always remain the same, or is the "9" some kind of release or version number that could change with time?

The virtualSchema change should allow you to query www.biomart.org. The other server (plants.ensembl.org) is not run by us, it is run by Ensembl, so I can't comment on their naming scheme and whether it may change with time. I imagine that it will, though, when they release version 10.

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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

Dan Staines

>> One thing that I noticed was that the virtual schema we had to use was
>> plant_mart_9.  Will this always remain the same, or is the "9" some
>> kind of release or version number that could change with time?
>
> The virtualSchema change should allow you to query www.biomart.org
> <http://www.biomart.org>. The other server (plants.ensembl.org
> <http://plants.ensembl.org>) is not run by us, it is run by Ensembl, so
> I can't comment on their naming scheme and whether it may change with
> time. I imagine that it will, though, when they release version 10.

The naming scheme uses the Ensembl Genomes (as opposed to Ensembl)
release number, and should be stable for the foreseeable future - we
increment the number by 1 for each EG release, so the next one (July)
will be plant_mart_10.

Thanks,

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
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Re: [BioMart Users] Alerts for database migrations, attribute name changes and the like

David Croft
Hi Dan,

>
>>> One thing that I noticed was that the virtual schema we had to use was
>>> plant_mart_9.  Will this always remain the same, or is the "9" some
>>> kind of release or version number that could change with time?
>>
>> The virtualSchema change should allow you to query www.biomart.org
>> <http://www.biomart.org>. The other server (plants.ensembl.org
>> <http://plants.ensembl.org>) is not run by us, it is run by Ensembl, so
>> I can't comment on their naming scheme and whether it may change with
>> time. I imagine that it will, though, when they release version 10.
>
> The naming scheme uses the Ensembl Genomes (as opposed to Ensembl)
> release number, and should be stable for the foreseeable future - we
> increment the number by 1 for each EG release, so the next one (July)
> will be plant_mart_10.
>
Is there a generic virtual schema name that always points to the current
plant Mart?  If not, will plant_mart_9 continue to work forever, even
after the next Ensembl Genomes release is out?

Cheers,

David Croft.
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