[biomart-users] xml in meta__template__xml and meta__conf__xml. What's the diff?

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[biomart-users] xml in meta__template__xml and meta__conf__xml. What's the diff?

joe carlson
Here is an old question I've had about biomart 0.7 which I cannot quite figure out.

The xml in the table meta_conf__xml__dm and meta_template__xml__dm is similar (after decompressing meta_template__xml_dm, of course) but not exactly the same. Our biomart has long gotten to the point that updating the filters and attributes using marteditor is tedious and error prone. So I've been updating the xml by starting with a template created in marteditor and adding to the entries as needed.

It's been working fine. But I've never quite understood the distinction between the 2 xml's. And cannot quite follow the code to find when one is used and not the other. Is there a simple explanation?

Thanks,

Joe Carlson

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Re: [biomart-users] xml in meta__template__xml and meta__conf__xml. What's the diff?

Arek Kasprzyk
Hi Joe,

if the memory serves me right ... 

Template xml captures common elements between different datasets that are very similar (we refer to them sometimes as 'partitions of the same dataset'). A good example is species in Ensembl dataset. In such cases individual dataset xml are generated from the template xml taking into account small differences between them e.g filling out place holders with species names etc.



a.

On 24 July 2017 at 22:47, <[hidden email]> wrote:
Here is an old question I've had about biomart 0.7 which I cannot quite figure out.

The xml in the table meta_conf__xml__dm and meta_template__xml__dm is similar (after decompressing meta_template__xml_dm, of course) but not exactly the same. Our biomart has long gotten to the point that updating the filters and attributes using marteditor is tedious and error prone. So I've been updating the xml by starting with a template created in marteditor and adding to the entries as needed.

It's been working fine. But I've never quite understood the distinction between the 2 xml's. And cannot quite follow the code to find when one is used and not the other. Is there a simple explanation?

Thanks,

Joe Carlson

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