Thank you Arek and JunJun for your fast reply, concern and excellent explanations.
Cheers, Núria ________________________________ De: Arek Kasprzyk [mailto:[email protected]] Enviado el: miércoles, 07 de septiembre de 2011 0:38 Para: Junjun Zhang CC: QUERALT, NURIA (IDIBAPS); [email protected] Asunto: Re: [BioMart Users] OUTER JOIN between tables Let's do it properly. Why don't you make a proposal taking into account all use cases and I'll review it. We can take it offlline a On Tue, Sep 6, 2011 at 6:28 PM, Junjun Zhang <[email protected]> wrote: OK, let's make 'left join' the default behaviour. However, we will have to bare it in mind that there are use cases that require 'inner join' between data marts. For example, find the common genes that are over expressed in breast cancer and pancreatic cancer datasets. I understand that we do not support this type of query in the ICGC data portal at this time, but since this is a frequently requested use case we should properly design and implement support for that in the near future. Let's discuss details later. Cheers, Junjun From: Arek Kasprzyk <[email protected]> Date: Tue, 6 Sep 2011 17:55:24 -0400 To: jzhang <[email protected]> Cc: "[email protected]" <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [BioMart Users] OUTER JOIN between tables <snip> >2. left join with inter mart querying needs to be solved with in list >annotation at the same time Just wanted to confirm with you that I understand the 'in list annotation' use case correctly. Do you think the query should behave as inner join for 'in list annotation' and BioMart should support both left join and inner join between different marts? If so, then that's what I see it as well. For that we can make 'left join' the default behaviour (as it's more common) and provide a mechanism to override this in case deployer wants alter that to 'inner join'. </snip> I would just do everything as default left join. In this way people would not be loosing their identifiers when trying to annotate stuff that does not exist in a given mart. For inter-mart querying just the same. We can discuss more technical details offline at some point a
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