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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