On 18/05/10 4:30 PM, "Kan, Zhengyan" <[email protected]> wrote:
> Hi, everyone:
>
> Thanks for your helpful replies. It is encouraging to know that the
> problem already has a solution, I guess I just need to find out how
> COSMIC is converted into a Biomart.
>
> I understand that as long as data is transformed into 'reverse-star'
> schema, it can be turned into a Biomart. But I'm not sure whether
> reverse-star is suitable for all types of data sets. For each Biomart
> dataset, my understanding is that it centers on a hub, an entity that
> other tables are linked to through foreign-key relationships. For
> COSMIC, I cannot find a single hub that links all the tables together. I
> had to create multiple data sets, each centered around concepts such as
> 'sample', 'gene' and 'paper'.
Yes, this is exactly how you approach the problem. These correspond to entry
points for end users. If you want to search samples you go through sample
entry point, if you want to search genes you go through gene entry point
etc. You can also have mutation as entry point if you think that this is how
your users want to interact with the data. The usual routine is to first
collect the set of 'use cases' from the users and then decide on how many
different datasets (entry points) you need.
a
>
> It seems to me that COSMIC is more suitable for a 'star' schema with
> 'mutation' being the entity that holds everything together. If a data
> set is more suitable for a 'star' schema, does this mean that it is not
> suitable to be transformed into a Biomart?
>
> Zhengyan (George) Kan
>
> -----Original Message-----
> From: Syed Haider [mailto:[email protected]]
> Sent: Friday, May 14, 2010 7:39 PM
> To: Kan, Zhengyan
> Cc: [email protected]
> Subject: Re: [mart-dev] dataset not suitable for biomart?
>
> Hi George,
>
> BioMart reverse-star schema is independent of any biological concepts,
> hence can be used to model any kind of 'omics data. As far as the COSMIC
>
> goes, could you please let us know what difficulties did you face ? we
> are happy to help.
>
> Best
> Syed
>
> On 15/05/2010 01:47, Kan, Zhengyan wrote:
>> Hi, Bio-mart team:
>>
>> I wonder if there are some data sets not suitable for transformation
>> into Biomart. In my experience, I had difficulties transforming the
>> COSMIC database into Biomart as the data is very decentralized. It may
>> just be my lack of knowledge about the Biomart system though.
>>
>> My understanding is that Biomart uses a 'top-down', reverse-star
> schema.
>> Should this type of schema applicable to all genomic data sets or just
> a
>> limited spectrum?
>>
>> Many thanks!
>>
>> Zhengyan (George) Kan
>> Computational Biology
>> Pfizer, La Jolla
>>
>>
