On 15/04/10 4:53 AM, "Leandro Hermida" <[email protected]> wrote:
> Hi everyone,
>
> Would anyone be able to give a comparison and contrast of BioMart and
> Intermine?
>
> -Leandro
>
Hi Leandro,
Here it is my (naturally biased ;) comparison.
The key features that distinguish BioMart from flymine/intermine/modmine etc
are as follows:
1. Generic (data agnostic) platform.
A. BioMart makes no assumptions about underlying data. It can be as
easily applied to biological as well as non-biological data
2. Scalability
A. BioMart uses a query optimized schema that has been designed for
efficient retrieval of large datasets
B. Parallel query processing (only available in 0.8) will further
improve the scalability of the system
3. Data federation
A. BioMart has the ability to federate databases.
B. This will be further enhanced in 0.8 for both speed and number of
databases that can be federated
4. Ease of deployment
A. BioMart includes tools to facilitate deployment from relational
sources. (MEditor, MBuilder)
B. In addition (0.8) will allow to create 'virtual marts' without the
need to replicate data. This feature will be particularly useful for small
datasets or fast prototyping
5. Established software.
BioMart is being used in a number of well established project both in
academia and industry (at least 35 public data sources are currently
using BioMart software) (see biomart.org) and can be utilized for the
federation purposes. It also has a large deployer and user community
6. Programmatic access and third party plugins
BioMart has much richer programmatic interface and a growing number of
third party plugins (see biomart.org)
In short:
BioMart is a particularily good fit if you are thinking either about large
collaborative project (such as ICGC) or about a single data source that
needs to be deployed quickly and take advantage of other data sources in
public domain that can be used to enhance the querying capabilities of your
data source through the federation mechanism
Hope that helps,
a
