[Bioc-devel] Updates: biomaRt

Steffen Durinck steffen.durinck at esat.kuleuven.be
Mon Dec 12 14:59:26 CET 2005

The initial release of biomaRt contained a large amount of hard coded
queries and didn't make advantage of the xml description (describing the
database) present in each BioMart database.
Here we want to highlight the incorporation of this xml description in the
biomaRt package.  Additional to the original set of biomaRt functions
(getGene, getGO, getOMIM, getINTERPRO and getHOMOLOG), the package now has
a second set of more advanced functions (listMarts, useMart, listDatasets,
useDataset, listFilters, listAttributes and getBM).  These new functions
enable data retrieval of many more fields equivalent to other BioMart
API's as for example http://www.ensembl.org/Multi/martview
The functions are also more robust to database changes as they don't
contain any hard coded queries and any new BioMart database can be
included without code changes in the package.

The current BioMart databases that can be queried with biomaRt are:

 Ensembl: http://www.ensembl.org/Multi/martview
 Uniprot, VEGA, SNP_mart and MSD:  http://www.ebi.ac.uk/BioMart/martview

New BioMart databases that have recently been released are:

 Wormbase: http://www.wormbase.org/biomart/martview
 Gramene: http://www.gramene.org/Multi/martview
 HapMap:  http://hapmart.hapmap.org/BioMart/martview

As soon as public MySQL access to these new BioMarts becomes available
they will be incorporated in the biomaRt package.


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