Comparison between remart and biomaRt

18 August 2026

While we tried as much as possible to reproduce the biomaRt interface, there are some differences between the two packages, and limitations that we won’t be able to overcome.

Interface

New species / speciesL argument

In biomaRt, the mart argument was used to specify the database to connect to, this usually contained some information about the species of interest. This enabled for example the conversion of gene symbols to Ensembl gene IDs (since multiple species can have the same gene symbol). In remart, the mart argument is no longer required, and the species of interest is specified via the new species argument in getBM() and speciesL argument in getLDS().

Limitations

Because remart queries Ensembl at execution time, a result is determined by the current Ensembl service and annotation release rather than by a bundled snapshot. For reproducible analyses, record the date of access, the Ensembl identifiers queried, the requested attributes, and the version of remart.

Additionally, Ensembl is the supported backend; arbitrary BioMart databases are not.