Retrieve Ensembl Biomart marts and datasets for a query organism — organismBM • biomartr
Description: This function returns either all available biomart connections for all available organisms for which biomart access is possible, or (when specified) returns all organism specific biomart connections.

# Retrieve Ensembl Biomart marts and datasets for a query organism

Source: `R/organismBM.R`
`organismBM.Rd`

This function returns either all available biomart connections for all available organisms for which biomart access is possible, or (when specified) returns all organism specific biomart connections.

    organismBM(organism = NULL, update = FALSE, mute_citation = TRUE)

## Arguments

organism

  a character string specifying the scientific name of a query organism. Default is `organism` = `NULL`. In this case all available biomart connections are returned.

update

  a logical value specifying whether or not the local listMart.txt and listDatasets.txt files shall be updated by remote access to BioMart.

mute_citation

  logical value indicating whether citation message should be muted.

## Details

This function collects all available biomart connections and returns a table storing the organism for which biomart connections are available as well as the corresponding mart and database.

## Note

When you run this function for the first time, the data retrieval procedure will take some time, due to the remote access to BioMart. The corresponding result is then saved in a *.txt file named "_biomart/listDatasets.txt" in the `tempdir` directory, allowing subsequent queries to perform much faster.

## References

http://biomart.org/

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber, Nature Protocols 4, 1184-1191 (2009).

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma and Wolfgang Huber, Bioinformatics 21, 3439-3440 (2005).

## See also

`getMarts`, `getDatasets`, `biomart`, `organismFilters`, `organismAttributes`

## Author

Hajk-Georg Drost

## Examples

    if (FALSE) {
    # returning all available biomart connections
    head(organismBM(), 20)
    # retrieving all available datasets and biomart connections for
    # a specific query organism (scientific name)
    organismBM(organism = "Homo sapiens")
    # you can also update the downloaded version using
    # the "update = TRUE" argument
    head(organismBM(update = TRUE), 20)
    }