Package ubic.gemma.core.loader.util.biomart

Class BiomartEnsemblNcbiFetcher

java.lang.Object

ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher

public class BiomartEnsemblNcbiFetcher
extends Object

BioMart is a query-oriented data management system. In our particular case we are using it to map ensembl, ncbi and hgnc ids. To construct the query we pass the taxon and the attributes we wish to query for. Note the formatting of taxon for biomart consists of latin name without the point e.g. 'hsapiens'. For more information visit the biomart website. Note that Gemma now includes Ensembl ids imported for NCBI genes, using the gene2ensembl file provided by NCBI.

Author:

ldonnison

Field Summary

Fields

Modifier and Type	Field	Description
static String	BIOMARTPATH

Constructor Summary

Constructors

Constructor	Description
BiomartEnsemblNcbiFetcher()

Method Summary

Modifier and Type	Method	Description
String[]	attributesToRetrieveFromBioMartForProteinQuery(String biomartTaxonName)	Method that based on the taxon supplied constructs an array of attributes that can be queried on.
Map<Taxon,File>	fetch(Collection<Taxon> taxa)	Main method that iterates through each taxon supplied and calls the fetch method for each taxon.
File	fetchFileForProteinQuery(String bioMartTaxonName)	Given a biomart taxon formatted name fetch the file from biomart and save as a local file.
String	getBiomartTaxonName(Taxon gemmaTaxon)	Biomart taxon names are formatted as the scientific name all lowercase with the genus name shortened to one letter and appended to species name E.g.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BIOMARTPATH

public static final String BIOMARTPATH

See Also:

Constant Field Values

Constructor Detail

BiomartEnsemblNcbiFetcher

public BiomartEnsemblNcbiFetcher()

Method Detail

attributesToRetrieveFromBioMartForProteinQuery

public String[] attributesToRetrieveFromBioMartForProteinQuery(String biomartTaxonName)

Method that based on the taxon supplied constructs an array of attributes that can be queried on. For example if hsapiens is supplied then hgnc_id can be supplied as a query parameter.

Parameters:

biomartTaxonName - Biomart formatted taxon name

Returns:

An Array of strings representing the attributes that can be used to query biomart.

fetch

public Map<Taxon,File> fetch(Collection<Taxon> taxa)
                            throws IOException

Main method that iterates through each taxon supplied and calls the fetch method for each taxon. Which returns a biomart file for each taxon supplied.

Parameters:

taxa - Collection of taxa to retrieve biomart files for.

Returns:

A map of biomart files as stored on local file system keyed on taxon.

Throws:

IOException - if there is a problem while manipulating the file

fetchFileForProteinQuery

public File fetchFileForProteinQuery(String bioMartTaxonName)
                              throws IOException

Given a biomart taxon formatted name fetch the file from biomart and save as a local file.

Parameters:

bioMartTaxonName - taxon name from biomart

Returns:

biomart file

Throws:

IOException - when there is a problem while manipulating the file

getBiomartTaxonName

public String getBiomartTaxonName(Taxon gemmaTaxon)

Biomart taxon names are formatted as the scientific name all lowercase with the genus name shortened to one letter and appended to species name E.g. Homo sapiens > hsapiens

Parameters:

gemmaTaxon - taxon object

Returns:

Biomart taxon formatted name.

Throws:

RuntimeException - The taxon does not contain a valid scientific name.