uk.ac.ed.inf.utils
Class EntrezUtils

java.lang.Object
  uk.ac.ed.inf.utils.EntrezUtils

public class EntrezUtils
extends java.lang.Object

Utilities for Entrez services.

Version:

12 Dec 2007

Author:

Luna De Ferrari luna.deferrari-at-ed.ac.uk

Constructor Summary

EntrezUtils()

Method Summary

static java.lang.String	eSummaryToString(XmlNode xmlTree) Test method to print an an Entrez eSummary xml report
static XmlNode	getESummaryXML(java.lang.String db, java.lang.String id) Gets an XML tree of elements (SimpleElement) from eSummary Entrez service.
static java.lang.String	getNameForEntrezGeneId(java.lang.String id) Get the entrez gene name for an entrez gene id
static java.lang.String	getPubMedUrl(java.lang.String pubMedIds) Generates pubMed URL adding pubMed ids (as list separated by commas)
static void	main(java.lang.String[] args) Mains for testing
static java.lang.String	xmlElementToString(XmlNode xml) Test method to print to string a single Entrez eSummary xml element

Methods inherited from class java.lang.Object

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

Constructor Detail

EntrezUtils

public EntrezUtils()

Method Detail

eSummaryToString

public static java.lang.String eSummaryToString(XmlNode xmlTree)

Test method to print an an Entrez eSummary xml report

Parameters:

xmlTree -

Returns:

to string

getESummaryXML

public static XmlNode getESummaryXML(java.lang.String db,
                                     java.lang.String id)
                              throws java.io.IOException

Gets an XML tree of elements (SimpleElement) from eSummary Entrez service. Example: // http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary .fcgi?db=gene&id=55111&retmode=xml

Parameters:

db - a database (for example for Entrez gene = 'gene')

id - if database = gene > an entrez gene id

Returns:

an xml simple element

Throws:

java.io.IOException

See Also:

XmlNode

getNameForEntrezGeneId

public static java.lang.String getNameForEntrezGeneId(java.lang.String id)
                                               throws java.io.IOException

Get the entrez gene name for an entrez gene id

Parameters:

id - the entrez gene id, eg. 1956 (EGFR)

Returns:

the entrez gene name, eg. 'EGFR' (for entrez gene id 1956)

Throws:

java.io.IOException

getPubMedUrl

public static java.lang.String getPubMedUrl(java.lang.String pubMedIds)

Generates pubMed URL adding pubMed ids (as list separated by commas)

Parameters:

pubMedIds - eg. 16381840,15608222

Returns:

pubMed fetch url, eg: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd =retrieve&db=pubmed&list_uids=16381840,15608222&dopt=citation

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException

Mains for testing

Parameters:

args -

Throws:

java.io.IOException

xmlElementToString

public static java.lang.String xmlElementToString(XmlNode xml)

Test method to print to string a single Entrez eSummary xml element

Parameters:

xml -

Returns:

the string value of the xml element