Package ubic.gemma.core.loader.entrez.pubmed

Class PubMedSearch

java.lang.Object

ubic.gemma.core.loader.entrez.pubmed.PubMedSearch

public class PubMedSearch
extends Object

Search PubMed for terms, retrieve document records.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
PubMedSearch()

Method Summary

Modifier and Type	Method	Description
Collection<BibliographicReference>	searchAndRetrieveByHTTP(Collection<String> searchTerms)	Search based on terms
Collection<BibliographicReference>	searchAndRetrieveIdByHTTP(Collection<String> searchTerms)
Collection<String>	searchAndRetrieveIdsByHTTP(String searchQuery)	Gets all the pubmed ID's that would be returned from a pubmed search string, using two eUtil calls.
Collection<String>	searchAndRetrieveIdsByHTTP(Collection<String> searchTerms)	Gets all the pubmed ID's that would be returned given a list of input terms, using two eUtil calls.

Methods inherited from class java.lang.Object

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

Constructor Detail

PubMedSearch

public PubMedSearch()

Method Detail

searchAndRetrieveByHTTP

public Collection<BibliographicReference> searchAndRetrieveByHTTP(Collection<String> searchTerms)
                                                           throws IOException,
                                                                  SAXException,
                                                                  ParserConfigurationException,
                                                                  ESearchException

Search based on terms

Parameters:

searchTerms - search terms

Returns:

BibliographicReference representing the publication

Throws:

IOException - IO problems

SAXException - sax exception

ParserConfigurationException - parser config exception

ESearchException

searchAndRetrieveIdByHTTP

public Collection<BibliographicReference> searchAndRetrieveIdByHTTP(Collection<String> searchTerms)
                                                             throws IOException

Throws:

IOException

searchAndRetrieveIdsByHTTP

public Collection<String> searchAndRetrieveIdsByHTTP(Collection<String> searchTerms)
                                              throws IOException,
                                                     SAXException,
                                                     ParserConfigurationException,
                                                     ESearchException

Gets all the pubmed ID's that would be returned given a list of input terms, using two eUtil calls.

Parameters:

searchTerms - search terms

Returns:

The PubMed ids (as strings) for the search results.

Throws:

IOException - IO problems

SAXException - SAX exception

ParserConfigurationException - config problems

ESearchException

searchAndRetrieveIdsByHTTP

public Collection<String> searchAndRetrieveIdsByHTTP(String searchQuery)
                                              throws IOException,
                                                     SAXException,
                                                     ParserConfigurationException,
                                                     ESearchException

Gets all the pubmed ID's that would be returned from a pubmed search string, using two eUtil calls.

Parameters:

searchQuery - - what would normally be typed into pubmed search box for example "Neural Pathways"[MeSH]

Returns:

The PubMed ids (as strings) for the search results.

Throws:

IOException - IO problems

SAXException - SAX exception

ParserConfigurationException - config problems

ESearchException