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(String apiKey)

Method Summary

Modifier and Type	Method	Description
BibliographicReference	retrieve(String pubMedId)	Retrieve a single PubMed record by ID.
Collection<BibliographicReference>	retrieve(Collection<String> pubmedIds)	Retrieve multiple PubMed records by ID.
Collection<String>	search(String searchQuery, int maxResults)	Gets all the pubmed ID's that would be returned from a pubmed search string, using two eUtil calls.
Collection<String>	search(Collection<String> searchTerms, int maxResults)	Gets all the pubmed ID's that would be returned given a list of input terms, using two eUtil calls.
Collection<BibliographicReference>	searchAndRetrieve(String searchQuery, int maxResults)	Search based on terms and retrieve the PubMed records.

Methods inherited from class java.lang.Object

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

Constructor Detail

PubMedSearch

public PubMedSearch(String apiKey)

Method Detail

search

public Collection<String> search(Collection<String> searchTerms,
                                 int maxResults)
                          throws IOException

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

search

public Collection<String> search(String searchQuery,
                                 int maxResults)
                          throws IOException

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

searchAndRetrieve

public Collection<BibliographicReference> searchAndRetrieve(String searchQuery,
                                                            int maxResults)
                                                     throws IOException

Search based on terms and retrieve the PubMed records.

This is more efficient than calling search(String, int) and then retrieve(Collection) as it bypasses the intermediary query to get PubMed IDs.

Parameters:

searchQuery - search terms

Returns:

BibliographicReference representing the publication

Throws:

IOException

retrieve

@Nullable
public BibliographicReference retrieve(String pubMedId)
                                throws IOException

Retrieve a single PubMed record by ID.

Throws:

IOException

See Also:

EntrezUtils.fetchById(String, String, EntrezRetmode, String, String)

retrieve

public Collection<BibliographicReference> retrieve(Collection<String> pubmedIds)
                                            throws IOException

Retrieve multiple PubMed records by ID.

Throws:

IOException

See Also:

EntrezUtils.fetchById(String, String, EntrezRetmode, String, String)