Class PubMedSearch
java.lang.Object
ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
Search PubMed for terms, retrieve document records.
- Author:
- pavlidis
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionRetrieve a single PubMed record by ID.retrieve(Collection<String> pubmedIds) Retrieve multiple PubMed records by ID.Gets all the pubmed ID's that would be returned from a pubmed search string, using two eUtil calls.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.searchAndRetrieve(String searchQuery, int maxResults) Search based on terms and retrieve the PubMed records.
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Constructor Details
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PubMedSearch
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Method Details
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search
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
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search
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
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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 thenretrieve(Collection)as it bypasses the intermediary query to get PubMed IDs.- Parameters:
searchQuery- search terms- Returns:
- BibliographicReference representing the publication
- Throws:
IOException
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retrieve
Retrieve a single PubMed record by ID.- Throws:
IOException- See Also:
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retrieve
Retrieve multiple PubMed records by ID.- Throws:
IOException- See Also:
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