BioLit

BioJava module: BioLit

The BioJava - BioLit module allows to perform web service request to the webservices provided by BioLit. BioLit allows to access information from open access articles that are published in PubMedCentral.

This library is used by the RCSB-PDB web site to dynamically request the data from the BioLit RESTful web services. For an example see here: http://www.rcsb.org/pdb/explore/literature.do?structureId=1aoi

Source Code Examples

import org.rcsb.biolit.io.TermParser;
 
/** Get PDB codes that are cited in the same articles as the query PDB id.
 *
 *
 */
public class GetRelated
{
 
   public static void main(String[] args){
      String pdb = "1hiv";
 
      TermParser parser = new TermParser();
      try{
         List<String> ids = parser.fetch(pdb);
 
         for (String id : ids)
         {
            System.out.println(id);
         }
      } catch (Exception e){
         e.printStackTrace();
      }
   }
}

Running this code will provide you with a list of PDB that have been cited in the same article as 1HIV:

1A3C
1A6Q
1A7J
1AAC
1AC5
1AH7
1AK1
1AKO
1AMJ
1BTL
1HIV
2LZM
1A2P
1GVP
1BAZ
1CLL
1EER
3PVI
5PTI

For more examples see the "demos" subdirectory in SVN.

Source Code

Developer access to the module is available via here:

svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/branches/modules/biojava-biolit/trunk biojava-biolit

Anonymous access is via here:

svn co svn://code.open-bio.org/biojava/biojava-live/branches/modules/biojava-biolit/trunk biojava-biolit