Package net.bioclipse.managers

Class OscarManager

java.lang.Object
net.bioclipse.managers.OscarManager
All Implemented Interfaces:
IBactingManager, net.bioclipse.managers.business.IBioclipseManager
public class OscarManager extends Object implements IBactingManager
Bioclipse manager that adds text mining functionality.

  • Constructor Details

    • OscarManager

      public OscarManager(String workspaceRoot)
      Creates a new OscarManager.
      Parameters:
      workspaceRoot - location of the workspace, e.g. "."

  • Method Details

    • findNamedEntities

      public List<String> findNamedEntities(String text)
      Extracts named entities from a text.
      Parameters:
      text - Text with named entities (chemical names).
      Returns:
      List of named entities.

    • findResolvedNamedEntities

      public List<net.bioclipse.core.domain.IMolecule> findResolvedNamedEntities(String text) throws net.bioclipse.core.business.BioclipseException
      Extracts molecules from a text for which the corresponding named entities are recognized as chemicals.
      Parameters:
      text - Text with chemical names.
      Returns:
      List of IMolecules.
      Throws:
      net.bioclipse.core.business.BioclipseException

    • extractText

      public String extractText(String html)
      Extracts plain text from a HTML document.
      Parameters:
      html - HTML string from which the text should be extracted.
      Returns:
      The resulting text

    • getManagerName

      public String getManagerName()
      Specified by:
      getManagerName in interface net.bioclipse.managers.business.IBioclipseManager

    • doi

      public List<String> doi()
      Description copied from interface: IBactingManager
      Lists the DOIs of the articles associated to this manager.
      Specified by:
      doi in interface IBactingManager
      Returns:
      a List of String with DOIs