Changes to Query.java

1. HashMap< mbDataSourceBase, Vector< mbQueryResult > > m_hashmapResultsByDataSource
2. HashMap< mbQueryResult.DATATYPE, Vector< mbQueryResult > > m_hashmapResultByDataType

The first hashmap are the results indexed by data source. The second hashmap are the results by data type.

mbDataSourceBase

void QueryTermToSourceTerm^?( Vector< SearchParam^? > vTerms); // NOTE: since BonFire services aren't stable and not sure if they can // support our needs, this will have to be re-evaluated

Sample datasource plugin:

MBAT3.0 Core Object Classes

mbAnnotatedObject (represents an object with annotations in mbat3.0)

mbQueryResult

public class mbQueryResult {
   public enum DATATYPE {
      UNKNOWN,
      IMAGE2D,
      IMAGE3D,
      PROBE,
      GENE,
      GENE_ALIAS,
      GENE_EXPRESSION,
      STRUCTURE,
      DATATYPE_COUNT
   }
   
   // datasource
   private mbDataSourceBase m_mbDataSource;
   // annotated objects for this result, indexed by datatype
   private HashMap< DATATYPE, mbAnnotatedObject > m_hashmapResultSet;
}

Class hierarchy of query results:

               mbQueryResult
                   ^
                   |

ABAResult     CCDBResult    BMDBResult 

public class mbResult
{
    DataType m_dataType; // Image2D, Probe, etc.
    DataSource m_dataSourceRef; // ABA, BMDB, CCDB, etc
    Vector< Annot > m_vAnnotations; // annotation pairs

    Vector< mbResult > m_vChildren;  // hierarchy/ontology results
}

GUI Interfaces

1. DataSource centric:

     ----------------------------------------------
     | DataSource: CCDB                           |
     ----------------------------------------------
   
         ------------------------------------------
         | Image2D                                |
         ------------------------------------------
   
         ------------------------------------------
         | Probe                                  |
         ------------------------------------------
     

2. DataType centric:

     ----------------------------------------------
     | DataType: Image2D                          |
     ----------------------------------------------
   
         ------------------------------------------
         | CCDB                                   |
         ------------------------------------------
   
         ------------------------------------------
         | ABA                                    |
         ------------------------------------------
   
     ----------------------------------------------
     | DataType: Probe                            |
     ----------------------------------------------
   
         ------------------------------------------
         | BMDB                                   |
         ------------------------------------------
   
         ------------------------------------------
         | GENSAT                                 |
         ------------------------------------------
     

3. Hierarchy/Ontology centric:

     -------------  ------------------------------
     | TreeView  |  | Node Details               |
     |           |  |                            |
     |           |  |                            |
     |           |  |                            |
     |           |  |                            |
     |           |  |                            |
     |           |  |                            |
     -------------  ------------------------------
    

An image volume such as Analyze or NIFTI.

Talk with Rob Williams about GN results. See if we can converge results types from other individual researchers and GN database.

ExpressionLevelGroup (might not need this)

Annotation Display

• Annotations/metadata displayed in results table after a query
• Options:
  1. "Standard" 5 columns per datatype (need consensus from PIs)
  2. Customizable columns (end-user interactively chooses columns to display )

• Note: Microarray probe annotations are trickiest since they have nested annotations (ie: each probe has structure tags and each structure tag has annotations)

Required Data Source Information per Plugin

• user credentials (preferences file)

• Mapping of MBAT query parameter terms to data source parameters terms

• Internally, query plugin maps user parameter value to data source value
  • gene and structure may get very complicated to lookup using BonFire^? services

public interface DataSource
{
   boolean hasQueryTermSearch();
   boolean hasKeywordSearch();
   boolean hasSemanticSearch();

   Vector< MBATResult > searchByQueryTerms( Vector< SearchParam > vQueryTerms );
   Vector< MBATResult > searchByKeyword( String sKeywords );
   Vector< MBATResult > searchBySemantic( String sRDF );

   void QueryTermToSourceTerm( Vector< SearchParam > vTerms); NOTE: since !BonFire services aren't stable and not sure if they can support our needs, this will have to be re-evaluated 
}

public class ABASource implements DataSource
{
   Vector< MBATResult > searchByQueryTerms( Vector< SearchParam > vQueryTerms );

   boolean hasQueryTermSearch() { return true; }
   boolean hasKeywordSearch() { return false; }
   boolean hasSemanticSearch() { return false; }
}

               MBATResult
                   ^
                   |

Probe        Image2DSeries      Image3D      NumericData      ExpressionLevel

• Separate GUI elements and objects if possible, for example:
  • SearchParam : object to hold search parameter
  • JSearchParam extends SearchParam : GUI object for SearchParam
• Eliminate Adapter type of classes (ie: AnnotContainerAbstract)

Required Data Source Information

• Display name (ie: Allen Brain Atlas)
• Data types supported (ie: 2D image, microarray, etc)
• connString (ie: URL)
• parameters
• UMD ID (only needed to query UMD server for connString/parameters? if we use XML based configuration, won't need this?)

• Mapping of data source column names to MBAT column names
• Mapping of MBAT query terms to data source terms

Current Data Types to be Displayed in MBAT

Current Data Types Displayed in MBAT

• Image2DSeries

  An ordered list of references to one or more 2-D image files. The following image file formats are supported: [INSERT LIST]

• ExpressionLevel

  A microarray expression level for a particular anatomical structure or region. The structure or region may be expressed by name (i.e. "cerebellum") or the geometric coordinates in an atlas.

  The expression value may be numerical or it may be an English word indicating a relative expression level (i.e. "low", "mid", "high").

Current Data Sources

Planned Data Sources