Genomic Maps Implementers Report

1
Genomic Maps Implementers Report

• 10 Sep 2001

2
Genomic Maps Specification Overview

• DsLSRControlledVocabularies
• DsLSRGenomicMaps
• valuetype Mappable
• interface Map
• interface OrderedMap, CytogeneticElement,
  LinearMap
  
• interface MapsQueryLanguageType
• valuetype Assignment
• MappableAssignment and SubMapAssignment
• valuetypes Position, RelativePosition,
  RelativeMetricPosition
  
• interface MapCorrelation

3
Update

• Implementation of basic functionality proceeding
  well.
  
• Target dates
• All major functionality coded 12 Oct (Comment
  deadline)
  
• Implementation delivery 16 Nov (FTF
  Recommendation Report deadline)
  
• Will basic functionality be sufficient?

4
Issue 4495 Request for Conformance Points

• Some aspects of the Genomic Maps Specification
  are not required for a functional implementation
  
• Support for map correlations was an optional
  requirement in the RFP
  
• Support for nested maps can be provided in
  several ways in addition to the one specified in
  the Genomic Maps Adopted Specification
  
• A basic genomic maps service would be much
  simpler to implement, maintain, and use

5
Proposed Resolution

• Add the following Conformance Points to the
  Genomic Maps Specification
  
• (1) Base Maps
• (2) Nested Maps
• (3) Correlated Maps

6
Conformance Point 1. Base Maps

• Implements all modules and interfaces, with the
  following exceptions
  
• ignore the recursion_depth parameter for query
  operations (implicitly setting it to 0).
  
• support only the MappableAssignment subtype of
  Assignment.
  
• support Mappable as the type of
  left_flanking_entity and right_flanking_entity in
  the interface relativePosition (i.e., does not
  support Map as a type for left_flanking_entity
  and right_flanking_entity).
• additional exceptions listed under the Nested
  Maps conformance point
  
• Mandatory conformance point.

7
Conformance Point 2. Nested Maps

• Implements all modules and interfaces, with the
  following exceptions
  
• the interface MapCorrelation and its factory
  MapCorrelationFactory
  
• the interface AssignmentPairIterator and the data
  types AssignmentPair and MapPair.
  
• Optional conformance point.

8
Conformance Point 3. Correlated Maps

• Implements all modules and interfaces, with the
  following exceptions
  
• exceptions (a), (b), and (c) listed under Base
  Maps conformance point.
  
• An optional conformance point.

9
Conformance Point Summary

• Implementation must satisfy
• Conformance point (1) Base Maps
• May optionally satisfy either or both of
• Conformance point (2) Nested Maps
• Conformance point (3) Correlated Maps