Issue 4495: Request for Conformance Points (genomic_map-ftf) Source: GlaxoSmithKline plc (Dr. W. David Benton, wdavid.benton@gsk.com w.david.benton@gsk.com w_david_benton@gsk.com W.David.Benton@gsk.com) Nature: Severity: Summary: Issue: Some aspects of the Genomic Maps Specification are not required for a functional implementation. Specifically, support for map correlations was an optional requirement in the Genomic Maps RFP and support for nested maps can be provided in several ways in addition to the one specified in the Genomic Maps Adopted Specification (e.g., the maps in the underlying map database could be preprocessed to integrate nested maps into unified maps, while, if necessary, keeping the original map fragments as individually available maps). Therefore, an adequately functional Genomic Maps service can be implemented that does not support map correlations or nested maps. This "Base Maps" service would be much simpler to implement, maintain, and use. Proposed Resolution: Add the following Conformance Points to the Genomic Maps Specification: (1) Base Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: (a) Base Maps implementations ignore the recursion_depth parameter for query operations (implicitly setting it to 0). (b) Base Maps implementations support only the MappableAssignment subtype of Assignment. (c) Base Maps implementations support Mappable as the type of left_flanking_entity and right_flanking_entity in the interface RelativePosition. They are not required to support Map as a type for left_flanking_entity and right_flanking_entity. (d) the additional exceptions listed under the Nested Maps conformance point below. This is a mandatory conformance point. (2) Nested Maps. Implements all modules and interfaces as described in Chapter 3, with the following exceptions: (a) the interface MapCorrelation and its factory MapCorrelationFactory (b) the interface AssignmentPairIterator and the data types AssignmentPair and MapPair. This is an optional conformance point. (3) Correlated Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: exceptions (a), (b), and (c) listed under Base Maps above. This is an optional conformance point. Therefore a Genomic Maps implementation must satisfy conformance point (1) Base Maps and may optionally satisfy either or both of conformance points (2) Nested Maps and (3) Correlated Maps. Resolution: see above Revised Text: 1.2 Compliance Points There are four compliance points to this specification: (1) "Base Maps", (2) "Nested Maps", (3) "Correlated Maps" and (4) "LQSLink". These compliance points make use of the interfaces described in IDL modules DsLSRControlledVocabularies, DsLSRGenomicMaps and DsLSRLQSLink, but to varying degrees. The modules are described in detail in Chapter 3; the compliance points are given below. (1) Base Maps. Implements all modules and interfaces described in modules DsLSRControlledVocabularies and DsLSRGenomicMaps, with the following exclusions: (a) "Base Maps" implementations ignore the recursion_depth parameter for query operations (implicitly setting it to 0). (b) "Base Maps" implementations support only the MappableAssignment subtype of Assignment. (c) "Base Maps" implementations support Mappable as the type of left_flanking_entity and right_flanking_entity in the interface RelativePosition. They are not required to support Map as a type for left_flanking_entity and right_flanking_entity. (d) the additional exclusions listed under the Nested Maps conformance point below. "Base Maps" is a mandatory conformance point. (2) Nested Maps. Implements all modules and interfaces as described in modules DsLSRControlledVocabularies and DsLSRGenomicMaps, with the following exclusions: (a) the interface MapCorrelation and its factory MapCorrelationFactory (b) the interface AssignmentPairIterator and the data types AssignmentPair and MapPair. "Nested Maps" is an optional conformance point. (3) Correlated Maps. Implements all modules and interfaces described in modules DsLSRControlledVocabularies and DsLSRGenomicMaps, with the following exclusions: (a) exclusions (a), (b), and (c) listed under Base Maps above. "Correlated Maps" is an optional conformance point. (4) LQSLink. The interface described in the DsLSRLQSLink module is optional. A compliant Genomic Maps implementation must satisfy conformance point (1) "Base Maps" and may satisfy none or more of conformance points (2) "Nested Maps" and (3) "Correlated Maps" and (4) "LQSLink". Disposition: Accepted Actions taken: August 14, 2001: received issue Discussion: Resolution: Replace the last paragraph of 1.1 ("To be complian ... DsLSRLQSLink is optional") with the following, as a separate new section, 1.2: End of Annotations:===== From: webmaster@omg.org Message-Id: <200108141827.f7EIR2t29806@emerald.omg.org> Date: 14 Aug 2001 14:30:52 -0400 To: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Subject: Issue/Bug Report Content-Type: Text/html; charset=windows-1252 X-UIDL: )=hd98>^d9!nJe9HX>!! Name: David Benton Company: GlaxoSmithKline mailFrom: w_david_benton@gsk.com Notification: Yes Specification: Genomic Maps Section: 3 FormalNumber: dtc/99-12-01 Version: 1.0 RevisionDate: 12/20/99 Page: 3-4 - 3-15 Nature: Revision Severity: Significant HTTP User Agent: Mozilla/4.0 (compatible; MSIE 5.01; Windows NT) Description Genomic Maps Specification Issue: Request for Conformance Points Issue: Some aspects of the Genomic Maps Specification are not required for a functional implementation. Specifically, support for map correlations was an optional requirement in the Genomic Maps RFP and support for nested maps can be provided in several ways in addition to the one specified in the Genomic Maps Adopted Specification (e.g., the maps in the underlying map database could be preprocessed to integrate nested maps into unified maps, while, if necessary, keeping the original map fragments as individually available maps). Therefore, an adequately functional Genomic Maps service can be implemented that does not support map correlations or nested maps. This "Base Maps" service would be much simpler to implement, maintain, and use. Proposed Resolution: Add the following Conformance Points to the Genomic Maps Specification: (1) Base Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: (a) Base Maps implementations ignore the recursion_depth parameter for query operations (implicitly setting it to 0). (b) Base Maps implementations support only the MappableAssignment subtype of Assignment. (c) Base Maps implementations support Mappable as the type of left_flanking_entity and right_flanking_entity in the interface RelativePosition. They are not required to support Map as a type for left_flanking_entity and right_flanking_entity. (d) the additional exceptions listed under the Nested Maps conformance point below. This is a mandatory conformance point. (2) Nested Maps. Implements all modules and interfaces as described in Chapter 3, with the following exceptions: (a) the interface MapCorrelation and its factory MapCorrelationFactory (b) the interface AssignmentPairIterator and the data types AssignmentPair and MapPair. This is an optional conformance point. (3) Correlated Maps. Implements all modules and interfaces described in Chapter 3, with the following exceptions: exceptions (a), (b), and (c) listed under Base Maps above. This is an optional conformance point. Therefore a Genomic Maps implementation must satisfy conformance point (1) Base Maps and may optionally satisfy either or both of conformance points (2) Nested Maps and (3) Correlated Maps.