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| - !! Overview |
| + !!! Intended audience |
| + This document is intended for __SEEK and Kepler developers__. |
| + |
| + It is a __DRAFT DESIGN DOCUMENT__ and does not reflect functionality as it |
| + currently exists in Kepler or SEEK. Comments and feedback are appreciated. |
| + |
| + !!! Overview |
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| - The following lists the semantic mediation service interfaces: |
| + The following lists the semantic-mediation service interfaces: |
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| - search( ConceptExpression, Set<ResourceType>, RemoteFlag ) :: Set<ResourceID> |
| + Set<ResourceID> search( ConceptExpression, Set<ResourceType>, RemoteFlag ) |
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| - query( QueryExpression, RemoteFlag ) :: Set<QueryResult> |
| + Set<QueryResult> query( QueryExpression, RemoteFlag ) |
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| - compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) :: Boolean |
| - |
| - searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) :: Set<ResourceID> |
| + Boolean match( ResourceID, ConceptExpression, RemoteFlag ) |
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| - compose( ResourceID, Connection, ResourceID, RemoteFlag ) :: Set<StructMapping> |
| + Boolean compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) |
| + |
| + Set<ResourceID> searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) |
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| - merge( ResourceID, Connection, ResourceID, RemoteFlag ) :: Set<StructMapping> |
| + Set<StructMapping> compose( ResourceID, Connection, ResourceID, RemoteFlag ) |
| At line 19 added 1 line. |
| + Set<StructMapping> merge( ResourceID, Connection, ResourceID, RemoteFlag ) |
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| - semanticType( ResourceID, String, RemoteFlag ) :: ConceptExpression // summarizing annotations |
| + ConceptExpression semanticTypeConcepts( ResourceID, String, RemoteFlag ) // for summarizing annotations |
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| - !! {{Search}}: Simple Concept-Based Searching |
| + !!! {{Search}}: Simple Concept-Based Searching |
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| - {{{search( ConceptExpression, Set<ResourceType>, RemoteFlag ) :: Set<ResourceID>}}} |
| + {{{Set<ResourceID> search( ConceptExpression, Set<ResourceType>, RemoteFlag )}}} |
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| - The service returns a set of resources (as LSIDs) that have semantic annotations "matching" the given search term. |
| + The service returns a set of resources (as LSIDs) that have semantic types "matching" the given search term. |
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| - getResourceType( ResourceID ) :: ResourceType |
| + ResourceType getResourceType( ResourceID ) |
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| - getSemanticAnnotations( RemoteSearchFlag ) :: Set<SemanticAnnotationID> |
| + Set<SemanticTypeID> getSemanticAnnotations( RemoteSearchFlag ) |
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| - getOntology( OntologyID ) :: Set<Ontology> |
| + Set<Ontology> getOntology( OntologyID ) |
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| - The first operation returns the resource type of a given resource identifier (an LSID). The second operation returns the set of semantic annotations known to the kepler object manager (including annotations stored on remote repositories depending on the value of the remote flag). The last operation returns the ontology for a given ontology identifier (also a resource id). |
| + The first operation returns the resource type of a given resource identifier (an LSID). The second operation returns the set of semantic types known to the kepler object manager (including semantic types stored on remote repositories depending on the value of the remote flag). The last operation returns the ontology for a given ontology identifier (also a resource id). Note that this last operation could be used with an ontology service, e.g., the simple one described at the end of this page[simple ontology service|1]. |
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| - ! Optimized Remote Searching |
| + !! Optimized Remote Searching |
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| - In general, the {{search}} operation requires access to all semantic annotations to find matching resources. For example, consider a search expression {{A and B}}, i.e., a resource must contribute to both concept {{A}} and concept {{B}}. To find appropriate matches for this search term, the algorithm must look for annotations that explicitly state {{A and B}} as well as those that state only {{A}} and only {{B}} (which taken together make {{A and B}}). Note that an annotation that states only {{A}} may be in one repository, while an annotation that states only {{B}} may be in another. Thus, for remote searches, the {{search}} algorithm must obtain and consider all remote annotations to find matching resources, making the {{search}} operation inherently centralized. |
| + In general, the {{search}} operation requires access to all semantic types to find matching resources. For example, consider a search expression {{A and B}}, i.e., a resource must contribute to both concept {{A}} and concept {{B}}. To find appropriate matches for this search term, the algorithm must look for semantic types that explicitly state {{A and B}} as well as those that state only {{A}} and only {{B}} (which taken together make {{A and B}}). Note that a semantic type that states only {{A}} may be in one repository, while a semantic type that states only {{B}} may be in another. Thus, for remote searches, the {{search}} algorithm must obtain and consider all remote semantic types to find matching resources, making the {{search}} operation inherently centralized. |
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| - getRepositories() :: Set<RepositoryID> |
| + Set<RepositoryID> getRepositories() |
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| - getResources( RepositoryID, Set<ResourceType> ) :: Set<ResourceID> |
| + Set<ResourceID> getResources( RepositoryID, Set<ResourceType> ) |
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| - partialSearch( RepositoryID, ConceptExpression, ResourceID ) :: Set<ConceptExpression> |
| + Set<ConceptExpression> partialSearch( RepositoryID, ConceptExpression, ResourceID ) |
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| - !! {{Query}}: Complex Concept-Based Searching |
| + !!! {{Query}}: Complex Concept-Based Searching |
| + |
| + {{{ |
| + Set<QueryResult> query( QueryExpression, RemoteFlag ) |
| + }}} |
| + |
| + |
| + |
| At line 71 added 2 lines. |
| + !!!{{Match}}: Checking Matching Resources |
| + |
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| - query( QueryExpression, RemoteFlag ) :: Set<QueryResult> |
| + Boolean match( ConceptExpression, ResourceID, RemoteFlag ) |
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| + The arguments for this service are: |
| + # A resource whose semantic types are to be checked; |
| + # A concept expression; and |
| + # A flag denoting whether local or remote repositories are searched |
| + |
| + The service returns true if the resource has a semantic type matching the concept expression. Note that given a set of resources {{R}} returned by the {{search}} service for a concept expression {{c}} and remote flag value {{m}} (either true or false), for each {{r}} in {{R}}, {{match(r, c, m)}} is true. That is, {{r}} is a {{match}} for search {{c}}. |
| + |
| + The {{match}} service is included primarily to support browsing of ontologies. |
| + |
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| - !! {{Compatible}}: Checking Semantically Well-Formed Connections |
| + !!! {{Compatible}}: Checking Semantically Well-Formed Connections |
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| - compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) :: Boolean |
| + Boolean compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) |
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| - !! {{SearchCompatible}}: Searching for Semantically Well-Formed Connections |
| + !!! {{SearchCompatible}}: Searching for Semantically Well-Formed Connections |
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| - searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) :: Set<ResourceID> |
| + Set<ResourceID> searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) |
| Line 93 was replaced by line 118 |
| - !! {{Compose}}: Suggesting Well-Structured Actor Connections |
| + !!! {{Compose}}: Suggesting Well-Structured Actor Connections |
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| - compose( ResourceID, Connection, ResourceID, RemoteFlag ) :: Set<StructMapping> |
| + Set<StructMapping> compose( ResourceID, Connection, ResourceID, RemoteFlag ) |
| Line 99 was replaced by line 124 |
| - !! {{Merge}}: Suggesting Simple Merging of Heterogeneous Datasets |
| + !!! {{Merge}}: Suggesting Simple Merging of Heterogeneous Datasets |
| Line 102 was replaced by line 127 |
| - merge( ResourceID, Connection, ResourceID, RemoteFlag ) :: Set<StructMapping> |
| + Set<StructMapping> merge( ResourceID, Connection, ResourceID, RemoteFlag ) |
| Line 106 was replaced by line 131 |
| - !! {{SemanticType}}: Summarizing Semantic Annotations |
| + !!! {{SemanticType}}: Summarizing Semantic Annotations |
| Line 109 was replaced by line 134 |
| - semanticType( ResourceID, String, RemoteFlag ) :: ConceptExpression |
| + ConceptExpression semanticType( ResourceID, String, RemoteFlag ) |
| At line 110 added 31 lines. |
| + |
| + |
| + !!! A Simple Ontology Interface |
| + |
| + [simple ontology interface|#1] |
| + |
| + {{{ |
| + interface ISimpleOntologyAccess { |
| + |
| + Set<ConceptID> getConcepts( OntologyID ) |
| + |
| + Set<RoleID> getRoles( OntologyID ) :: Set<RoleID> |
| + |
| + Set<ConceptID> getMatchingConcepts( OntologyID, String ) |
| + |
| + Set<ConceptID> getMatchingRoles( OntologyID, String ) |
| + |
| + Set<ConceptID> getSubConcepts( OntologyID, ConceptID, DirectFlag ) |
| + |
| + Set<ConceptID> getSuperConcepts( OntologyID, ConceptID, DirectFlag ) |
| + |
| + Set<RoleID> getSubRoles( OntologyID, RoleID, DirectFlag ) |
| + |
| + Set<RoleID> getSuperRoles( OntologyID, RoleID, DirectFlag ) |
| + |
| + Booolean satisfies( ConceptExpression, ConceptExpression ) |
| + |
| + } |
| + }}} |
| + |
| + !!! Comments |
