| Line 1 was replaced by lines 1-5 |
| - !! Concept-Based Searching |
| + !!! 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. |
| At line 2 added 126 lines. |
| + !!! Overview |
| + |
| + The following lists the semantic-mediation service interfaces: |
| + |
| + {{{ |
| + interface ISemanticMediation { |
| + |
| + Set<ResourceID> search( ConceptExpression, Set<ResourceType>, RemoteFlag ) |
| + |
| + Set<QueryResult> query( QueryExpression, RemoteFlag ) |
| + |
| + Boolean match( ResourceID, ConceptExpression, RemoteFlag ) |
| + |
| + Boolean compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) |
| + |
| + Set<ResourceID> searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) |
| + |
| + Set<StructMapping> compose( ResourceID, Connection, ResourceID, RemoteFlag ) |
| + |
| + Set<StructMapping> merge( ResourceID, Connection, ResourceID, RemoteFlag ) |
| + |
| + ConceptExpression semanticTypeConcepts( ResourceID, String, RemoteFlag ) // for summarizing annotations |
| + |
| + } |
| + }}} |
| + |
| + The rest of this page describes each of these services and their dependencies. |
| + |
| + |
| + !!! {{Search}}: Simple Concept-Based Searching |
| + |
| + {{{Set<ResourceID> search( ConceptExpression, Set<ResourceType>, RemoteFlag )}}} |
| + |
| + The arguments for this service are: |
| + # A search term represented as a description-logic concept expression; |
| + # A set of resource types, e.g., "actor" and/or "dataset"; and |
| + # A flag denoting whether local or remote repositories are searched |
| + |
| + The service returns a set of resources (as LSIDs) that have semantic types "matching" the given search term. |
| + |
| + We assume that (via a GUI) an initial search string has been converted to a description-logic concept expression. A concept expression can be single concept (like "Biomass") or a complex formula (including nested disjunctive and conjunctive formulas, and so on). We assume each concept is associated to the ontology it is defined in (e.g., where the ontology is implied by the concept identifier). |
| + |
| + The {{search}} service depends on the following kepler object manager services: |
| + {{{ |
| + ResourceType getResourceType( ResourceID ) |
| + |
| + Set<SemanticTypeID> getSemanticAnnotations( RemoteSearchFlag ) |
| + |
| + Set<Ontology> getOntology( OntologyID ) |
| + }}} |
| + |
| + 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]. |
| + |
| + !! Optimized Remote Searching |
| + |
| + 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. |
| + |
| + We may reduce the cost of {{search}} by adding additional services that can be executed locally at each repository and by altering the search algorithm, making it slightly less centralized. The additional services are: |
| + |
| + {{{ |
| + Set<RepositoryID> getRepositories() |
| + |
| + Set<ResourceID> getResources( RepositoryID, Set<ResourceType> ) |
| + |
| + Set<ConceptExpression> partialSearch( RepositoryID, ConceptExpression, ResourceID ) |
| + }}} |
| + |
| + Using these operations, the {{search}} algorithm would procede as follows, assuming that the remote flag has been selected. With the {{getRepositories}} service, the algorithm first obtains the available repositories from the local kepler object manager. The algorithm selects the first returned repository and with the {{getRepositories}} service, obtains the relevant resources in the respository. For each resource in the repository, the {{partialSearch}} service is used, which returns the parts of the concept expression that the resource matches (e.g., just the concept {{A}}). The algorithm then moves to the next repository, performing the same steps. However, for those resources already having partial matches (from the previous step), the algorithm reformulates the search term given to {{partialSearch}} to include only the additional required parts of the concept expression (e.g., just the concept {{B}}). Once a complete match is found, the resource is considered a match and is not further checked. Finally, the algorithm repeats the process until all repositories have been examined. |
| + |
| + |
| + !!! {{Query}}: Complex Concept-Based Searching |
| + |
| + {{{ |
| + Set<QueryResult> query( QueryExpression, RemoteFlag ) |
| + }}} |
| + |
| + |
| + |
| + |
| + !!!{{Match}}: Checking Matching Resources |
| + |
| + {{{ |
| + Boolean match( ConceptExpression, ResourceID, RemoteFlag ) |
| + }}} |
| + |
| + |
| + 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. |
| + |
| + |
| + !!! {{Compatible}}: Checking Semantically Well-Formed Connections |
| + |
| + {{{ |
| + Boolean compatible( ResourceID, Connection, ResourceID, StructTypeFlag, RemoteFlag ) |
| + }}} |
| + |
| + |
| + |
| + !!! {{SearchCompatible}}: Searching for Semantically Well-Formed Connections |
| + |
| + {{{ |
| + Set<ResourceID> searchCompatible( ResourceID, Port, StructTypeFlag, RemoteFlag ) |
| + }}} |
| + |
| + |
| + !!! {{Compose}}: Suggesting Well-Structured Actor Connections |
| + |
| + {{{ |
| + Set<StructMapping> compose( ResourceID, Connection, ResourceID, RemoteFlag ) |
| + }}} |
| + |
| + !!! {{Merge}}: Suggesting Simple Merging of Heterogeneous Datasets |
| + |
| + {{{ |
| + Set<StructMapping> merge( ResourceID, Connection, ResourceID, RemoteFlag ) |
| + }}} |
| + |
| + |
| + !!! {{SemanticType}}: Summarizing Semantic Annotations |
| + |
| Line 4 was replaced by line 134 |
| - search( ConceptExpression, Set<ResourceType>, RemoteSearchFlag ) :: Set<Resource> |
| + ConceptExpression semanticType( ResourceID, String, RemoteFlag ) |
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| - Given a search expression (represented as a description logic concept expression), a list of resource types (e.g., "actor", "dataset", etc.), and whether the search should be local or include remote repositories, this operation returns a set of resources that have semantic annotations that "match" the given search expression. |
| + |
| + !!! 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 ) |
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| - Here, we assume that an initial search string has been converted to a description-logic concept expression, which can be a simple concept id (like "Biomass") or a more complex formula (including nested disjunctive and conjunctive formulas, etc.) |
| + Set<ConceptID> getMatchingRoles( OntologyID, String ) |
| + |
| + Set<ConceptID> getSubConcepts( OntologyID, ConceptID, DirectFlag ) |
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| - The search operation also assumes that the following data structures have been implemented: |
| + Set<ConceptID> getSuperConcepts( OntologyID, ConceptID, DirectFlag ) |
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| - * {{{ |
| - interface SemanticAnnotation { |
| - } |
| - }}} |
| + Set<RoleID> getSubRoles( OntologyID, RoleID, DirectFlag ) |
| Line 18 was replaced by lines 159-164 |
| - leverages the following other services provided by the Kepler Object Manager: |
| + Set<RoleID> getSuperRoles( OntologyID, RoleID, DirectFlag ) |
| + |
| + Booolean satisfies( ConceptExpression, ConceptExpression ) |
| + |
| + } |
| + }}} |
| Lines 20-21 were replaced by line 166 |
| - * {{getAnnotations( RemoteSearchFlag ) :: Set<SemanticAnnotation>}} |
| - * A set of ontology operations to determine |
| + !!! Comments |
