Summary
Description of the profile
The semantic models managed by the Semantic Infrastructure enable enhanced reasoning.
Architectural implications of semantic models on the Semantic Infrastructure, with respect to reasoning, are reflected in the following capabilities:
- semantic models that provide normative descriptions of the utilized terms, where the models may range from a simple dictionary of terms to an ontology showing complex relationships and capable of supporting enhanced reasoning. This is a refinement of the Artifact metadata capability.
- mechanisms to support the storage, referencing, and access to these semantic models. This is a refinement of the Artifact store capability.
- one or more mechanisms to support the storage, referencing, and access to conversion relationships between semantic models, and the mechanisms to carry out such conversions.
This functional profile supports reasoning and using an OWL DL representation of models, and research and clinical data. This addresses a requirement from the BRIDG stakeholder communities. (BRIDG) explicitly called for this capability. This also addresses the CDISC requirement for ontologies
Reason specializes capabilities architecturally implied by its associated concepts of Artifact , Change , Semantic Model . The implied architectural capabilities are described in the following paragraphs.
Artifact An artifact is a managed resource within the Semantic Infrastructure.
An artifact is associated with the following capabilities:
- descriptions to enable the artifact to be visible, where the description includes a unique identifier for the artifact and a sufficient, and preferably a machine processible, representation of the meaning of terms used to describe the artifact, its functions, and its effects;
- one or more discovery mechanisms that enable searching for artifacts that best meet the search criteria specified by the service participant; where the discovery mechanism will have access to the individual artifact descriptions, possibly through some repository mechanism;
- accessible storage of artifacts and artifact descriptions, so service participants can access, examine, and use the artifacts as defined.
Change Artifact descriptions change over time and their contents will reflect changing needs and context.
Architectural implications of change on the Semantic Infrastructure are reflected in the following capabilities:
- mechanisms to support the storage, referencing, and access to normative definitions of one or more versioning schemes that may be applied to identify different aggregations of descriptive information, where the different schemes may be versions of a versioning scheme itself;
- configuration management mechanisms to capture the contents of the each aggregation and apply a unique identifier in a manner consistent with an identified versioning scheme;
- one or more mechanisms to support the storage, referencing, and access to conversion relationships between versioning schemes, and the mechanisms to carry out such conversions.
Semantic Model Artifact Descriptions make use of defined semantics, where the semantics may be used for categorization or providing other property and value information for description classes.
Architectural implications of semantics on the Semantic Infrastructure are reflected in the following capabilities:
- semantic models that provide normative descriptions of the utilized terms, where the models may range from a simple dictionary of terms to an ontology showing complex relationships and capable of supporting enhanced reasoning. This is a refinement of the Artifact metadata capability.
- mechanisms to support the storage, referencing, and access to these semantic models. This is a refinement of the Artifact store capability.
- configuration management mechanisms to capture the normative description of each semantic model and to apply a unique identifier in a manner consistent with an identified versioning scheme. This is a refinement of the Change configurationManagement capability.
- one or more mechanisms to support the storage, referencing, and access to conversion relationships between semantic models, and the mechanisms to carry out such conversions.
Capabilities
- configurationManagement
- discovery
- identity
- metadata
- ontologyModelReasoning
- provenance
- reasonOverClinicalOutcomeMeasurements
- semanticConversion
- store
- transition
- versioning
Requirements traceability
Requirement |
Source |
Capability |
|---|---|---|
Represent caBIG information models as ontologies in order to be able to use Semantic Web technology to reason over information models and the data that conforms those models |
Gap Analysis::Reason::117.1 - Represent caBIG Information models as ontologies |
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Support reasoning and querying on Ontology models (T-Box) and instance data (A-Box) |
Gap Analysis::Reason::125 - Reasoning and querying on Ontology models |
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This is representational model of the BRIDG Level 2 and Level 3 content that can be used to reason over BRIDG-derived artifacts. The new model will become a “canonical quality control” by which new content – when presented for inclusion in the evolving 3.x model – will be able to be “analyzed” for semantic consistency “on its way in” so that semantic inconsistencies can be addressed. The BRIDG model is a complex ontology that incorporates all of the HL 7 artifacts into the version 3 side of the model and links these to the UML side of the model via mappings at the class and attribute level. |
Gap Analysis::BRIDG::BRIDG-1 - Store data elements in a publicly available ontology repository |
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The caEHR provides a means for performing outcome measurements, and aggregating those measurements for analysis. These outcome measurements are defined as being time interval values based on clinical observations. Representation of clinical outcome measurement details is required. This should include the set of observations that a clinical outcome requires, and any constraints that might be necessary. These constraints may need to be represented as rules or value set bindings. This would more likely be a specific profile for an observation class or set of classes with criterion classes associated. These would also be associated with the detailed clinical models that represent the observation.code attribute in added detail. In addition, aggregations occur across measurements. Aggregations may have measurements for single patients or informal collections of patients. In addition it may operate upon formal collections of patients in the form of study cohorts. These measurements may be defined in the form of a treatment plan. The purpose of the KR data for outcomes would allow reasoning to determine related measurements, related cohorts, possible cohort definition criteria, and treatment plan details. |
Gap Analysis::caEHR::caEHR 3 - Support reasoning on clinical outcome measurements |
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Use ontologies to help create high-quality data element definitions and avoid duplicate definitions. In particular, Layer 2 of BRIDG 3.0 has an OWL-based ontology of the BRIDG DAM semantics that can be used to help support this normalization and harmonization process. *Source * * CDISC SHARE: Pathway into the Future for Standards Development and Delivery, April 10, 2010, Brow W. Kisler, CDISC Senior Director and CDISC SHARE Pilot Report. |
Gap Analysis::CDISC::CDISC-10 - Use Ontologies to Help Create High Quality Data Element Definitions |
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Service Oriented Architecture is an architectural paradigm for organizing and utilizing distributed capabilities that may be under the control of different ownership domains. Consequently, it is important that organizations that plan to engage in service interactions adopt governance policies and procedures sufficient to ensure that there is standardization across both internal and external organizational boundaries to promote the effective creation and use of SOA-based services. SOA governance requires numerous architectural capabilities on the Semantic Infrastructure: Governance is expressed through policies and assumes multiple use of focused policy modules that can be employed across many common circumstances This is elaborated in the inherited Policy profile. Governance requires that the participants understand the intent of governance, the structures created to define and implement governance, and the processes to be followed to make governance operational. This is provided by capabilities specialized from the inherited Management Profile. Governance policies are made operational through rules and regulations. This is provided by the following capabilities, most of which are specializations of the inherited Artifact Profile: * descriptions to enable the rules and regulations to be visible, where the description includes a unique identifier and a sufficient, and preferably a machine process-able, representation of the meaning of terms used to describe the rules and regulations; * one or more discovery mechanisms that enable searching for rules and regulations that may apply to situations corresponding to the search criteria specified by the service participant; where the discovery mechanism will have access to the individual descriptions of rules and regulations, possibly through some repository mechanism; * accessible storage of rules and regulations and their respective descriptions, so service participants can understand and prepare for compliance, as defined. * SOA services to access automated implementations of the Governance Processes. Governance implies management to define and enforce rules and regulations.. This is elaborated in the inherited Management profile. Governance relies on metrics to define and measure compliance. This is elaborated in the inherited Metric profile. |
Semantic Profile::OASIS SOA::Governance Model |
discovery from inherited abstract profile Artifactidentity from inherited abstract profile Artifactmetadata from inherited abstract profile Artifactstore from inherited abstract profile Artifact |
A service description is an artifact, usually document-based, that defines or references the information needed to use, deploy, manage and otherwise control a service. This includes not only the information and behavior models associated with a service to define the service interface but also includes information needed to decide whether the service is appropriate for the current needs of the service consumer. Thus, the service description will also include information such as service reachability, service functionality, and the policies and contracts associated with a service. A service description artifact may be a single document or it may be an interlinked set of documents. Architectural implications of service description on the Semantic Infrastructure are reflected in the following functional decomposition: * Description will change over time and its contents will reflect changing needs and context. This is elaborated in the inherited Change profile. * Description makes use of defined semantics, where the semantics may be used for categorization or providing other property and value information for description classes. This is elaborated in the inherited Semantic Model profile. * Descriptions include reference to policies defining conditions of use and optionally contracts representing agreement on policies and other conditions. This is elaborated in the inherited Policy profile. * Descriptions include references to metrics which describe the operational characteristics of the subjects being described. This is elaborated in the inherited Metrics profile. * Descriptions of the interactions are important for enabling auditability and repeatability, thereby establishing a context for results and support for understanding observed change in performance or results. This is elaborated in the inherited Interaction profile. * Descriptions may capture very focused information subsets or can be an aggregate of numerous component descriptions. Service description is an example of a likely aggregate for which manual maintenance of all aspects would not be feasible. This is elaborated in the inherited Composition profile. * Descriptions provide up-to-date information on what a resource is, the conditions for interacting with the resource, and the results of such interactions. As such, the description is the source of vital information in establishing willingness to interact with a resource, reachability to make interaction possible, and compliance with relevant conditions of use. This is elaborated in the inherited Interoperability profile. Policy capabilities are specialization of Artifact capabilities. |
Semantic Profile::OASIS SOA::Service Description Model |
versioning from inherited abstract profile ChangeconfigurationManagement from inherited abstract profile Changetransition from inherited abstract profile Changediscovery from inherited abstract profile Artifactidentity from inherited abstract profile Artifactmetadata from inherited abstract profile Artifactstore from inherited abstract profile ArtifactsemanticConversion from inherited abstract profile Semantic Model |
One of the key requirements for participants interacting with each other in the context of a SOA is achieving visibility: before services can interoperate, the participants have to be visible to each other using whatever means are appropriate. The Reference Model analyzes visibility in terms of awareness, willingness, and reachability. Visibility in a SOA ecosystem has the following architectural implications on mechanisms providing support for awareness, willingness, and reachability: Mechanisms providing support for awareness will likely have the following minimum capabilities: * creation of Description, preferably conforming to a standard Description format and structure; * publishing of Description directly to a consumer or through a third party mediator; * discovery of Description, preferably conforming to a standard for Description discovery; * notification of Description updates or notification of the addition of new and relevant Descriptions; * classification of Description elements according to standardized classification schemes. In a SOA ecosystem with complex social structures, awareness may be provided for specific communities of interest. The architectural mechanisms for providing awareness to communities of interest will require support for: * policies that allow dynamic formation of communities of interest; * trust that awareness can be provided for and only for specific communities of interest, the bases of which is typically built on keying and encryption technology. The architectural mechanisms for determining willingness to interact will require support for: * verification of identity and credentials of the provider and/or consumer; * access to and understanding of description; * inspection of functionality and capabilities; * inspection of policies and/or contracts. The architectural mechanisms for establishing reachability will require support for: * the location or address of an endpoint; * verification and use of a service interface by means of a communication protocol; * determination of presence with an endpoint which may only be determined at the point interaction but may be further aided by the use of a presence protocol for which the endpoints actively participate. |
Semantic Profile::OASIS SOA::Service Visibility Model |
discovery from inherited abstract profile Artifact |
configurationManagement
Description
Mechanisms to support the storage, referencing, and access to normative definitions of one or more versioning schemes that may be applied to identify different aggregations of descriptive information, where the different schemes may be versions of a versioning scheme itself.
Requirements addressed
Overview of possible operations
discovery
Description
One or more discovery mechanisms that enable searching for artifacts that best meet the search criteria specified by the service participant; where the discovery mechanism will have access to the individual artifact descriptions, possibly through some repository mechanism.
Requirements addressed
Overview of possible operations
identity
Description
Descriptions which include a unique identifier for the artifact.
Requirements addressed
Overview of possible operations
metadata
Description
A representation of the meaning of terms used to describe the artifact, its functions, and its effects.
Requirements addressed
Overview of possible operations
ontologyModelReasoning
Description
Support reasoning and querying on Ontology models (T-Box) and instance data (A-Box)
Represent caBIG information models as ontologies in order to be able to use Semantic Web technology to reason over information models and the data that conforms those models
Store data elements in a publicly available ontology repository
Use Ontologies to Help Create High Quality Data Element Definitions.
Requirements addressed
- CDISC-10 - Use Ontologies to Help Create High Quality Data Element Definitions
- 125 - Reasoning and querying on Ontology models
- 117.1 - Represent caBIG Information models as ontologies
- BRIDG-1 - Store data elements in a publicly available ontology repository
Overview of possible operations
provenance
Description
While the Resource identity provides the means to know which subject and subject description are being considered, Provenance as related to the Description class provides information that reflects on the quality or usability of the subject. Provenance specifically identifies the entity (human, defined role, organization, ...) that assumes responsibility for the resource being described and tracks historic information that establishes a context for understanding what the resource provides and how it has changed over time. Responsibilities may be directly assumed by the Stakeholder who owns a Resource or the Owner may designate Responsible Parties for the various aspects of maintaining the resource and provisioning it for use by others. There may be more than one entity identified under Responsible Parties; for example, one entity may be responsible for code maintenance while another is responsible for provisioning of the executable code. The historical aspects may also have multiple entries, such as when and how data was collected and when and how it was subsequently processed, and as with other elements of description, may provide links to other assets maintained by the Resource owner.
Requirements addressed
Overview of possible operations
reasonOverClinicalOutcomeMeasurements
Description
The caEHR provides a means for performing outcome measurements, and aggregating those measurements for analysis. These outcome measurements are defined as being time interval values based on clinical observations.
Representation of clinical outcome measurement details is required. This should include the set of observations that a clinical outcome requires, and any constraints that might be necessary. These constraints may need to be represented as rules or value set bindings.
This would more likely be a specific profile for an observation class or set of classes with criterion classes associated. These would also be associated with the detailed clinical models that represent the observation.code attribute in added detail.
In addition, aggregations occur across measurements. Aggregations may have measurements for single patients or informal collections of patients. In addition it may operate upon formal collections of patients in the form of study cohorts. These measurements may be defined in the form of a treatment plan. The purpose of the KR data for outcomes would allow reasoning to determine related measurements, related cohorts, possible cohort definition criteria, and treatment plan details.
Requirements addressed
Overview of possible operations
semanticConversion
Description
One or more mechanisms to support the storage, referencing, and access to conversion relationships between semantic models, and the mechanisms to carry out such conversions.
Requirements addressed
Overview of possible operations
store
Description
Accessible storage of artifacts and artifact descriptions, so service participants can access, examine, and use the artifacts as defined.
Requirements addressed
Overview of possible operations
transition
Description
One or more mechanisms to support the storage, referencing, and access to conversion relationships between versioning schemes, and the mechanisms to carry out such conversions.
Requirements addressed
Overview of possible operations
versioning
Description
Configuration management mechanisms to capture the contents of the each aggregation and apply a unique identifier in a manner consistent with an identified versioning scheme.
