Table of Contents
Introduction
As a means towards engaging this larger community and contributing to the creation of solutions for its needs, the BIG Health Consortium was formed, a non-governmental organization that is affiliated with caBIG, but which has a complementary agenda that is focused on enabling the integration of research, care delivery, and patient-driven decision making in practical ways. As a consequence, the institutional stakeholders associated with BIG Health Consortium extend well beyond the cancer centers, universities, and cooperative groups that make up the core NCI-funded constituencies that have participated in caBIG since its original incarnation. The extended community thus goes beyond what is considered caBIG-proper today, and includes groups that are not yet connected to caGrid.
Background
The caDSR has a suite of tools and APIs that support workflows for metadata development, browsing and retrieval. In addition, the caDSR has been adapted to support the UML model-driven development paradigm adopted by caBIG. UML-defined information models such as those from the BRIDG project, caArray, caTissue, and others are each registered in the caDSR through conversion of the model elements into ISO11179 metadata constructs. This functionality, and the workflows that it supports, has evolved over an 8-year period and is now quite mature. It satisfies the current requirements for semantic representation in the current caBIG developer and user community, but it is ill-suited to serve the new requirements for decentralization and indefinite scalability in the broader health care community. The goal of this program is therefore to harvest and recycle the best elements of the first generation of caBIG metadata infrastructure, and to then incorporate those elements into a redesigned and modernized technology stack that is engineered from the start to support a federated deployment topology with far less centralized administration.
Scope
DRAFT
Project Scope
The Knowledge Repository (KR) project is charged with supporting the activities defined in Initiative 1 of the caBIG Semantic Infrastructure effort. Therefore, the document on the Vocabulary Knowledge Center Wiki that describes Initiative 1 is the starting point for defining the high-level scope of this project. The NCI caBIG Semantic Infrastructure and Operations (SIO) group's representatives (Denise Warzel & Dave Hau), referred to here as NCI representatives, will provide direction and ensure that we interpret Initiative 1 in a way that aligns with the vision and mission of SIO, caBIG, and NCI.
The scope statements below represent our current understanding of the scope of this project. However, as we gain further understanding of the needs of the NCI stakeholder community, these scope statements will evolve. Therefore, these statements serve to guide our near- to mid-term activities, but do not constrain the ultimate scope of the project.
The scope for Release 1, which will be delivered in March of 2011, will be specified in the Release 1 Scope document. That document is derived from the prioritization of lower-level requirements that are specified in the KR Software Requirements Specification document. Furthermore, there are multiple touch-points among initiatives. The #Inter-Initiative Touch-Points section below describes those and how they affect the scope of this project.
Scope Statements
- S1: ISO 11179 ed. 3 Registry Support
- S2: UML Model Repository Support
- S3: ISO 21090 Support
- S4: Semantic Transformation Support
- S5: Distributed, Federated Repositories
- S6: Service Oriented Architecture
- S7: Semantic Integration Tooling
- S8: Semantic Infrastructure Interoperability
S1: ISO 11179 ed. 3 Registry Support
Description:
Provide design and reference implementation of a ISO 11179 ed. 3 compliant metadata repository.
Source:
Initiative 1 explicitly calls for "a production realization of the PIM of the distributed ISO 11179 Ed3 repository..."
Justification:
According to the standard, the purposes of ISO/IEC 11179 are:
- Standard description of data
- Common understanding of data across organizational elements and between organizations
- Re-use and standardization of data over time, space, and applications
- Harmonization and standardization of data within an organization and across organizations
- Management of the components of data
- Re-use of the components of data
To the extent that ISO 11179 achieves these purposes, it provides support for data integration. This aligns with caBIG goals of supporting translational research, which benefits from data integration.
S2: Model Repository Support
Description:
Provide the design and reference implementation of Model Repository, initially to include representations of UML Models, but also to allow recording/registering of other types of end user models that represent the information model for a given application.
Source:
Initiative 1 calls for "...model repositories and tooling including storage and sharing of DAMs and of 'lower-level" models derived from DAMs." It describes the need to use UML-based information models such as BRIDG and LS-DAM to provide a "shared semantic view." It describes the need to enable "model repositories to be decomposed into data description..." We interpret this to mean that there should be some alignment of UML information models to ISO 11179 metadata elements, similar to what is currently in use within caBIG. The purposes for this alignment include 1) encouraging reuse of data elements; 2) enabling description of semantic relationships among UML models. However, alternatives should be considered that may not include ISO 11179, but do support creation of a shared semantic view.
Justification:
BRIDG and LS-DAM represent the consensus, shared semantic views of the clinical research and care and life sciences domains. By providing the capability to describe the semantic relationships among these models and other UML-based information models, the repository would enable view-based data integration, which can support query re-writing or construction of data warehouses.
Additional Notes
One of the goals of this effort is to reduce barriers to sharing metadata. Therefore, the repository should be not be restricted to recording only UML or 11179 metadata elements. Instead, it should allow users to record metadata in any form (e.g. spreadsheets, XSDs, etc.). The ISO 11179 ed. 3 model allows for this kind of unconstrained recording of metadata. So, ultimately, we may be able to use that feature of 11179 in order to achieve the goal of lowering barriers.
S3: ISO 21090 Support
Description:
Extend the 11179 Value Domain to support representation of ISO 21090 Heathcare datatypes and accommodate UML models that use these datatypes.
Source:
Initiative 1 does not explicitly call for ISO 21090 support. However, it might be inferred from a call for support of DAMs such as BRIDG which use these datatypes. The Statement of Work for the Knowledge Repository project specifically calls for "Extension of ISO 11179 Value Domain Datatype to include representation of ISO 21090 Healthcare data types" and "support for representation of complex ISO 21090 Healthcare data types" by the services that this project produces.
Justification:
According to the ISO 21090 standard, its purpose is to:
- provide set of data type definitions for representing and exchanging basic concepts that are commonly encountered in healthcare environments in support of information exchange in the healthcare environment,
- specify a collection of healthcare related data types suitable for use in a number of health related information environments,
- declare the semantics of these data types using the terminology, notations and data types defined in ISO 11404 rev 2005,
- provide UML definitions of the same data types using the terminology, notation and types defined in Unified Modeling Language (UML) version 2.0,
- define an XML (Extensible Markup Language) based representation of the data types suitable for use when exchanging information between information processing entities.
To the extent that use of these datatypes will support interoperability, this item aligns with the caBIG goal to "Connect scientists and practitioners through a shareable and interoperable infrastructure."
Additional Notes
The system should provide support for selecting and describing specific 21090 types, and allow localization of 21090 data types (constraining/expanding).
S4: Semantic Transformation Support
Description:
The system should allow metadata that has been stored in the repository to be queried and manipulated from the perspective of multiple views. Therefore, we will define isomorphic transformation between all supported views. ISO 11179 and UML are the currently identified views.
Source:
Initiative 1 calls for "...transformation capabilities to allow model repositories to be decomposed into data descriptions that can be reused through the existing infrastructure to support deployment of these semantics in practical end user solutions via software engineering techniques such as forms development and forms generation. "
Here, the main requirement seems to be, enabling use of the existing infrastructure, which is oriented toward a ISO 11179 view of metadata.
The RFP expands the notion of transformation to include higher-level services such as comparison. This is captured here in a separate scope item.
Justification:
There are existing tools (e.g. form builders) that rely on a ISO 11179 view of metadata. This project should support them.
S5: Distributed, Federated Repositories
Description:
The architecture of the 11179 and UML repositories should enable physical distributed and logical federation. The architecture should support distributed linking of content and federated workflows (e.g. versioning, curation, query) over that content.
Source:
The sub title of Initiative 1 is "Distributed, federated metadata repositories and model repositories and operations." It indicates that the "...architecture for the distributed metadata repository (MDR) will be decentralized in nature, allowing multiple peer repositories to be present at the same time, for sharing of data elements."
Justification:
According to the SI Conops Initiatives overview, "The need for all semantic metadata to be formally recorded in a single central repository would limit or preclude application of the semantic infrastructure to very large, diverse communities such national health care. Distributed, federated metadata resources will clearly be required."
S6: Semantic Service Oriented Architecture
Description:
The architecture of the metadata and model repositories will be service-oriented, according to the principles defined here. Functionality will be exposed through semantically annotated service interfaces.
Source:
The Si Conops calls for the use of the Services Aware Interoperability Framework (SAIF), which prescribes a SOA-based approach.
Justification:
NCI is using SOA as it strategy to "ensure working interoperability between differing systems that need to access or exchange specific classes of information and/or coordinate cross-application behaviors."
S7: Semantic Integration Tooling
Description:
This project will produce tooling that utilizes the distributed, federated metadata and model repository services to support an updated and revised semantic integration workflow (i.e. the ECCF) that enables decentralized and localized additions of models and data elements.
Source:
Initiative 1 calls for "Development of a set of user applications or services as needed for creation, management, search and retrieval and of metadata." And, the SI Conop Mission statement calls for:
- Employ the Enterprise Compliance and Conformance Framework to represent frameworks and models in an implementation independent manner;
- Build and adapt tools and interfaces for generation, curation, storage and use of semantic information, and for convenient lookup, retrieval and transformation of this information by both end-users and applications;
Justification:
The semantic infrastructure requirements have both run-time and design-time aspects. The primary design-time requirements involve application of the ECCF to build systems that achieve Working Interoperability.
S8: Semantic Infrastructure Interoperability
Description:
The NCI's approach to metadata registries should support some level of interoperability with registries of other agencies and external groups.
Source:
<source>
Justification:
<justification>
Inter-Initiative Touch-Points
<working>
Users and Characteristics
An Actor models a type of role played by an entity that interacts with the subject (e.g., by exchanging signals and data), but which is external to the subject. Actors may represent roles played by human users, external hardware, or other subjects. Note that an actor does not necessarily represent a specific physical entity but merely a particular facet (i.e., "role") of some entity that is relevant to the specification of its associated use cases. Thus, a single physical instance may play the role of several different actors and, conversely, a given actor may be played by multiple different instances.
While UML 2 does not permit associations between Actors, this constraint is often violated in practice since the generalization/specialization relationship between actors is useful in modeling overlapping behaviours between actors. The actors below are represented as having a hierarchical relationship for ease of understanding; however, these relationships can easily be removed.
- Cancer Researcher: plans and performs activities related to discovery of new knowledge, drugs, and treatments in the field of oncology
- Clinical Researcher: works directly with patients and/or patient data while performing cancer research
- Basic Science Researcher: works with scientifically generated data while performing cancer research
- Protocol Designer: defines the methods used to perform cancer research
- Information Technologist: designs, develops, and manages the software and hardware necessary to perform cancer research
- Business Analyst: analyzes the business processes and describes the goals and activities of the user community
- Information Modeler: designs, defines, and describes the data that will be captured during cancer research activities
- Software Engineer: implements the software systems that are used to manage and perform cancer research
- Systems Architect: designs the software and hardware systems that are used to manage and perform cancer research
- System Administrator: manages the software and hardware systems that are used to perform cancer research
- Metadata Specialist: having a deep understanding of semantics and syntactic, assists Cancer Researchers and Information Technologists on modeling and managing metadata
- Forms Author: constructs data collection forms based on a library of common data elements
- Metadata Curator: works hands-on with Cancer Researchers and Information Technologists to model and manage their metadata
- Metadata Systems Specialist: manages centralized metadata systems and assists with the design of metadata systems
- Terminologist: a metadata expert that manages and maintains the semantic concepts that underlie information models
- Compatibility Reviewer: while the nature of "caBIG Compatibility" may change as need dictates, the role of the Compatibility Reviewer will likely continue to be a Metadata Specialist that reviews a variety of documents/artifacts to determine the level of interoperability that a system meets
- Patient: any person who receives medical attention, care, or treatment
- Subject: a Patient that is participating in Cancer Research
Related Documentation
End User |
Analysis |
Technical |
Management |
|---|---|---|---|
Knowledge Repository Project Page |
Architecture Guide |
Vision and Scope |
Resources
The following is a list of documents that provide background material, requirements, and related topics:
- Con Ops Supplemental Page for Requirements Gathering: https://wiki.nci.nih.gov/display/VCDE/Supplemental+Page+for+Requirements+Gathering
- Semantic Requirements Forum: https://cabig-kc.nci.nih.gov/Vocab/forums/viewforum.php?f=34
- Con Ops Stakeholders: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/SI_Conop_Stakeholders
- Con Ops Requirements: https://wiki.nci.nih.gov/display/VCDE/Requirements+Questionnaires
- Con Ops Use Cases: https://wiki.nci.nih.gov/display/VCDE/Use+Cases+for+Semantic+Requirements
Terms & Definitions
Term |
Definition |
|---|---|
MUST |
This word means that the definition is an absolute requirement of the specification. |
MUST NOT |
This phrase means that the definition is an absolute prohibition of the specification. |
WILL |
This word means that the definition is an absolute future requirement of the specification. |
WILL NOT |
This phrase mean that the definition is an absolute future prohibition of the specification. |
SHOULD |
This word means that there may exist valid reasons in particular circumstances to ignore a particular item, but the full implications must be understood and carefully weighed before choosing a different course. |
SHOULD NOT |
This phrase means that there may exist valid reasons in particular circumstances when the particular behavior is acceptable or even useful, but the full implications should be understood and the case carefully weighed before implementing any behavior described with this label. |
MAY |
This word means that a requirement is truly optional. The developer may choose to include the item based on the needs of their design. |
Assumptions and Dependencies
Usability
The user interface shall be designed for ease-of-use by the designated end-users, shall use terms common to the user's normal business environment, and shall require little to no additional training on the system. Drop down menus, Google-like searches, and tooltips should be used wherever appropriate.
Accessibility
The user interface should be accessible via a web browser.
General Assumptions
Following is a list of basic assumptions:
- Federated Discovery Services: Knowledge Repository Services will be distributable and discoverable in a federated manner
- Security Considerations: services and underlying data will be secured using the caBIG security architecture
- Subscriptions/Notifications: services requiring subscription and notification functionality will be enabled by the caBIG pub/sub architecture
- ISO 11179 Ed 3: the Knowledge Repository will comply with ISO 11179 Ed 3 specifications. See here for our analysis.
- Ability to have non-administered items: the Knowledge Repository will provide for non-administered items in the ISO 11179 notion
- Duplication/identification: in compliance with the Federated Discovery Services assumption, reference of data, data duplication, and unique identification of data will be handled
Dependencies
TBD
Functional Requirements
Model Services
Some basic description of model services.
ID |
Requirement |
Source |
Release |
|---|---|---|---|
MOS-1 |
The Model Service MUST support the abilities to record new model elements. |
|
|
MOS-2 |
The Model Service MUST support the abilities to record new assertions. |
|
|
MOS-3 |
The Model Service MUST support the abilities to record new rules. |
|
|
MOS-4 |
The Model Service SHOULD support the abilities to record queries. |
|
|
MOS-10 |
Discover |
|
|
MOS-11 |
Federated query |
|
|
MOS-12 |
Find related metadata |
|
|
MOS-20 |
Compare |
|
|
MOS-21 |
Harmonize |
|
|
MOS-30 |
Merge |
|
|
MOS-40 |
Graphical/visualize |
|
|
MOS-50 |
Version |
|
|
MOS-60 |
Retire |
|
|
MOS-70 |
Update |
|
|
MOS-80 |
Delete/unregister |
|
|
MOS-90 |
Transform |
|
|
MOS-100 |
Validate |
|
|
MOS-110 |
Reuse |
|
|
MOS-111 |
Copy |
|
|
MOS-120 |
Extend |
|
|
MOS-121 |
Extend classes |
|
|
MOS-122 |
Add relationships |
|
|
MOS-123 |
Extend attribute value list |
|
|
MOS-130 |
Constrain |
|
|
MOS-131 |
Subset classes |
|
|
MOS-132 |
Subset/constrain attribute value lists |
|
|
MOS-140 |
Find related services |
|
|
MOS-150 |
Find related documentation |
|
|
Metadata Services
Some basic description of metadata services.
ID |
Requirement |
Source |
Release |
|---|---|---|---|
MDS-1 |
Data Element |
|
|
MDS-2 |
Record (no rules) |
|
|
MDS-3 |
New assertions |
|
|
MDS-4 |
Update |
|
|
MDS-5 |
Version |
|
|
MDS-6 |
Validate business rules |
|
|
MDS-7 |
Retire |
|
|
MDS-8 |
Delete/rollback |
|
|
MDS-9 |
Discover reusable content |
|
|
MDS-10 |
Usage information |
|
|
MDS-11 |
Search/query |
|
|
MDS-12 |
Federated search/query |
|
|
MDS-13 |
Compare |
|
|
MDS-14 |
Create new from existing |
|
|
MDS-15 |
Discover related models |
|
|
MDS-16 |
Discover related metadata items |
|
|
MDS-17 |
Discover related services |
|
|
MDS-18 |
Discover related rules |
|
|
MDS-19 |
Discover related forms |
|
|
MDS-101 |
Value Domain |
|
|
MDS-102 |
Record (no rules) |
|
|
MDS-103 |
New assertions |
|
|
MDS-104 |
Update |
|
|
MDS-105 |
Version |
|
|
MDS-106 |
Validate business rules |
|
|
MDS-107 |
Retire |
|
|
MDS-108 |
Delete/rollback |
|
|
MDS-109 |
Discover reusable content |
|
|
MDS-110 |
Usage information |
|
|
MDS-111 |
Search/query |
|
|
MDS-112 |
Federated search/query |
|
|
MDS-113 |
Compare |
|
|
MDS-114 |
Create new from existing |
|
|
MDS-115 |
Discover related models |
|
|
MDS-116 |
Discover related metadata items |
|
|
MDS-117 |
Discover related services |
|
|
MDS-118 |
Discover related rules |
|
|
MDS-119 |
Discover related forms |
|
|
MDS-120 |
Create subset/constrain |
|
|
MDS-120 |
Extend (create new from existing) |
|
|
MDS-120 |
Semantic transformations (Explicitly based on mapping e.g. to the same Value Meaning) |
|
|
MDS-120 |
Syntactic transformations ( Source representation to Target representation) |
|
|
MDS-201 |
Data Element Concept |
|
|
MDS-202 |
Record (no rules) |
|
|
MDS-203 |
New assertions |
|
|
MDS-204 |
Update |
|
|
MDS-205 |
Version |
|
|
MDS-206 |
Validate business rules |
|
|
MDS-207 |
Retire |
|
|
MDS-208 |
Delete/rollback |
|
|
MDS-209 |
Discover reusable content |
|
|
MDS-210 |
Usage information |
|
|
MDS-211 |
Search/query |
|
|
MDS-212 |
Federated search/query |
|
|
MDS-213 |
Compare |
|
|
MDS-214 |
Create new from existing |
|
|
MDS-215 |
Discover related models |
|
|
MDS-216 |
Discover related metadata items |
|
|
MDS-217 |
Discover related services |
|
|
MDS-218 |
Discover related rules |
|
|
MDS-219 |
Discover related forms |
|
|
MDS-220 |
Discover related data elements |
|
|
MDS-222 |
Discover related value sets |
|
|
MDS-223 |
Create data element from existing data element concept and value domain |
|
|
MDS-224 |
Create new data element concept from existing data element concept |
|
|
Registry-Registry Service
ID |
Requirement |
Source |
Release |
|---|---|---|---|
RRS-1 |
Import Content |
|
|
RRS-10 |
Export Content |
|
|
RRS-20 |
Update Content |
|
|
RRS-30 |
Search |
|
|
RRS-40 |
Submit Content |
|
|
RRS-50 |
Register Content |
|
|
RRS-60 |
Update Registration |
|
|
General Service
ID |
Requirement |
Source |
Release |
|---|---|---|---|
GEN-1 |
Annotate with concepts |
|
|
GEN-10 |
Subscribe to changes |
|
|
GEN-20 |
Reuse (classify/categorize) |
|
|
Metadata Registry Tools
ID |
Requirement |
Source |
Release |
|---|---|---|---|
|
Clinician friendly browser |
|
|
|
Information specialist browser |
|
|
|
Customizable browser |
|
|
|
Portal that integrates tools |
|
|
|
Workflow management to support ECCF artifact creation |
|
|
|
Interface of browser/editing models and metadata with modeling tools |
|
|
Non-functional Requirements
Performance
Performance refers to the qualitative or quantitative measure of how well a system reacts in a user workflow. This can be measured in time from a user or system perspective, as well as the amount of resources (CPU, memory, etc.) that software must consume to complete a task.
ID |
Requirement |
|---|---|
PE-1 |
Where not otherwise specified, web pages should be completely returned within seconds of request. |
Auditing, Logging, and Provenance
Auditing, logging, and provenance is the process of recording events in an automated and/or manual way within a certain scope in order to provide an audit trail that can be used to understand the activity of the system and/or to diagnose problems.
ID |
Requirement |
|---|---|
ALP-1 |
The application will address Title 21 Code of Federal Regulations (21 CFR Part 11) Electronic Records where appropriate and reasonable. |
ALP-10 |
The system must audit each and every user action that results in database access (read or write). Examples include: add/edit study or participant data, user login, query etc.
|
ALP-20 |
Auditing information must be accessible in a timely manner to system administrators. |
ALP-30 |
Auditing features must at least be available through standard database logging/auditing. |
ALP-40 |
Logging must be implemented in all the architectural layers - presentation, business logic and data access layers |
Fault Handling
Fault handling is a mechanism designed to handle the occurrence of exceptions, special conditions that change the normal flow of software or user execution.
ID |
Requirement |
|---|---|
FH-1 |
Any runtime exceptions or errors must be reported to the user in a graphical window containing the probable cause of the problem and how to rectify that. |
FH-10 |
The exceptions and errors shall be divided into two groups:
|
Quality of Service
Quality of service is the ability to provide sufficient uptime and availability of software to guarantee a certain level of performance to access and data flow.
ID |
Requirement |
|---|---|
QS-1 |
The system must be adequately validated during the system development lifecycle. |
QS-10 |
The system must provide the functionality to generate and manage accurate data records during the development processes. |
QS-20 |
The system development lifecycle must include validity checks for all data fields. |
Usability
In design, Usability is the study of the ease with which people can employ a particular tool or other human-made object in order to achieve a particular goal.
ID |
Requirement |
|---|---|
US-1 |
An intuitive user friendly graphical user interface must be developed. |
PE-10 |
Web page requests must resolve in a timely manner. Where not otherwise specified, this is on the order of seconds. |
PE-20 |
The application will address section 508 of the Rehabilitation Act of 1973 where appropriate and reasonable. |
Security
Security is the protecting of information and information systems from unauthorized access, use, disclosure, disruption, modification or destruction.
ID |
Requirement |
|---|---|
SE-1 |
The system must limit access to authorized individuals. |
SE-10 |
Electronic Signatures should meet necessary requirements as described in 21 CFR part 11. |
SE-20 |
The application will address section 508 of the Rehabilitation Act of 1973 where appropriate and reasonable. |
SE-30 |
System developers must adhere to the caBIG™ Data Sharing & Intellectual Capital Policy and Procedures |
Portability
Portability is the software codebase feature to be able to reuse the existing code instead of creating new code when moving software from an environment to another. The prerequirement for portability is the generalized abstraction between the application logic and system interfaces.
ID |
Requirement |
|---|---|
PO-1 |
Operating system native libraries should not be used. |
PO-10 |
All the paths for the local file system must not be hard coded. Example C:\myDir etc. |
