Semantic Infrastructure (SI) MDR Requirements Summary
CBIIT’s mission is to provide and advocate for the appropriate use of data science, informatics, and information technology (IT) to support and accelerate the NCI Mission to prevent cancer, treat cancer, and improve cancer outcomes. An important role of the NCI Semantic Infrastructure (SI) is to support the NCI research mission through community definition and collection of metadata. Data that have well defined linked metadata can improve the use, interpretation, and reuse of data and the extraction of information and knowledge from these data. Supporting both human readable and machine-readable definitions and metadata has been an important driver for the NCI Semantic Infrastructure. These general metadata characteristics are also among the key principles for data citation , and are noted to enable data access, verifiability and discoverability.
The primary goals for updating the metadata services are to:
- Simplify and streamline community creation, curation, maintenance, and discovery;
- Support content harmonization leveraging automated means for identification of overlapping content;
- Support interoperability and integration of data elements, modules of elements, and semantics into existing and novel workflows; and
- Support knowledge extraction.
SI Data Semantics Outline
1 Executive Summary
1.1 Mission and Goals
2 Overview, Background, Alternatives
2.1 Background
2.2 Lessons Learned
2.3 Purpose and Scope
2.4 Stakeholders
2.4.1 Personas
2.4.1.1 Mary Metadata Curation Specialist
2.4.1.2 Danny Data Manager
2.4.1.3 Alice Application developer
2.4.1.4 Ralph Researcher/Analyst
2.4.1.5 Harry Harmonization Specialist
2.4.1.6 Pete Principal Investigator
2.5 Alternatives and Analysis
- compare the NCI requirements with open source and commercial metadata repository software.
2.5.1 NLM CDE Repository
2.5.2 Semantics Manager - SOA Software - Akana
2.5.3 OneData – Software AG
2.5.4 Constellation – DOD
2.5.5 SALUS
2.5.6 Colectica
2.5.7 cTAKES, YTEX, MetaMap, UNIM
2.5.8 TransMart
2.5.9 DataType Registry – CNRI
2.5.10 Oxford University Metadata Registry
2.5.11 DataOne- USGS (Earth)
2.5.12 openMDR – Ohio State
2.5.13 USHIK
2.5.14 Mayo
2.5.15 IMOS
2.5.16 Elsevier
2.5.17 CEDAR
2.5.18 BRICS
3 Requirements and High Level Use Cases
3.1 Functional Requirements
3.1.1 Core Services
3.1.1.1 Search
- provide the ability for end users to find content based on user search criteria.
3.1.1.2 Faceted browsing
- provide users with the ability to see related content, without tacit knowledge of the underlying 11179 metamodel or specific information model or content in the repository
3.1.1.3 Curation and Maintenance
- provide a way to record and maintain structured content with minimal effort and training
3.1.1.4 Download
- provide a human accessible mechanism for getting content out of the repository to meet a variety of end user stories
3.1.1.5 Password administration
- provide user password maintenance services consistent with NIH policies.
3.1.1.6 Compare
- provide customers with the ability to identify and select similar items and view features and attributes of the items side-by-side.
3.1.1.7 Application Programming Interfaces
- provide internal and external customers with a programmatic access to repository contents.
3.1.1.8 Subscription and Notification
- provide users of NCI metadata with information about important changes.
3.1.1.9 Administration
- provide the ability to setup and configure the repository for its use; user accounts and privileges; customizing lookup tables to reflect preferred values, naming conventions and business rules.
3.1.2 New Metadata Services
3.1.2.1 Standards Collaboration
- provide the ability for users to discuss existing content and evolve the content to meet community needs.
3.1.2.2 Harmonization activities
- provide the ability to help detect similar items; support reviewing, comparing, adding “mapping” metadata, recording decisions.
3.1.2.3 Registration, Submission, and Governance
- support a procedure wherein content from various areas in NIH can be developed and maintained as needed to meet specific use cases, while at the same time submitted for central harmonization and elevation to preferred standard for the community. The process, roles and responsibilities are described in ISO 11179-6 Registration.
3.1.2.4 Reproducibility of Results
- provide a mechanism for researchers’ to record structured information about research studies so that the published data and conclusions can be reproduced.
3.1.2.5 Data Discovery Metadata, HPC, and Cloud (Big Data Initiatives) (Ian Fore, Eric Stahlberg)
- provide metadata to support emerging and existing national and international standards to share, discover, interpret and use data.
3.1.2.6 Team Science Data Management (Kara Hall)
- providing support for the unique characteristics when science is conducted as a collaboration.
3.1.2.7 Metadata Driven Software Development (TBD)
- facilitate reuse of the metadata to automate or semi-automate user interface design (drop downs, screen labels, etc), data structure creation, data validation, data transmission, data transformations
3.1.2.8 Reporting and Content Quality Metrics (Dianne Reeves)
- provide customizable reporting and statistics to support metadata curators and content administrators to improve registry content and best practices.
3.1.2.9 Semantic Web Metadata Services (Gilberto Faragoso)
- The goal of these services are to provide the abilty to leverage the semantics of CDEs to explore the meaning of the CDE, the meaning of directly related data, discovery of related data elements, data, and information using semantic web technologies.
3.1.3 New API Services
3.1.3.1 Conformance Testing
- provide a means to test conformance to a specific item’s metadata specification
3.1.3.2 CRUD
- provide dynamic registration and maintenance of metadata via application programming interfaces.
3.1.3.3 Mapping and Transformation
- leverage the infrastructure’s semantic and representational metadata to enable automated aggregation of similar or related data.
3.1.3.4 Standard Interfaces
- develop interfaces for a number of national standards for exchanging forms and data elements are emerging through ONC SDC, FHIR and IHE, transformations to other popular systems such as REDCap.
3.2 Non-Functional Requirements
3.2.1 Usability
- simplify and streamline creation and reuse of metadata
3.2.2 Constraints and Dependencies
3.2.3 Extensibility and Customization
- ability to easily extend and customize the architecture to include new kinds of content beyond those as 11179 administered items
3.3 Technical Requirements- NIH, CBIIT
3.3.1 Security
3.3.2 External API Integration
The repository needs the ability to retrieve content from other entities offering similar services.
4 Assumptions and Dependencies
5 Architecture and Constraints
5.1 Architecture Review and Refactor
5.2 Existing Metadata Migration
6 NCI Extensions
7 Performance Metrics
Annex A User prioritized Search Features
Annex B HPC & Cloud Computing
Annex C Advisory Group and Charter
Annex D Interview guide for requirements elicitation
References
Appendix A – Reporting and content quality
The above outline is presented in full detail in the following document (draft): Extended MDR RequirementsV10.9.docx
