Knowledge Capture™ Data Management for Biobanking

 

The Challenge

A critical impediment to life science R&D productivity is segregation of logistical, research, pre-clinical, and clinical trial data into information silos. Compartmentalized information inhibits sharing of knowledge within organizations and across collaborations, hinders valuable translation between pre-clinical research and clinical development, and restricts efficient evaluation of results across clinical trials.

The Solution: the KnowledgeCapture™ Data Management System

Based on a 3-year, multi-million research grant from the U.S. National Institute of Standards and Technology (NIST) Advanced Technology Program (ATP), KnowledgeCapture™ enables convenient web-based acquisition, retrieval and analysis of information. KnowledgeCapture™ consists of the following four components:

KnowledgeCapture™ Information Requirements Modeling Methodology

Researchers require high-quality annotation to derive greatest benefit from biospecimens – annotation that must be sufficiently granular, tissue-specific, diagnosis-relevant, and based on industry data standards. KnowledgeCapture™ provides an easily manipulated yet highly structured documentation tool in which to model and edit information requirements. The KnowledgeCapture™ engagement begins with discussion and analysis of your information needs, and your specifications become your custom disease model.

The KnowledgeCapture™ Library of Biomedical Concepts (DiseaseLink™)

Based on a "starter kit" of 75 disease models developed under the ATP grant, DiseaseLink™ has evolved into a library of more than 3,000 preconstructed data elements and linked structured value sets for use in requirements modeling and forms. Specifically focused on the information needs of translational research, these biomedical concepts cover domains as diverse as clinical presentation, molecular diagnostics, risk factors, surgical pathology and biorepository science. This unified, central vocabulary guarantees the harmonization and integration of data, enabling researchers to customize disease or research models that are completely comparable across disparate silos.

KnowledgeCapture™ Forms

Annotation and query forms are defined using concepts selected from the DiseaseLink™ Library and are designed according to the work flow, organization, and data display names you prefer. Forms are added to BIGR® using an administrative transaction and are immediately available for use, and can easily be modified to accomodate your evolving annotation and query needs.  The DiseaseLink™ Library can be expanded to include additional data elements required to meet your needs.

KnowledgeCapture™ Software Development Kit

The rich metadata annotation of your information requirements is used by the KnowledgeCapture™ Software Development Kit (SDK) to generate a custom database schema and provide support for robust data annotation and query capabilities in BIGR®. The SDK enables BIGR® to:

  • Display, enter and query data via web-based user interfaces
  • Check data validity in context upon entering through server-side validation
  • Transform the entered data to the format stored in the associated database
  • Integrate into new or existing host applications via Application Programming Interfaces (APIs)

The KnowledgeCapture™ SDK minimizes the development effort and increases the quality and reliability of the resulting system.

Additional Information about DiseaseLink™

DiseaseLink™ was created by HealthCare IT’s team of clinical researchers, molecular biologists, medical librarians and biomedical informatics specialists in conjunction with clinicians and scientists at academic medical research centers. HealthCare IT’s clinical informatics development group continues to expand and refine the DiseaseLink™ Library, which includes:

  • Extensive use of structured data elements and values with associated text note fields
  • SNOMED-CT CUIs augmented by local extensions to fill clinical ontology gaps and to support tissue intake and tracking
  • Diagnosis concepts precoordinated for a high degree of granularity and specificity
  • Surgical pathology based on CAP Synoptic Reports and AJCC6
  • Gene tests conforming to HUGO Gene Nomenclature Committee
  • Chromosomal aberration tests conforming to the International System for Human Cytogenetic Nomenclature
  • Occupation and environmental exposure based on the Bureau of Labor Statistics SOC
  • Disease Model elements and values prototyped in the ISO 11179 standard of the NCI caBIG™ Cancer Data Standards Repository

KnowledgeCapture™ delivers the richness and robustness of a customized software solution with the ease of use found in off-the-shelf applications.