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The Importance of Data Standards to Integrative Queries
This The common infrastructure that will result from CTIIP and its sub-projects depends on data interoperability, which is greatly aided by adherence to data standards. While standards such as Annotation and Image Markup (AIM) and Digital Imaging and Communications in Medicine (DICOM) exist, vendors of data viewers and other tools required for the analysis of imaging data have not widely adopted them. Digital pathology, unlike its more mature radiographic counterpart, has yet to standardize on a single storage and transport media. The result of this lack of uniformly accepted standards is that outside a given laboratory of small collaborative groups, the integration of pathology data with radiographic, genomic, and proteomic data is all but impossible. The lack of standards in pre-clinical and pathology prevents the standards in pre-clinical and pathology prevents the ability to share and leverage data across studies and institutions.
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CBIIT has worked extensively for several years in the area of data standards for both clinical research and healthcare, working with the community and Standards Development Organizations (SDOs), such as the Clinical Data Interchange Standards Consortium (CDISC), Health Level 7 (HL7) and the International Organization for Standardization (ISO). From that work, EVS and caDSR is harmonized with the BRIDG, SDTM, and HL7 RIM models. Standardized Case Report Forms (CRFs), including those for imaging, have also been created. The CBIIT project work provides the bioinformatics foundation for semantic interoperability in digital pathology and co-clinical trials integrated with clinical and patient demographic data and data contained in TCIA / TCGA.
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work provides the bioinformatics foundation for semantic interoperability in digital pathology and co-clinical trials integrated with clinical and patient demographic data and data contained in TCIA / TCGA.
Digital Pathology and Integrated Query System
Digital pathology, unlike its more mature radiographic counterpart, has yet to standardize on a single storage and transport media. The result of this lack of uniformly accepted standards is that outside a given laboratory of small collaborative groups, the integration of pathology data with radiographic, genomic, and proteomic data is all but impossible.
This sub-project addresses the lack of uniformly accepted standards within digital pathology and the simultaneous need for integration of pathology data with radiographic, genomic, and proteomic data.
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1) AIM 1 - Integrated query system for existing TCGA data (including improved pathology systems)
a) HistopathologyHistopathology
i) Incorporate Openslide with caMicrosocope enabling caMicrosocope to directly serve whole slide pathology images from the majority of digital pathology vendors.
ii) Incorporate support for basic image analysis algorithms into caMicroscope.
iii) Standards-based image annotation utilizing the Annotation Image Markup (AIM) standard.
b) Integrative Integrative Queries
i) Programmatic Access to Data to TCGA-related image data.
ii) Extend software to support data mashups between image-derived information from TCIA and clinical and molecular metadata from TCGA.
Integrative Query System
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