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Upcoming Speaker:
February 27, 2019
Dr. Thomas Klumpp
Design and Implementation of a Multipurpose BRIDG-Harmonized Cancer Research Information System
An invitation: If you are interested in presenting your work to our diverse audience of informaticists; basic, translational, and clinical researchers; software developers; and others interested in exploring the uses of informatics in cancer research, contact Eve Shalley at eve.shalley@nih.gov or 240-276-5194.
Welcome to the CBIIT Speaker Series Wiki
The NCI Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series presents talks from innovators in the research and informatics community. The biweekly presentations allow thought leaders to share their work and discuss trends across a diverse set of domains and interests. The goals of the Speaker Series are: to share leading edge research; to inform the community of new tools, trends, and ideas; to inspire innovation; and to provide a forum from which new collaborations can begin.
Speakers represent many different institutions, and the topics they address are wide-ranging. View a list of all past speakers, and view their presentations on our NCI CBIIT Speaker Series YouTube playlist!
For help accessing NCI CBIIT Speaker Series files, go to Help Downloading Files.
Location: 9609 Medical Center Drive, Rockville, Maryland 20850
Speaker Series Guidelines for Speakers: Download Word document
Questions or suggestions? If you have questions or would like to recommend a speaker, please email Eve Shalley at eve.shalley@nih.gov.
Upcoming Speakers:
February 27, 2019: Thomas Klumpp, Thomas Jefferson University Medical Center
March 27, 2019: Samir Courdy, Huntsman Cancer Institute, and Joyce Niland, City of Hope
CBIIT Speakers
A major barrier to the conduct of biomedical research is how difficult it is to share biomedical research data, both within and between institutions. Data located in different data repositories are almost always organized, categorized, and represented in different ways. This problem has been referred to as “the Chasm of Semantic Despair.” In an attempt to address this problem, the Cancer Informatics group at the NCI, in collaboration with their colleagues at the FDA, ISO, HL7, and CDISC, developed a new international standard data model for biomedical research called the Biomedical Research Integrated Doman Group (BRIDG) model. The purpose of the BRIDG model is to “bridge” the large number of Chasms of Semantic despair that exist both within and between academic medical centers, pharmaceutical companies, and government regulators. The Sidney Kimmel Cancer Center at Thomas Jefferson University in Philadelphia, has successfully designed and implemented a cancer research information system based on the NCI-BRIDG model. In this talk. Dr. Klumpp will describe how the BRIDG model has been implemented in the cancer research information system at Thomas Jefferson and the benefits of such an integrated system.
FDA, CDC, NIH (NCATS) are developing a FHIR based infrastructure that facilitates interactions with the four most prevalent Common Data Models (CDMs) - Sentinel , OMOP, i2b2/ACT and PCORNet - from a single portal. The infrastructure allows investigators the ability to create a universal query that can be run against all four CDMs, a secure transport and aggregation of the cross CDM query results, and the ability to submit the results directly to the FDA as a CDISC STDM file.
Building a web-based API (Application Programming Interface) has been rapidly adopted in the bioinformatics field as a new way of disseminating the underlying biomedical knowledge. While researchers benefit from the simplicity and the high accessibility (A) of available APIs, the findability (F), interoperability (I) and reusability (R) across APIs are largely not well-handled by the community. BioThings API project (http://biothings.io) is tasked to build a FAIR API ecosystem to better serve the underlying inter-connected biomedical knowledge. BioThings API provides three components in its API development ecosystem. First, it provides a family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs. Second, BioThings API packages its API-development best practice into a reusable SDK (Software Development Kit) to help other bioinformaticians to build the same high-quality API to distribute their own specific knowledge. Third, BioThings API provides a platform to foster the findability and interoperability across the community-developed biomedical APIs. Through the SmartAPI application (http://smart-api.info), it provides tools for authoring API metadata following the community supported OpenAPI standard and hosts standardized interactive API documentation. It also defines a set of OpenAPI extensions to provide biomedical-specific semantic annotations, such as what specific biomedical identifiers an API parameter accepts and what specific biomedical entity types an API response contains. Powered by these semantic annotations, a new web application called BioThings Explorer was developed to allow researchers to navigate the scope of the distributed biomedical API landscape and build the desired knowledge extraction workflows by identifying and combining required APIs.
In this talk, Dr. Smith will describe the work he and his lab are doing to progress the state of Informatics for Computational Mass Spectrometry to further proteomic research.