NIH VideoCast - NLM Informatics and Data Science Lecture Series: Semantic Annotations, Reuse, and Reproducibility

Skip Navigation

NLM Informatics and Data Science Lecture Series: Semantic Annotations, Reuse, and Reproducibility

Loading... Loading video...

144 Views

Air date:	Wednesday, June 6, 2018, 2:00:00 PM Time displayed is Eastern Time, Washington DC Local
Views:	Total views: 144 (80 Live, 64 On-demand)
Category:	Special
Runtime:	01:00:10
Closed captioning:	Check box to display CC outside of the video Note: You can drag the captioning window around and resize it
Description:	NLM Informatics and Data Science Lecture Series Biomodeling (or biosimulation modeling) has the potential to revolutionize patient-specific health care and precision medicine. To increase our knowledge and management of complex pathologies, biomodeling provides the ability to produce detailed, mechanistic simulations of the dynamic biological processes and their participants. The development of these biomodels can be viewed as analogous to software development. To be effective and to scale to larger systems, the models must include clear documentation (semantic annotations), be developed in a reproducible manner, and be designed to allow for plug-and-play reuse so that researchers can build from the efforts of others. In the presentation, Dr. Gennari will report on his group’s efforts to standardize practices for semantic annotation, and to demonstrate the value of those annotations both for semantic searching over model repositories and for model merging and model reuse tasks. Over the last several years, they have succeeded in building community-wide agreement on both the importance of semantic annotation and the format of these annotations. In addition, using their annotation and model reuse tool, they have developed several demonstration examples of model merging that leverage the use of semantic annotation. Finally, as an important consequence of their work, he will also report on the initiation of a new Center for Reproducible Biomedical Modeling. Brief Bio: John Gennari has been a professor in biomedical and health informatics at the University of Washington for over 15 years. His doctorate and background is in computer science, but he began working in biomedical informatics in the early ‘90s, beginning with work on the Protégé knowledge representation and ontology development system. He has had a wide range of experiences on large, multi-institutional, multi-disciplinary projects, and this led to his research focus of knowledge reuse and knowledge sharing. His expertise is in ontology development, standards and semantic web tools. Dr. Gennari is the Graduate Program Director at UW, overseeing the PhD and research M.S. programs. He is currently on the NLM Biomedical Informatics, Library and Data Sciences Review Committee.

NLM Title:	Semantic annotations, reuse, and reproducibility / Dr. John Gennari.
Author:	Gennari, John H. National Institutes of Health (U.S.),
Publisher:
Abstract:	(CIT): Biomodeling (or biosimulation modeling) has the potential to revolutionize patient-specific health care and precision medicine. To increase our knowledge and management of complex pathologies, biomodeling provides the ability to produce detailed, mechanistic simulations of the dynamic biological processes and their participants. The development of these biomodels can be viewed as analogous to software development. To be effective and to scale to larger systems, the models must include clear documentation (semantic annotations), be developed in a reproducible manner, and be designed to allow for plug-and-play reuse so that researchers can build from the efforts of others. In the presentation, Dr. Gennari will report on his group"s efforts to standardize practices for semantic annotation, and to demonstrate the value of those annotations both for semantic searching over model repositories and for model merging and model reuse tasks. Over the last several years, they have succeeded in building community-wide agreement on both the importance of semantic annotation and the format of these annotations. In addition, using their annotation and model reuse tool, they have developed several demonstration examples of model merging that leverage the use of semantic annotation. Finally, as an important consequence of their work, he will also report on the initiation of a new Center for Reproducible Biomedical Modeling.
Subjects:	Biological Phenomena Computer Simulation Models, Biological Reproducibility of Results Semantics
Publication Types:	Lecture Webcast

NLM Classification:	QH 324.8
NLM ID:	101729819
CIT Live ID:	27905
Permanent link:	https://videocast.nih.gov/watch=27905

Related Videos...