Objective and Scope
Topics of interest include, but are not limited to, the following:
All attendees will be expected to be interested in building an OBO Foundry compliant biobank ontology or providing use cases for a biobank ontology.
Oct. 6, 2014 Schedule
Introduction (30 min)
The merged ontology can be obtained here:
Presentations (1.5 h)
Dave Parrish is the Senior Director for Laboratory Informatics at Data in Motion and key driver of the sampleminded product strategy. He is currently fully engaged at the NIAID Integrated Research Facility (IRF) in Frederick Maryland establishing a unified research operation management system (ROMS). The IRF ROMS is a collection of commercial information management systems integrated through shared models of research data and the IRF operational workflows. The ROMS supports the complete study lifecycle from study design and review through study execution and data archive
Mr. Parrish has more than 20 years of experience developing knowledge-based solutions at the intersection of clinical research and data management. His expertise has evolved around three specific dimension of informatics: (1) Data Management and Data Warehousing, (2) Clinical Vocabularies and Controlled Terminologies, and (3) Development of Clinical Trials Ontologies, each focused on applying a pragmatic solution to clinical research. Over his career he has been at the forefront of adopting leading-edge information systems in support of clinical research. Mr. Parrish has supported a broad range information management activities—from software product development to clinical trials data center operations—that required skills to effectively involve users in the planning and implementation of client-directed, problem-oriented solutions.
10:00 AM-10:15 AM Break
Discussion (1 h 45 min)
11:40 AM-12:00 PM: Wrap-up and future plans
Recommended installation before the workshop
Organizers (in alphabetical order)
Mathias Brochhausen, PhD, MA is Assistant Professor in the Division of Biomedical Information, University of Arkansas for Medical Sciences. He has served as ontologist in multiple extramurally funded projects. He participates in the development and curation of multiple ontologies related to the Open Biomedical Ontologies Foundry, (OMRSE, IAO, d-acts, BFO). Since he joined UAMS in 2011 he has been involved in multiple funded projects as on ontologist. The focus of his research is ontology-driven medical information systems, ontology development, formal ontology, logical models in medical computation.
Dr. Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.
Chris Stoeckert's research has focused on biomedical data integration. His group has worked on genomic databases including the EuPathDB project and the Beta Cell Genomics component of the Beta Cell Biology Consortium. Both projects involve the integration of genomes from multiple species, their annotation, and functional genomics datasets of various types. He is on the Board of the FGED Society which promotes data sharing. He is one of the founders and core developers of the Ontology for Biomedical Investigations. His work on data integration is motivated by biological discovery particularly in the area of transcriptional regulatory networks.
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in Ontology for Biomedical Investigation (OBI) development and building application ontologies based on OBI (e.g. , Biobank Ontology, Beta Cell Genomics Ontology (BCGO)). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations.
Papers are limited to 2-3 pages in the IEEE conference proceedings US Letter format:
Papers should be submitted electronically as a PDF file via the Easychair system at Scientific paper:
Submission Type: Scientific paper