The NIH's Clinical and Translational Science Award (CTSA) program has always emphasized the need for data standards to promote sharing and comparison of data across the CTSA Consortium and beyond. Yet creation and adoption of such standards is still painfully slow. Urgent action remains necessary. History shows the high value of standard terms, definitions, and symbols (i.e. ontology) to science.
The focus of this meeting is to explore new and existing uses of common ontologies to support creation, sharing, and analysis of clinical data.
This meeting is designed to bring together clinical and translational scientists from across the CTSA Consortium who are interested in using ontologies to promote discoverability and interoperability of biomedical data.
Richard H. Scheuermann, PhD, Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and Adjunct Professor of Pathology at U.C. San Diego
Dr. Scheuermann has applied his deep knowledge of molecular immunology and infectious disease to the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, and the development of novel methods for gene expression, protein network, flow cytometry, and comparative genomics data analysis. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database (IRD; www.fludb.org), the Virus Pathogen Resource (ViPR; www.viprbrc.org) and the Immunology Database and Analysis Portal (ImmPort; https://immport.niaid.nih.gov/) supported by the U.S. National Institutes of Health.
8am – Registration & Breakfast
8:45am – Welcoming remarks // Oliver He, Barry Smith, Kanchan Lota
Session I: Microbiomes and Host-Microbiome Interactions // Oliver He
9am – OMP: The Ontology for Microbial Phenotypes // Deborah A. Siegele/Jim Hu
9:20am – The MicrO Ontology: Enabling the Acquisition of Higher-Order Knowledge of Phenotypes from Prokaryotic Taxonomic Descriptions and the Construction of Very Large Character Matrices // Carrine E. Blank
9:40am – MEOWL: Microbial Environments described using OWL // Ramona L. Walls
10:30am – Break
10:45-11:50am – Development and Applications of the Ontology of Host-Microbiome Interactions (OHMI)
10:45-11:05am – Brief OHMI Introduction and OHMI Representation of Rheumatism-Associated Host-Microbiome Interactions // Oliver HE
11:05-11:20am – Ontology of Host-Microbiome Interactions Use Case at UPenn // Jie Zheng/Daniel Beiting
11:20-11:35am – Ontology of Host-Microbiome Interactions Use Case at MUSC // Jihad Obeid/Alesander Alekseyenko
11:35-11:50am – Ontology of Host-Microbiome Interactions Use Case at Duke // Anna Maria Masci
11:50am-12:15pm – Discussion on the Morning Session Topics
12:15pm – Lunch
Session II: CTSA Breaking Topics: Informatics Metrics
1pm – Ontological Representation of Software to Make it FAIR // Bill Hogan
1:30pm – FAIR Principles and the Immune Epitope Database (IEDB) // James Overton
2pm – Using Cyberinfrastructure to Make Life Sciences Data FAIR: Lessons Learned // Ramona Walls
2:30pm – Measuring Interannotator Agreement in the Florida Annotated Corpus for Translational Science – The Difficult Ontological Task // Amanda Hicks
3pm – Break
3:30pm – Discussion
6:30pm - Dinner at Local Ann Arbor Restaurant
4:15pm – Keynote Address 1: Identification and Representation of Cellular Biomarkers Using High-Content Single Cell Cytometry and Sequencing Technologies // Richard H. Scheuermann, PhD
Chris Stoeckert, Research Professor of Genetics, Institute of Biomedical Informatics, University of Pennsylvania
Dr. Stoeckert works on databases supporting the mining of complex datasets. Currently, he is co-investigator of the NIAID EuPath Bioinformatic Research Center supporting research on eukaryotic pathogens and a co-investigator of the NIA Genomics Alzheimers Disease Storage Site project supporting research of AD and related dementias. That and prior database work has gotten him involved in development of data standards. He is a core developer of the Ontology for Biomedical Investigations (OBI), leads the development of the Ontology for Biobanking (OBIB), and serves on the OBO Foundry Operations Committee and Editorial Working Groups. He is faculty director of the TURBO (Transforming & Unifying Research with Biomedical Ontologies) project at Penn aimed at semantic harmonization and integration of clinical data.
8am – Registration & Breakfast
8:20am – Remarks from Dr. Bob Dysko
8:30am – Key Note Address 2: Ontology Support of Clinical, Epidemiological, and Microbiome Data Exploration // Dr. Chris Stoeckert
9:30am – Break
Session III: Infectious Disease Ontology (IDO) and Related Ontologies // Lindsay Cowell/Barry Smith
9:45am – The Present State of the Infectious Disease Ontology // Lindsay Cowell/Barry Smith
10am – Infectious Disease Ontology Round Table // Lindsay Cowell, Barry Smith, Oliver He, Chris Stoeckert, Richard Scheuermann
11:45am – The Antibody Ontology // Alex Deihl
12:15pm – Networking Lunch
Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium // Bill Hogan
1pm – Clinical Microbiology Data // Gigi Lipori
2pm – Working Session: Building the Microbiome Ontology // Barry Smith
1:30pm – Tissue Collection and Data management in the Microbiome Clinical Studies // Dominick Lemas
3pm – Break
5pm – Close
Travel & Lodging Info
We have secured $2000 as a travel fund, owing to Dr. Bob Dysko (the director of the Unit for Laboratory Animal Medicine in the University of Michigan Medical School), to support four slots of junior scholars to attend the workshop.
If you are interested, please submit a short vita with a rationale for attendance to Dr. Oliver He at yongqunh@med.umich.edu.
20 hotel rooms have been reserved in Bell Tower, 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: http://www.belltowerhotel.com/.
You can reserve a room in the Bell Tower Hotel for arriving Tuesday, October 24th 2017 and departing Friday, October 27th (or Thursday, Oct 26th) 2017. For attendees to book a room, the rate is $179 per night and taxable. Note that the group block of rooms are under “Ontology Workshop”. Any remaining rooms by September 24th 2017 that have not be reserved, will be released back to the hotel.
Note: the Bell Tower Hotel is only two blocks away from the Michigan League where our workshop will be held.
20 hotel rooms have been reserved in Holiday Inn Near the University of Michigan, 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: http://www.hiannarbor.com. You can reserve a room in Holiday Inn for the nights of Oct 24-26. Our group rate for a single-bed or double-bed room will be $110 (+tax) per night. Reservations at our group rate will be accepted until October 10, 2017. Any additional reservations received after this date will be subjected to available space and prevailing rates. Note: Holiday Inn is about 15 minutes driving from the Michigan League.
Workshop Participants Will Include
Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)
Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)
Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)
Cowell, Lindsay (UT Southwestern, Dallas, Texas)
Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)
Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)
He, Yongqun (Oliver) (University of Michigan Medical School, Ann Arbor, MI)
Hicks, Amanda (Health Outcomes and Policy, University of Florida, Gainesville, FL)
Hogan, William (Bill) (Health Outcomes and Policy, University of Florida, Gainesville, FL)
Hu, Jim (Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX)
Huang, Yvonne J. (Division of Pulmonary & Critical Care Medicine, University of Michigan Health System, Ann Arbor, MI)
Hur, Junguk (Dept. of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota)
Lin, Asiyah Yu (FDA, Silver Spring, MD)
Lipori, Gigi (UF Health, Gainesville, FL)
Masci, Anna Maria (Duke University, Durham, NC)
Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)
Scheuermann, Richard (J. Craig Venter Institute, La Jolla, CA)
Seekatz, Anna (Division of Infectious Diseases, University of Michigan Medical School)
Siegele, Deborah A (Dept. of Biology, Texas A&M University, College Station, TX)
Smith, Barry (National Center for Ontological Research, University at Buffalo, Buffalo, NY)
Smith, Sam (DataSmith LLC.)
Soergel, Dagobert (University at Buffalo)
Stoeckert, Chris (University of Pennsylvania Perelman School of Medicine, Philadelphia, PA)
Walls, Ramona L. (CyVerse, Tucson, Arizona)
Wu, Jianfeng (School of Public Health, University of Michigan, Ann Arbor, MI)
Zheng, Jie (University of Pennsylvania Perelman School of Medicine, Philadelphia, PA)