Microbiology for the CTSA: Ontological Approaches

Sixth Annual Workshop of the Clinical and Translational Science Ontology Group

Announcement

The Clinical and Translational Science Ontology Group (CTSOG) invites you to join us this October in Ann Arbor, Michigan to discuss the state of the art in ontologies and terminologies towards standardized data and metadata and data integration in various areas of clinical and translational microbiology. Example areas of discussion include microbiomes, host-microbiome interactions, microbial pathogens (e.g., bacteria, viruses, and parasites), infectious diseases, host immunity, vaccines and drugs treating infectious diseases, and vaccine and drug adverse events and safety. We will focus on how ontologies can be developed and used to support clinical and translational microbiology data recording, standardization, and analysis.

Our workshop will include an education session that will be used to discuss: What are critical needs in microbiology that ontology can help to address? What do microbiologists need to know to use and develop ontologies? What experience do microbiologists need to acquire to use and develop ontologies? What do ontologists need to know to develop ontologies with and for microbiologists? How to generate use cases to demonstrate the usage of ontology in microbiology?

Organizers

Workshop Co-organizers: Yongqun “Oliver” He (University of Michigan Medical School, Ann Arbor, MI), Amanda Hicks (University of Florida College of Medicine, Gainesville, FL)

CTSOG Co-chairs: Bill Hogan (University of Florida College of Medicine, Gainesville, FL), Barry Smith (University at Buffalo, Buffalo, NY)

Sponsor

The Michigan Institute for Clinical & Health Research (MICHR), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards (CTSA). We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.

Date

October 25 (Wednesday) - 26 (Thursday), 2017

Venue

Insert hotel / venue information here Ann Arbor, MI, USA.

Schedule Day 1: October 25

Wednesday Morning

8:00am Registration and Breakfast

8:45am XXXX Welcoming remarks

Session: Microbiomes and Host-Microbiome Interactions

Session coordinators: Oliver He,

9:00am

10:30am Break

11:00am Oliver: Development and application of the Ontology of Host-Microbiome Interactions (OHMI)

12:00: Lunch

Wednesday Afternoon

Session: Education session

Session coordinators: Amanda Hicks

In this session, we will discuss: What are critical needs in microbiology that ontology can help to address? What do microbiologists need to know to use and develop ontologies? What experience do microbiologists need to acquire to use and develop ontologies? What do ontologists need to know to develop ontologies with and for microbiologists? How to generate use cases to demonstrate the usage of ontology in microbiology?

1:00pm Gigi Lipori, TBD

3:00pm Break

3:30pm

4:15pm Keynote address 1, by Dr. Richard Scheuermann, Director of Informatics at J. Craig Venter Institute.

6:30pm Dinner (Note: A nice Ann Arbor restaurant will be reserved)

Schedule Day 2: October 26

Thursday Morning

Session: Infectious Disease Ontology (IDO) and related ontologies and topics

Session coordinators: Lindsay Cowell, Barry Smith

8:00am Registration and Breakfast

8:30am Keynote address 2, by Dr. Chris Stoeckert. Professor of Genetics at the University of Pennsylvania School of Medicine)

10:00am Break

10:30am Lindsay: The Present State of the Infectious Disease Ontology

11:00am Barry: Immunology Ontology: A Survey

12:00 Lunch

Thursday - Afternoon

Session: Sharing Clinical Microbiology Data Across the CTSA Consortium

Session coordinators: Bill Hogan,

1:00pm

2:00pm Wrap-up session

4:00pm Close

Rationale

The 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. But the creation and adoption of such standards often takes decades. Translational science requires a consistent set of standard ontologies spanning all scales, from molecule to organism to population. In this year's meeting we focus on resources for describing data at the scale of micro-organisms XXX

This workshop will convene stakeholders interested in identifying ways to XXX

Goals

The Clinical and Translational Science Ontology Group was established in 2012 to leverage the use of common ontologies to support different aspects of information-driven clinical and translational research. The focus of this meeting is to explore new and existing uses of common ontologies to support creation, sharing, and analysis of clinical data.

Like its predecessors in the series, 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.

Persons interested in attending or in presenting at the meeting should write to [mailto:].

Travel Fund Application

We will have funding to support 4 attendees with $500 each. Please submit your letter of intend to ... by date.

Hotel Room Reservation

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 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.

Participants will include

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)

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)

Soergel, Dagobert (University at Buffalo)

Stoeckert, Chris (University of Pennsylvania Perelman School of Medicine, Philadelphia, PA)

Wu, Jianfeng (School of Public Health, University of Michigan, Ann Arbor, MI)

Zheng, Jie (University of Pennsylvania Perelman School of Medicine, Philadelphia, PA)