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 25-26, 2017 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.

We are happy to announce two keynote speakers:

• Dr. Richard Scheuermann (J. Craig Venter Institute)

• Dr. Chris Stoeckert (UPenn)

This workshop will include four sessions.

• Session I. Microbiomes and Host-Microbiome Interactions organized by Oliver He

• Session II: Education session organized by Amanda Hicks

In this session we plan to discuss the following questions: 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? This is not a didactic session.

• Session III. Infectious Disease Ontology (IDO) and related ontologies and topics organized by Lindsay Cowell

• Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium organized by Bill Hogan

Organizers

Workshop Co-organizers:

Yongqun “Oliver” He (University of Michigan Medical School, Ann Arbor, MI), yongqunh@med.umich.edu

Amanda Hicks (University of Florida College of Medicine, Gainesville, FL), aehicks@ufl.edu

CTSOG Co-chairs:

Bill Hogan (University of Florida College of Medicine, Gainesville, FL), hoganwr@ufl.edu

Barry Smith (University at Buffalo, Buffalo, NY), phismith@buffalo.edu

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

Schedule Day 1: October 25

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks Oliver He, Barry Smith

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

Note: If you are interested in presenting at this session, please contact Oliver He (yongqunh@med.umich.edu).

9:00am: 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

9:20am: MEOWL: Microbial Environments described using OWL - Ramona L. Walls

9:40am: OMP: title provided later - Deborah A. Siegele / Jim Hu

10:30am: Break

11:00am-12 noon: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)

11:00-11:15 am: Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions - Oliver He

11:15-11:25 am: OHMI use case at UPenn: title provided later - Jie Zheng / Daniel Beiting

11:25-11:35 am: OHMI use case at MUSC: title provided later - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: OHMI use case at Duke: title provided later - Anna Maria Masci

11:45 am -12:00 noon: Microbiome ontology suite discussion - Barry Smith

12:00: Lunch

Wednesday Afternoon

Session II: Education session

Session coordinator: 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: Title TBD

2:00pm: If you are interested in presenting in this session, contact Amanda Hicks (aehicks@ufl.edu).

3:00pm: Break

3:30pm: If you are interested in presenting in this session, contact Amanda Hicks (aehicks@ufl.edu).

4:15pm: Keynote address 1: Title TBD Dr. Richard Scheuermann (J. Craig Venter Institute)

Richard Scheuermann is the Director of Informatics at the J. Craig Venter Institute. Since 2001, Dr. Scheuermann has applied his deep knowledge in molecular immunology and infectious disease toward the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, novel methods for the analysis of gene expression, protein network and flow cytometry data, and novel comparative genomics methods. These knowledge representation approaches and computational methods have been made available to the research community 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; www.immport.org) supported by the National Institutes of Health. At JCVI he is also expanding his bioinformatics research program into the area of human genomics.

6:30pm: Dinner (Note: A nice Ann Arbor restaurant will be reserved for those who wish to join. The cost of dinner is not included in the workshop.)

Schedule Day 2: October 26

Thursday Morning

8:00am: Registration and Breakfast

8:30am: Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration Dr. Chris Stoeckert (UPenn)

Chris Stoeckert

           Abstract: The challenge of working with Big Data is not only scale but in many situations, also the complexity of what the data is about. This is especially true of clinical and epidemiological data where data is obtained for critical variables but often in an ad hoc and inconsistent manner. Critical understanding of how these variables impact health and host microbiome interactions requires analyses across different studies and data sources. Ontologies are key to meeting this challenge through providing semantic harmonization of common and specialized types of data; the realist process approach followed by ontologies in Open Biomedical Ontologies (OBO) Foundry (http://obofoundry.org/) provides a common understanding of what the data is about. We are using application ontologies based on OBO Foundry ontologies to encode our understanding of data dictionaries in multiple projects. The projects range from the epidemiology and transmission patterns of malaria to enteric pathogen influence on morbidity and mortality in young children. An additional challenge is to transform ontologic representations into user-friendly web interface terminologies for data exploration. MicrobiomeDB (http://microbiomedb.org/mbio/) provides a web-based data-mining platform for interrogating microbiome experiments and makes use of our ontology and web interface terminology approach. The real power of ontologies will come from instantiation of data in these ontologies and the ability to do inferencing and searches of such data. A goal of the TURBO (Transforming and Unifying Research with Biomedical Ontologies) project at Penn is to instantiate an OBO Foundry-based application ontology with clinical data to support research starting with finding patient cohorts and biobank specimens.

           Chris Stoeckert is a Research Professor of Genetics and faculty in the Institute of Biomedical Informatics at the University of Pennsylvania. He 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 such as MIAME (Minimal Information About a Microarray Experiment), MAGE-TAB format standard for reporting microarray experiments, and the development of biomedical ontologies such as the MGED Ontology. 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.

10:00am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

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

11:00am: Immunology Ontology: A Survey - Barry Smith

12:00pm: Lunch

Thursday - Afternoon

Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium

Session coordinator: Bill Hogan

1:00pm: If you are interested in presenting during this session contact Bill Hogan (hoganwr@ufl.edu).

Gigi Lipori, title TBD

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 hope to have travel funds available for junior scholars. Check back for more information.

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

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)

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)