NCOR Wiki - User contributions [en]

Ontology for Precision Medicine: From Genomes to Public Health

2018-10-24T15:40:27Z

Aehicks: /* Participants will include */

Seventh Clinical and Translational Science Ontology Workshop

'''With a special subsection on: Ontology and the Opioid Crisis'''

== '''Announcement''' ==

'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us on February 19-20 or (most probably:) 20-21, 2019 in Orlando, Florida

''We are happy to announce as keynote speaker:''

* '''Janna Hastings (Babraham Institute, Cambridge, UK)'''

----
== '''Organizers''' ==

[https://hobi.med.ufl.edu/about/faculty-directory-2/hogan-bill/ William Hogan] (University of Florida, Gainesville, FL), hoganwr@ufl.edu

[http://ontology.buffalo.edu/smith Barry Smith] (University at Buffalo, Buffalo, NY), phismith@buffalo.edu

----
== '''Background''' ==

From genomes to public health, newer and larger datasets are increasingly available to inform precision approaches to the treatment and prevention of disease and disorders. Managing these datasets--especially their integration--for everything from managing the opioid epidemic to the learning health system to translational science--requires more and better ontologies. This workshop will briefly survey the state-of-the-art in ontology at the nexus of these trends, identify needs and opportunities for future work and collaborations, and develop one or more white papers charting the course for the future, including a set of recommendations for key stakeholders.

If you are interested in presenting cutting edge work in this area, please email a brief presentation proposal to Barry Smith (phismith@buffalo.edu) and Bill Hogan (hoganwr@ufl.edu). We are primarily interested in ontology, but also are interested to hear from experts in the CTSA network working in a diverse range of areas, from precision medicine, to the opioid epidemic, to precision public health.

For earlier meetings in the CTS Ontology Workshop series see [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group here].

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

== '''Sponsors''' ==

[http://ncor.us National Center for Ontological Research]

[https://hobi.med.ufl.edu/biomedical-informatics/ University of Florida Division of Biomedical Informatics]

[https://www.ctsi.ufl.edu/ University of Florida Clinical and Translational Science Institute]

== '''Date''' ==

February 20 (Wednesday) - 21 (Thursday), 2019

== '''Venue'''==

Orlando, Florida

Venue: TBD
A block of rooms will be available.

----

=='''Draft Schedule Day 1: February 20'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: TBD

10:00-10:30am: Break

12:15: Lunch

----

Wednesday Afternoon 

1:00pm: TBD

3:00pm: Break

3:30pm: TBD

4:15pm: '''Keynote address'''

6:30pm: Dinner

=='''Schedule Day 2: February 21'''==

Thursday Morning 

8:00am: Registration and Breakfast

8:20am: TBD

9:30-9:45am: Break

9:45am: TBD

12:15pm: Lunch

----

Thursday - Afternoon

1:00pm: TBD

4:00pm: ''Close''

=='''Rationale'''==

== '''Goals'''==

== '''Participants will include''' ==

Matthias Brochhausen (Little Rock, Arkansas)

Lindsay Cowell (Dallas, TX)

Janna Hastings (Cambridge, UK)

Oliver He (Ann Arbor, MI)

Amanda Hicks (Gainesville, FL)

William Hogan (Gainesville, FL)

Jihad Obeid (Charleston, SC)

Barry Smith (Buffalo, NY)

Chris Stoeckert (U Penn, PA)

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:52:00Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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 [http://ncorwiki.buffalo.edu/index.php/File:MicroOntology_CTSO.Oct2017.pptx Slides]

9:40am: ''MEOWL: Microbial Environments described using OWL'' - Ramona L. Walls [http://ncorwiki.buffalo.edu/index.php/File:Walls_CTSOG_meowl.pdf Slides]

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton [http://ncorwiki.buffalo.edu/index.php/File:Overton-FAIR-20171025.pdf Slides]

2:00pm: ''Using cyberinfrastructure to make life sciences data FAIR: lessons learned'' - Ramona Walls [http://ncorwiki.buffalo.edu/index.php/File:Walls-CyVerse_FAIR_CTSOG.pdf Slides]

2:30pm: ''Measuring Interannotator Agreement in the Florida Annotated Corpus for Translational Science - The difficult ontological task'' - Amanda Hicks [http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

8:30am: '''Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration ''' - Dr. Chris Stoeckert (UPenn) [http://ncorwiki.buffalo.edu/index.php/File:StoeckertOntologyClinicalEpidemiologyMIcrobiome.pptx Slides]

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert [http://ncorwiki.buffalo.edu/index.php/File:EuPath_ontology_for_IDO_session_2017.pptx Slides] , Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori [http://ncorwiki.buffalo.edu/index.php/File:Micro-Ontology-Presentation.pptx Slides]

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

File:Walls-CyVerse FAIR CTSOG.pdf

2017-10-30T16:51:10Z

Aehicks: Using cyberinfrastructure to make life sciences data FAIR: lessons learned

Using cyberinfrastructure to make life sciences data FAIR: lessons learned

File:Overton-FAIR-20171025.pdf

2017-10-30T16:49:38Z

Aehicks: FAIR principles and the Immune Epitope Database (IEDB)

FAIR principles and the Immune Epitope Database (IEDB)

File:Walls CTSOG meowl.pdf

2017-10-30T16:45:39Z

Aehicks: MEOWL: Microbial Environments described using OWL

MEOWL: Microbial Environments described using OWL

File:MicroOntology CTSO.Oct2017.pptx

2017-10-30T16:44:21Z

Aehicks: The MicrO ontology; enabling the acquisition of higher-order knowledge of phenotypes from prokaryotic taxonomic descriptions and the construction of very large character matrices

The MicrO ontology; enabling the acquisition of higher-order knowledge of phenotypes from prokaryotic taxonomic descriptions and the construction of very large character matrices

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:43:07Z

Aehicks: /* Schedule Day 2: October 26 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton

2:00pm: ''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 [http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

8:30am: '''Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration ''' - Dr. Chris Stoeckert (UPenn) [http://ncorwiki.buffalo.edu/index.php/File:StoeckertOntologyClinicalEpidemiologyMIcrobiome.pptx Slides]

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert [http://ncorwiki.buffalo.edu/index.php/File:EuPath_ontology_for_IDO_session_2017.pptx Slides] , Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori [http://ncorwiki.buffalo.edu/index.php/File:Micro-Ontology-Presentation.pptx Slides]

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

File:Micro-Ontology-Presentation.pptx

2017-10-30T16:41:10Z

Aehicks: Microbiology Data in the Real World�Thoughts and Examples from One Site

Microbiology Data in the Real World�Thoughts and Examples from One Site

File:StoeckertOntologyClinicalEpidemiologyMIcrobiome.pptx

2017-10-30T16:39:04Z

Aehicks: Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration

Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration

File:EuPath ontology for IDO session 2017.pptx

2017-10-30T16:37:02Z

Aehicks: The Infectious Disease Ontology Round Table - Stoeckert

The Infectious Disease Ontology Round Table - Stoeckert

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:26:56Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton

2:00pm: ''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 [http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

File:MUSC µBiome.pptx

2017-10-30T16:25:58Z

Aehicks: Ontology of Host-Microbiome Interactions use case at MUSC

Ontology of Host-Microbiome Interactions use case at MUSC

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:24:26Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton

2:00pm: ''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 [http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:14:27Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan,

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton

2:00pm: ''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[[:FACTS-CTSOG_2017]]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

Microbiology for the CTSA: Ontological Approaches

2017-10-30T16:08:38Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

----
== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

'''ULAM organizers:'''

Veronica Rieberger, Administrative Specialist, vrieberg@med.umich.edu

Teresa Fracala, Executive Assistant to Department Chair, ULAM, University of Michigan Medical School, fracalat@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholars attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

----

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: Welcoming remarks, by Oliver He [http://ncorwiki.buffalo.edu/images/7/73/He-openning.pdf Slides], Barry Smith, Kanchan Lota (MICHR managing director) [http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyCTSA_MICHR_Kanchan.pdf Slides]

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu [http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]

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

10:00-10:30am: Break

10:30-11:45 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI).

This section includes the following talks:'''

10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He [http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]

11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko

11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci

11:45-12:15: Discussion on the morning session topics

12:15: Lunch

----

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

Session coordinator: Amanda Hicks

1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan,

1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton

2:00pm: ''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[http://ncorwiki.buffalo.edu/images/6/6c/MicrobiologyFACTS-CTSOG-2017.pttx Slides]

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith

10:30am: Break

10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides], Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori

1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

Eventually five travel awards were given to：(i) Amanda Hicks, U. of Florida, our workshop co-chair. (ii) Anna Maria Masci, Duke University; (iii) Jie Zheng, UPenn; (iv) William Duncan, University at Buffalo; and (v) Asiyah Yu Lin, FDA. Congratulations!

== '''Participants''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Dipert, Randall (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

== '''Pictures taken from the event''' ==

[[File:IMG 6209-meetingRoom1.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6209-meetingRoom1.JPG|Attendees in the meeting room, Day 1]]

[[File:IMG_6287-together.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6287-together.JPG|Attendees together, Day 2. Note: some attendees not in]]

[[File:IMG_6219-Richard.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6219-Richard.JPG|Richard Scheuermann keynote presentation, Day 1]]

[[File:IMG 6260-Chris.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG 6260-Chris.JPG|Chris Stoeckert keynote presentation, Day 2]]

[[File:IMG_6274-Lindsay.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6274-Lindsay.JPG|Linsday Cowell presentation, Day 2]]

[[File:IMG_6301-Barry.JPG|thumb|150px|left|http://ncorwiki.buffalo.edu/index.php/File:IMG_6301-Barry.JPG|Barry Smith talking, Day 2]]

[[File:IMG_6279-ULAM3.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6279-ULAM3.JPG|UM-ULAM organizers: Veronica Rieberger, Oliver He, Teresa FracalaDinner, Day 2]]

[[File:IMG_6257-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6257-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6253-dinner.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6253-dinner.JPG|Dinner at Day 1]]

[[File:IMG_6284-lunch.JPG|thumb|150px|left|link=http://ncorwiki.buffalo.edu/index.php/File:IMG_6284-lunch.JPG|Lunch time, Day 2]]

File:FACTS-CTSOG 2017.pptx

2017-10-30T16:07:02Z

Aehicks:

Microbiology for the CTSA: Ontological Approaches

2017-10-12T21:15:49Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Ontological Representation of Software to Make it FAIR

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Measuring Interannotator Agreement in the Florida Annotated Corpus for Translational Science - The difficult ontological task

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Clinical Microbiology Data - Gigi Lipori

1:30pm: "Tissue Collection and Data Management in the Microbiome Clinical Studies" - Dominick Lemas

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T21:04:51Z

Aehicks: /* Schedule Day 2: October 26 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

Session I: Microbiomes and Host-Microbiome Interactions

Session coordinator: Oliver He

9:00am: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Clinical Microbiology Data - Gigi Lipori

1:30pm: "Tissue Collection and Data Management in the Microbiome Clinical Studies" - Dominick Lemas

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T17:13:45Z

Aehicks: /* Participants will include */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

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: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Ong, Edison (University of Michigan, Ann Arbor, MI)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T17:04:00Z

Aehicks: /* Participants will include */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

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: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

Duncan, Bill (Roswell Park, Buffalo NY)

Freddolino, Peter (Department of Biological Chemistry, University of Michigan Medical School)

Frederickson, Lynne (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Gross, Colin (University of Michigan, Ann Arbor, MI)

Guo, Kai (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)

Landis-Lewis, Zach (University of Michigan Medical School, Ann Arbor, MI)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

Lin, Asiyah Yu (FDA, Silver Spring, MD)

Lipori, Gigi (UF Health, Gainesville, FL)

Manion, Frank (University of Michigan, Ann Arbor, MI)

Masci, Anna Maria (Duke University, Durham, NC)

Obeid, Jihad (The Medical University of South Carolina, Charleston, SC)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

Wang, Haihe (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T16:53:09Z

Aehicks: /* Participants will include */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

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: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T16:44:52Z

Aehicks: /* Participants will include */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

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: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00-4pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

3:00-3:15 pm: break

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Diehl, Alexander D. (University at Buffalo, Buffalo, NY)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T16:30:15Z

Aehicks: /* Schedule Day 1: October 25 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''Schedule Day 1: October 25'''==

Wednesday Morning

8:00am: Registration and Breakfast

8:45am: ''Welcoming remarks'' Oliver He, Barry Smith, MICHR leadership (Michgan CTSA)

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: 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

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

2:30pm: Amanda Hicks, Title TBD

3:00pm: Break

3:30pm: Discussion

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T16:09:59Z

Aehicks: /* Schedule Day 2: October 26 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - Deborah A. Siegele / Jim Hu

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko (U Mich)

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-10-12T16:08:57Z

Aehicks: /* Schedule Day 2: October 26 */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - Deborah A. Siegele / Jim Hu

10:30-10:45am: Break

10:45-11:50 am: Development and applications of the Ontology of Host-Microbiome Interactions (OHMI)'''

10:45-11:05 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He

11:05-11:20 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:20-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:50 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

11:50-12:15: Discussion on the morning session topics

12:15: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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

8:20am: Remarks from Dr. Bob Dysko

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

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''Participants will include''' ==

Alekseyenko, Alexander (The Medical University of South Carolina, Charleston, SC)

Blank, Carrine E. (Department of Geosciences, University of Montana, Missoula, MT)

Brochhausen, Mathias (University of Arkansas for Medical Sciences, Little Rock, AR)

Cascalho, Marilia I. (Department of Surgery, University of Michigan Medical School)

Cowell, Lindsay (UT Southwestern, Dallas, Texas)

Diehl, Alexander (University at Buffalo, Buffalo, NY)

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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-08-25T16:45:54Z

Aehicks: /* Participants will include */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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

11:15-11:30 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:30-11:45 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:45-12:00 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Lemas, Dominick (Dept. of Health Outcomes and Policy, University of Florida)

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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-08-25T16:44:55Z

Aehicks: /* Travel Fund Application */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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

11:15-11:30 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:30-11:45 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:45-12:00 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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 new investigators 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 by August 30, 2017. Decisions will be made August 31, 2017.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-08-25T16:43:48Z

Aehicks: /* Announcement */

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: CTSO Breaking Topics: Informatics Metrics''' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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

11:15-11:30 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:30-11:45 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:45-12:00 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-08-25T14:42:06Z

Aehicks: /* Schedule Day 2: October 26 */

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: CTSO Breaking Topics: Informatics Metrics'' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

[https://www.michr.umich.edu/ MICHR] has also generated an announcement website for our workshop:
[https://microbiologyctsa17.splashthat.com/ https://microbiologyctsa17.splashthat.com/]

== '''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

'''MICHR organizer:'''

Jamie Racklyeft, Communication Director, MICHR, jracklye@med.umich.edu

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute and [https://ncats.nih.gov/ctsa CTSA] hub supported by the National Center for Advancing Translational Sciences at the National Institutes of Health.

We are grateful also to the MICHR and [https://medicine.umich.edu/medschool/leadership/george-mashour-md-phd Dr. George Mashour] (MICHR director) for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:MICHR-signature-acronym.png|thumb|350px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the previous ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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

11:15-11:30 am: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:30-11:45 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:45-12:00 noon: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

1:30pm James Overton, FAIR principles and the Immune Epitope Database (IEDB)

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''Infectious Disease Ontology Round Table'' - Barry Smith, Chris Stoeckert, Richard Scheuermann

11:45am: ''The Antibody Ontology'' - Alex Diehl

12:15pm: Lunch

Thursday - Afternoon

 Session IV: Sharing Clinical Microbiology Data Across the CTSA Consortium 

Session coordinator: Bill Hogan

1:00pm: Gigi Lipori, title TBD

1:30pm: Dominick Lemas, title TBD, topic - tissue collection and data management in the microbiome clinical studies

2:00pm: ''Working session: Building the Microbiome Ontology'' - Introduced by Barry Smith

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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Overton, James (Toronto, Ontario, Canada)

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)

Wang, Jiahao (University of Michigan, Ann Arbor, MI)

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

Zhang, Wei (Section of General Surgery, University of Michigan Medical School, Ann Arbor, MI)

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

Microbiology for the CTSA: Ontological Approaches

2017-08-21T18:43:30Z

Aehicks: /* Announcement */

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: CTSO Breaking Topics: Informatics Metrics'' organized by Amanda Hicks and Bill Hogan

*''' 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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-08-21T18:42:32Z

Aehicks: /* Schedule Day 1: October 25 */

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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

2:00pm: Ramona Walls, Using cyberinfrastructure to make life sciences data FAIR: lessons learned.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-08-17T18:38:23Z

Aehicks: /* Schedule Day 1: October 25 */

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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Bill Hogan and Amanda Hicks, Title TBD

2:00pm: Ramona Walls, Title TRD.

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-06-28T18:55:49Z

Aehicks: /* Schedule Day 1: October 25 */

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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Title TBD

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

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-06-28T18:55:09Z

Aehicks: /* Schedule Day 2: October 26 */

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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Title TBD

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

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

9:30-9:45am: Break

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

Session coordinators: Lindsay Cowell, Barry Smith

9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell

10:45am: ''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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-06-28T18:53:23Z

Aehicks: /* Schedule Day 1: October 25 */

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
Clinical laboratory data are a routine feature in research data repositories and their associated query mechanisms such as i2b2. However, the inclusion of microbiology data from the clinical laboratory are much less frequently present. Issues include which ontologies to use to identify micro-organisms, sensitivity tests, sensitivity test results, and the microbiology tests performed. Also, linking "bugs to drugs" (identified micro-organisms to their sensitivity tests/results) is often quite complicated to do accurately and reliably. This session will explore these and other issues, with an eye towards optimal modeling of clinical microbiology data for translational research.

== '''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

== '''Sponsors''' ==

* '''The Michigan Institute for Clinical & Health Research''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

* '''The Unit for Laboratory Animal Medicine''' ([http://animalcare.umich.edu/unit-laboratory-animal-medicine ULAM]) at the University of Michigan Medical School, We are also grateful to [http://animalcare.umich.edu/department/staff/robert-c-dysko-dvm-daclam Dr. Bob Dysko], the ULAM director in the University of Michigan Medical School, for his generous support of $4000 for catering and junior scholar attending the workshop (See more information below).

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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: The Ontology of Microbial Phenotypes (title TBA) - 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: Ontology of Host-Microbiome Interactions use case at UPenn - Jie Zheng / Daniel Beiting

11:25-11:35 am: Ontology of Host-Microbiome Interactions use case at MUSC - Jihad Obeid / Alexander Alekseyenko

11:35-11:45 am: Ontology of Host-Microbiome Interactions use case at Duke - Anna Maria Masci

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

12:00: Lunch

Wednesday Afternoon 

Session II: CTSO Breaking Topics: Informatics Metrics 

1:00pm: Title TBD

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

3:00pm: Break

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

4:15pm: '''Keynote address 2: Identification and representation of cellular biomarkers using high-content single cell cytometry and sequencing technologies ''' Dr. Richard Scheuermann (J. Craig Venter Institute)

[[File:Scheuermann R.jpg|thumb|150px|left|link=https://pbs.twimg.com/profile_images/1406857375/Scheuermann_R_400x400.jpg|Richard Scheuermann]] '''Abstract''': A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting for the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this presentation, we will present examples of state-of-the-art cellular biomarker characterization using high-content mass cytometry and single cell RNA sequencing, and discuss strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.

           ''Richard Scheuermann'', Ph.D., is the Director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an 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; https://www.fludb.org), the Virus Pathogen Resource (ViPR; https://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.

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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 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.

== '''Hotel Room Reservation'''==

20 hotel rooms have been reserved in [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-05-31T17:00:54Z

Aehicks: /* Rationale */

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''' ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]).

We are grateful also to the MICHR for sponsoring $3,000 for supporting two keynote speakers' attendance at the meeting.
[[File:Michr.jpg|thumb|300px|center|link=https://www.michr.umich.edu/|MICHR]]

== '''Date''' ==
October 25 (Wednesday) - 26 (Thursday), 2017

== '''Venue'''==

[http://conferences.umich.edu/venues/henderson/ Henderson Room at the Michigan League], University of Michigan, Ann Arbor, MI.

Address: 3rd floor, Michigan League, 911 N. University, Ann Arbor, MI 48109-1265 [https://www.google.com/maps/place/Michigan+League/@42.2790343,-83.7398302,17z/data=!3m1!4b1!4m5!3m4!1s0x883cae41112bb9cf:0x2163c675f6ac28e9!8m2!3d42.2790304!4d-83.7376361 Google map]
[[File:16-Michigan-League.jpg|thumb|300px|center|link=https://uunions.umich.edu/league|Michigan League]]

=='''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)

[[File:Stoeckert-photo.jpg|thumb|150px|left|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403|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.

== '''Goals'''==
The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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 [https://www.google.com/maps/place/Bell+Tower+Hotel/@42.33472,-84.215748,10z/data=!4m5!3m4!1s0x0:0x597a9dcf3d549001!8m2!3d42.2792424!4d-83.739903?hl=en-US Bell Tower], 300 S Thayer St, Ann Arbor, MI 48104. Tel: 800.562.3559 or 734.769.3010. Website: [http://www.belltowerhotel.com/ 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 [https://www.google.com/maps/place/Holiday+Inn+Near+the+University+of+Michigan/@42.3041809,-83.6919257,17z/data=!3m1!4b1!4m5!3m4!1s0x883cac1b75a197f1:0xbc6750e4373aaf8d!8m2!3d42.304177!4d-83.689737 Holiday Inn Near the University of Michigan], 3600 Plymouth Road, Ann Arbor, MI 48105. Tel: 734.769.9800. Website: [http://www.hiannarbor.com 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.

== '''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)

Microbiology for the CTSA: Ontological Approaches

2017-04-27T16:17:58Z

Aehicks: /* Announcement */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T16:14:33Z

Aehicks: /* Travel Fund Application */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T16:14:02Z

Aehicks: /* Travel Fund Application */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T16:13:33Z

Aehicks: /* Schedule Day 1: October 25 */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T16:10:53Z

Aehicks: /* Schedule Day 2: October 26 */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:58:44Z

Aehicks: /* Schedule Day 2: October 26 */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:57:14Z

Aehicks: /* Schedule Day 1: October 25 */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:56:38Z

Aehicks: /* Schedule Day 1: October 25 */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:46:43Z

Aehicks: /* Venue */ Deleted uninformative content

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:43:30Z

Aehicks: /* Announcement */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:43:04Z

Aehicks: /* Sponsor */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:42:29Z

Aehicks: /* Organizers */

Microbiology for the CTSA: Ontological Approaches

2017-04-27T15:40:34Z

Aehicks: /* Announcement */ Updated in light of new information.

Microbiology for the CTSA: Ontological Approaches

2017-04-14T20:08:25Z

Aehicks: Deleted "See here (need a link) for details."

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 (Ann Arbor, MI), Amanda Hicks (Gainesville, FL)

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

== '''Sponsor''' ==
The Michigan Institute for Clinical & Health Research ([https://www.michr.umich.edu/ MICHR]), a University of Michigan institute funded by the NIH Clinical and Translational Science Awards ([https://ncats.nih.gov/ctsa CTSA]). We are grateful also to the MICHR for sponsoring $3000 for supporting two keynote speakers' attendance at the meeting.

== '''Date''' ==
October 25-26, 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'''

9:00am

10:30am Break

11:00am

12:00: Lunch

Wednesday - Afternoon

1:00pm

3:00pm Break

3:30pm

4:15pm Keynote address 1

6:30pm Dinner

=='''Schedule Day 2: October 26'''==

Thursday - Morning

8:00am Registration and Breakfast

8:30am Keynote address 2

10:00am Break

10:30am

12:00 Lunch

Thursday - Afternoon

 Session: Sharing Clinical Microbiology Data Across the CTSA Consortium 

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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group 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 [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops 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:].

== '''Participants will include''' ==

Amanda Hicks (Health Outcomes and Policy, University of Florida, Gainesville, FL)

Yongqun (Oliver) He (University of Michigan Medical School, Ann Arbor, MI)

William Hogan (Health Outcomes and Policy, University of Florida, Gainesville, FL)

Richard Scheuermann (J. Craig Venter Institute, La Jolla, CA)

Dagobert Soergel (University at Buffalo)

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

Barry Smith (National Center for Ontological Research, University at Buffalo, Buffalo, NY)

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

Yvonne J. Huang (Division of Pulmonary & Critical Care Medicine, University of Michigan Health System, Ann Arbor, MI)

Anna Seekatz (Division of Infectious Diseases, University of Michigan Medical School)

Marilia I. Cascalho (Department of Surgery, University of Michigan Medical School)

Peter Freddolino (Department of Biological Chemistry, University of Michigan Medical School)

Carrine E. Blank (Department of Geosciences, University of Montana, Missoula, MT)

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

Lynne Frederickson (Taubman Health Sciences Library, University of Michigan, Ann Arbor, MI)

Asiyah Lin (FDA, Silver Spring, MD)

Lindsay Cowell (UT Southwestern, Dallas, Texas)

NCOR Wiki - User contributions [en]

Ontology for Precision Medicine: From Genomes to Public Health​

Microbiology for the CTSA: Ontological Approaches

File:Walls-CyVerse FAIR CTSOG.pdf

File:Overton-FAIR-20171025.pdf

File:Walls CTSOG meowl.pdf

File:MicroOntology CTSO.Oct2017.pptx

Microbiology for the CTSA: Ontological Approaches

File:Micro-Ontology-Presentation.pptx

File:StoeckertOntologyClinicalEpidemiologyMIcrobiome.pptx

File:EuPath ontology for IDO session 2017.pptx

Microbiology for the CTSA: Ontological Approaches

File:MUSC µBiome.pptx

Microbiology for the CTSA: Ontological Approaches

Microbiology for the CTSA: Ontological Approaches

Microbiology for the CTSA: Ontological Approaches

File:FACTS-CTSOG 2017.pptx

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Ontology for Precision Medicine: From Genomes to Public Health