Workshop on Ontologies for Stem Cells and Stem Cell Line Cells

Introduction:

Stem cells and stem cell lines are widely used in biomedical research. Stem cells are undifferentiated cells that can differentiate into specialized cells and can divide to produce more stem cells. To better study stem cells in vitro, thousands of stem cell lines, including embryonic and adult stem cell lines, and induced pluripotent stem cells (iPS/IPSCs), have been generated and used for different applications. With a large number of studies undergoing on stem cells and stem cell lines, many challenges have emerged, including the lack of community-based standards for representing stem cells and stem cell line cell development, formation, and characteristics.

The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively. CL can be used to represent stem cells, and CLO can be used to stem cell lines and stem cell line cells. However, the development of CLO and CLO for representing stem cells and stem cell line cells has just started, and many challenges still exist.

To support community-wide data and knowledge sharing and integration, we will organize a workshop, titled "Workshop on Ontologies for Stem Cells and Stem Cell Line Cells" (StemCellOW), to discuss the development and application of CL, CLO, and other ontologies in relation to in vivo stem cells and in vitro stem cell line cell studies.

Aims:

The workshop aims to translate stem cell biology into the ontology framework supported by CL and CLO, and related OBO Foundry ontologies. This includes defining key ontology terms, ontology hierarchy design, ontology design patterns for crucial cell processes (e.g., stem cell differentiation, division, gene expression, and reprogramming), modeling of experimental use cases, ontology applications, and discussion of continuous collaborations. This workshop is expected to become a platform for active interdisciplinary discussions among experts with different backgrounds.

Workshop Information:

The workshop information is as follows:

• Venue: North Campus Research Complex (NCRC) Building 16 Room B003E, University of Michigan, 2800 Plymouth Rd, Ann Arbor, MI 48109, USA. Check the venue in Google Map.

• Time: April 26-27 (Thursday-Friday), 2018

• Co-organizers:

  • Dr. Yongqun Oliver He, from the University of Michigan

  • Dr. Alexander D. Diehl, from the University at Buffalo

• Workshop administrator: Ms. Veronica Rieberger, from the University of Michigan

• Consultation: We also appreciate Dr. Sirarat (Sira) Sarntivijai's help in preparing the workshop.

• Sponsorship: The workshop is supported by an external data science research (eDSR) fund of the NIH Common Fund's Library of Integrated Network-based Cellular Signatures (LINCS) program.

Registration:

Please register for the workshop by filling up the following form: StemCellOW workshop registration form by April 5. Please feel free to contact us if you have any questions related to the registration.

Hotel Room Reservation:

We have reserved 10 rooms at Holiday Inn near the University of Michigan, 3600 Plymouth Road, Ann Arbor, MI 48105. Office: 734.769.9800 x 6175. Please reserve the rooms before April 11th to receive the $139.00 per day rate. This hotel has shuttle service for the guests to and from the meeting.

Hotel room book instruction: Click on the booking link "Cell Line Ontology Workshop". Scroll down to select your Check In and Check Out Dates, Group Code will automatically show up (if not, click "more options"). Click on Check Availability. From there the site will show you the room types that have been blocked, along with the group rate. Reserve your room type.

Schedule (tentative):

April 26 (Thursday, 1st day):

Morning:

• Registration and simple breakfast: 8:30-9:00 am

• 9:00 – 9:15 am: Introduction of the Workshop

• 9:15 – 10:15 am: Domain tutorial, by Daniel Cooper

  • Stem cell and cell line background introduction

  • Status, issues, and perspectives

  • Discussion

• Coffee break: 10:15 – 10:30 am

• 10:30 – 11:00 am: Alexander Diehl

  • Stem cell representation in CL

  • Stem cell related terms in GO

• 11:00 – 11:30 am: Oliver He

  • Stem cell line cell representation in CLO

  • Review of ontology for biomedical investigations for the stem cell research

• 11:30 – 12:00 am: Jens Hansen from Mount Sinai: Molecular Biology of the Cell Ontology

Lunch and discussion: 12:30 – 1:30 pm (lunch included)

Afternoon:

• 1:30 – 1:45 pm: Introduction by Alex and Oliver, and brief discussion to introduce the aims of the workshop.

• 1:45 – 2:15 pm: Daniel Cooper, LINCS, Standardization and Integration of Stem Cell Line Information in the National LINCS Research Consortium

• 2:15 – 2:45 pm: Edison Ong presents stem cell /cell line data integration with EBI and CLO, and CL.

• 2:45 – 2:50 pm: Sam Smith, The Micro-Macro Biological Ontology Project

• Coffee break: 2:45 - 3 pm

• 3:00 – 3:30 pm: Lucas Serra: Overview of cancer stem cells

• 3:30 – 4:00 William Duncan: Demonstration of technical power of ontology

• 4:00 – 5:30 pm: Discussion of needs and possibilities (coordinated by Alex):

  • Discuss the question: do we need some separate stem cell/cell line ontology that combines terms for CL, CLO, OBI, and GO? We have to consider the types of data.

  • Define related domains, e.g., which ontologies from biomedical domains to reuse or augment?

  • Define which are key top level ontology terms and their definitions.

Group dinner at own cost (restaurant to be determined): 6:00-8:30 pm

April 27 (Friday, 2nd day):

Morning:

• Chat and simple breakfast: 8:30 – 9:00 am

• 9:00 – 10:00 am: Sue O'Shea - iPSc induction and Dipolar disorder iPSc study use case

• Coffee break: 10:00 – 10:15 am

• 10:15 – 12:15 noon: coordinated by Oliver He

  • OBI introduction (by Oliver)

  • Design ontology design patterns for crucial cell processes

    • Stem cell and cell line cell differentiation and division

    • Stem cell and cell line cell reprogramming

    • Stem cell and cell line cell gene expression, interaction, pathways.

Lunch and discussion: 12:15 – 1:30 pm (lunch included)

Afternoon:

• 1:30 – 3:00 pm: Discussion of needs and possibilities (coordinated by Alex and Oliver):

  • Ontology applications

    • Use cases presented, and future plan

    • More use cases

  • Discussion of continuous collaborations.

  • Possible workshop paper to summarize our discussion results.

  • Possible collaborative grant applications.

• 3:00 pm: End of the workshop.

Travel Fund Application:

We have a small amount of travel fund. If you are interested, please submit a short vita with a rationale for attendance to Dr. Oliver He at yongqunh@med.umich.edu by March 25, 2018. Decisions will be made by March 27, 2018.

Travel fund awardees (congratulations!!):

• Cooper, Daniel (Molecular and Cellular Pharmacology, University of Miami, Miami, FL)

• Duncan, William (Roswell Park, Buffalo NY)

• Hansen, Jens (Pharmacological Sciences, Icahn School of Medicine at Mount Sinai)

• Serra, Lucas (Biomedical Informatics, University at Buffalo, Buffalo, NY)

Contact:

We welcome those interested in the topics to participate in our workshop. If you are interested, please contact:

• Oliver at yongqunh@med.umich.edu

• Alex at addiehl@buffalo.edu, or

• Veronica at vrieberg@med.umich.edu.

Participants:

The following is the list of attendees for the workshop. If you are also interested, please contact us.

• Cooper, Daniel (Molecular and Cellular Pharmacology, University of Miami, Miami, FL)

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

• Duncan, William (Roswell Park, Buffalo NY)

• Hansen, Jens (Pharmacological Sciences, Icahn School of Medicine at Mount Sinai)

• He, Yongqun (Oliver) (University of Michigan Medical School, Ann Arbor, MI)

• Lienczewski, Chrysta (Internal Medicine-Nephrology, University of Michigan Medical School, Ann Arbor, MI)

• O'Shea, Sue (Cell and Developmental Biology, University of Michigan Medical School)

• Ong, Edison (Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI)

• Serra, Lucas (Biomedical Informatics, University at Buffalo, Buffalo, NY)

• Smith, Sam (DataSmith LLC.)

• Tibi, Omar (Bioinformatics, John Hopkins Unversity, Baltimore, MD)

• Turali-Emre, Emine (Biomedical Engineering, University of Michigan)

• Walker, Kendal (Cell and Developmental Biology, University of Michigan Medical School)

  • Yang, Benjamin (Biomedical Engineering, University of Michigan)

A photo of attendees:

(Note: the top image came from: Russo E. (2005) Follow the Money—The Politics of Embryonic Stem Cell Research. PLoS Biol 3(7): e234. doi:10.1371/journal.pbio.0030234)