The Role of Ontology in Big Cancer Data

Date: May 12-13, 2015

Venue

• Day 1 (10am-5pm) will be in NCI's Shady Grove building (9609 Medical Center Dr, Rockville, MD, 20850), in Room 2W-32/34.

• Day 2 *9am-3pm) will be a public session in Balcony A, Natcher Conference Center, NIH Building 45, Bethesda, MD 20892

Goal of the meeting (to be expanded): To better understand the challenges involved in using big data for cancer research, and to explore the utility of ontologies in addressing these challenges.

Draft Schedule

Session 1: Addressing cancer big data challenges through imaging ontologies

Tuesday, May 12 in NCI Shady Grove building (9609 Medical Center Dr, Rockville, MD, 20850), Room 2W-32/34

10:00-13:00

Barry Smith (Buffalo): The cancer research ontology space: An introduction

will provide an introduction to the meeting with a survey of existing ontology resources, including NCI Thesaurus and OBO Foundry, and addressing opportunities and reasons for scepticism as concerns the use of ontologies in addressing cancer big data

Ilya Goldberg (NIA): The Role of Imaging Ontologies in Cancer Big Data

Metin Gurcan (Ohio) and John Tomaszewski (Buffalo): How Ontologies Can Help in Addressing the Big Data Challenges of Pathology Imaging?

TBD

13:00 Lunch

Session 2: Addressing Cancer Big Data Challenges with the Ontology for Biomedical Investigations (OBI)

14:00-17:00

Chris Stoeckert (Penn): Integration and alignment of ontologies for cancer metadata collection based on OBI

addresses the challenge that cancer research is multidisciplinary and requires standard terminology from multiple domains.

briefly describe OBI. Show how it has been used for collecting clinical and -omic metadata highlighting relevance to cancer data and integration of other ontologies for that purpose.

Gully Burns (UCSD): Applying OBI to cancer pathways via Knowledge Engineering from Experimental Design (KEfED)

addresses the challenge that much of what is known about cancer is only available in publications and requires text mining including the experimental basis for that knowledge.

application of OBI as semantic base for text mining and knowledge engineering.

Philippe Rocca-Serra: How can OBI contribute to unraveling cancer etiology? Scope, Gaps and Future Development of an interoperable semantic resource

addresses the challenge that cancer big data is multi-scale and requires agents to analyze.

demonstrate use of OBI in annotation and data discovery. Address alternatives to OBI and pros and cons.

Mathias Brochhausen (Arkansas): OBI-based integration of biobank data for cancer research

Session 3: Cancer Big Data and the Ontology of Disease

Wednesday, Mar 13 in Balcony A, Natcher

9:00-12:00

<-Comment

Larry Wright (NCI Enterprise Vocabulary Services): NCI-Thesaurus

Olivier Bodenreider (NLM): SNOMED-CT

->

Lynn Schriml (Baltimore): A Human Disease Ontology unified representation of cancer disease terms from

                                        COSMIC, https://icgc.org/ ICGC], TCGA, IntOGen and UniProt
         In progress: Disease classification: A genetic view of disease in DO 
                    (mutation types, inheritance types, specific mutations, chromosome locations)
             (IoM - Institute of Medicine proposals) -- another perspective on disease 
                                                     → The Role DO in Cancer Big Data Challenges

Use Case examples of Challenges: & Propose solutions Lindsay Cowell (UT Southwestern): HPV and cervical cancer, data in EHR - A BIg Data Challenge, what types of data do we need to represent. ?? IDO-HPV & cervical cancer

                  A large of samples, challenge of keeping and using the samples. 

Raja Mazumder (George Washington University): pan-cancer analysis Susan Mockus (The Jackson Laboratory, Genomic Medicine): cancer clinical genomics:

Session Wrap Up: Challenges, Needs, Action Item Solutions, short term steps, long term goals

        Potential Solutions: 30 min: action items, next steps 
  Write Up: White paper on the basis of the meeting

9:00-12:00

Lindsay Cowell (UT Southwestern): TBD

Lynn Schriml (Baltimore): TBD

Themes:

IoM proposals for a new disease taxonomy

Cancer clinical genomics

The Human Disease Ontology

The Human Phenotype Ontology

12:00 Lunch

Public Session: Cancer Big Data to Knowledge

13:00-15:00

Barry Smith (Chair)

With presentations by

Cathy Wu: Ontology and the Precision Medicine Initiative: The Role of OBO Foundry Ontologies in Protein-Centric Cancer Knowledge Network Discovery

Mark Musen: CEDAR: Making it Easier to Use Ontologies to Author Clinical Metadata

Warren Kibbe: TBD

Sponsors

• National Cancer Institute Center for Biomedical Informatics and Information Technology (CBIIT)
• National Center for Biomedical Ontology (NCBO)
• National Center for Ontological Research (NCOR)
• Center for Expanded Data Annotation and Retrieval ([CEDAR)

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Participants

will include:

• Evan Bolton (NIH / NLM / NCBI)
• Mathias Brochhausen (Biomedical Informatics, University of Arkansas for Medical Sciences)
• Gully Burns (Information Sciences Institute, University of Southern California)
• Sherri de Coronado (National Cancer Institute)
• Lindsay Cowell (UT Southwestern Medical Center)
• Peter Elkin (Department of Biomedical Informatics, University at Buffalo)
• Gilberto Fragoso (National Cancer Institute)
• Gang Fu (NIH / NLM / NCBI)
• Ilya Goldberg (Image Informatics and Computational Biology Unit, National Institute on Aging)
• Metin Gurcan (College of Medicine, Ohio State University)
• Warren Kibbe (National Cancer Institute / Disease Ontology)
• Raja Mazumder (Georgetown University / Protein Information Resource)
• Elvira Mitraka (University of Maryland, Baltimore)
• Susan Mockus, Jackson Laboratory for Genomic Medicine, Farmington, CT)
• Mark Musen (Stanford / National Center for Biomedical Ontology and Center for Expanded Data Annotation and Retrieval)
• Darren Natale (Georgetown University / Protein Ontology Consortium)
• Lynn Schriml (University of Maryland, Baltimore / Disease Ontology)
• Barry Smith (Buffalo / Open Biomedical Ontologies Foundry)
• John Tomaszewski (Pathology and Anatomical Sciences, Buffalo)
• Cathy Wu (Delaware / Protein Ontology)
• Wenjin J. Zheng (Center for Computational Biomedicine, University of Texas Health Science Center at Houston)