ONCONTO 2018: 2nd International Workshop on Oncology and Ontology

Organizer(s):

  • William Duncan
  • Alexander D. Diehl
  • Carmelo Gaudioso

Workshop type:

  • Discusion group (talks + discussion)

Workshop Abstract

To effectively treat and prevent cancer, we need to bring together data from multiple domains, such as electronic medical records, genomic data, tissue data, epidemiological data, and clinical trial data. Personalized medicine requires the integration of clinical and research findings from multiple disciplines, and cancer strikes each affected individual in a unique and specific way from the molecular, cellular, anatomical, genetic, and emotional perspectives. We aim to convene an interdisciplinary group of ontologists and cancer researchers through the ONCONTO workshop in order to advance the ontological representation of cancer and related entities to support both broader research in the domain and personalized treatment approaches. We will cover the following topics: revision and expansion of existing ontological resources for representing cancer and related biomedical entities; creation of new ontologies for the oncology domain that address gaps in representation; ontology-based data analysis of cancer patient or basic research data related to epidemiology, etiology, genomics, diagnosis, and treatment of cancer; use of ontologies for translational research related to cancer; and exploratory research or position papers related to ontologies and cancer.

Rational:

In order to effectively treat and prevent cancer, we need to bring together data from multiple domains, such as electronic medical records, genomic data, tissue data, epidemiological data, and clinical trial data. Each of these kinds of data often exists in distinct data silos maintained by research, clinical care, and government organizations. For example, the high level information about a patient's diagnosis (e.g., invasive ductal carcinoma) may be stored in an electronic medical record system, with detailed pathology information (e.g., the histological analysis of the tumor) stored in a separate specialized database. Furthermore these two data systems may be distinct from other systems that house genetic sequencing information of the patient's tumor or information about ongoing clinical trials that may effectively treat the tumor.

From an ontology and data science perspective, bringing these data sources together presents us with the challenge of developing a consistent and adequate formal representation of the oncology domain so that domain-specific data can be more easily integrated and analyzed. To date, some important ontologies and terminologies have been developed for this purpose. These include the NCI Thesaurus, SNOMED CT, the Ontology for General Medical Science, and the Disease Ontology. However, each of these has certain draw backs and gaps. The OWL implementations of the NCI Thesaurus and SNOMED CT contain a large number of classes, but linking between these classes using axioms is difficult. The Ontology for General Medical Science has an upper-level framework for representing disorders, diseases, and clinical findings, but work needs to be done to define cancer specific disorders and treatments. The Disease Ontology has a hierarchy of cancer types but does not have axioms linking the disease of cancer to the underlying disorder or anatomical location in which the cancer presents.

Topics include:

  • Revision and expansion of existing ontological resources for representing cancer and related biomedical entities and the creation of new ontologies for the oncology domain that address gaps in representation.
  • Ontology-based data analysis of cancer patient or basic research data related to epidemiology, etiology, genomics, diagnosis, and treatment of cancer.
  • Use of ontologies for translational research related to cancer and exploratory research or position papers related to ontologies and cancer.

We will organize our workshop into different sections based on the topics of presentations. Presentation time allocation will be determined after the number of each submission type is finalized. Panel discussions at the end of each section will be arranged based on time availability.

Submission

For the paper submission, we will allow three submission formats:

  • full research papers (6-10 pages) format
  • work in progress / late breaking results (2-4 pages)
  • a statement of interest (one page) for podium presentation

The paper format will be the same as the format used in ICBO.

All the papers will be submitted and handled through Easy Chair:

https://easychair.org/conferences/?conf=icbo2018 

Once you have logged into Easy Chair, choose ONCONTO 2018: 2nd International Workshop on Oncology and Ontology as the submission topic.

Workshop Schedule/Important Dates

  • Individual Workshop Papers Due: June 15, 2018
  • Notification of Acceptance:  June 25, 2018
  • Early Bird Registration:  July 1, 2018
  • Meeting:  August 7, 2018

Funding:
N/A