In conjunction with the 10th International Conference on Biomedical Ontology

July 30, 2019

9:00 - noon

Buffalo, NY, USA

Workshop schedule - July 30, 2019

• 9:00 Welcome
• 9:10 Danielle Mowery: Expanding the Hypertension Ontology to Leverage Information Extracted from Clinical Texts
• 9:40 Daniel Schlegel: GazOntology: A Tool for Building GATE Gazetteer Lists from Ontologies
• 10:00 Michael Bada: Facilitating Ontological Concept Annotation of Biomedical Text with Extension Classes
• 10:30 Break
• 10:40 Cooper Stansbury: Discovering and Managing Permissions from Informed Consent Documents
• 11:00 Peter Elkin: Biomedical Informatics Investigator: Ontology Driven Research
• 11:30 Discussion, wrap-up, next steps

Workshop topic and themes

Ontologies provide machine-interpretable semantic representations of biomedical information that can then be shared, queried, and reasoned about. Natural language processing techniques are increasingly being applied within the biomedical domain, allowing machines to automatically interpret and use the large amounts of unstructured textual data generated each day across the biomedical domain, including but not limited to that generated in the course of clinical care and research.

This workshop aims to explore and promote connections between work in ontologies and natural language processing techniques, with a focus on the domain of biomedicine. Work in both areas will benefit from this connection. For example, a significant hurdle in NLP, especially as applications increasingly require full natural language understanding, is the appropriate representation of the semantics of a particular word, phrase, sentence, or document. Ontologies encode useful domain and terminological knowledge and provide an ideal logical framework on which to build such semantic representations. Applications abound throughout biomedicine for these technologies, including in cohort identification, reporting, quality assurance, data integration, and clinical decision support. Similarly, NLP techniques can be useful for ontology creation, use, and evaluation, for instance in support of automated methods for generating and evaluating definitions for ontology terms. This workshop will provide a forum to discuss the state of the art in using NLP and ontologies together; disseminate research in these areas; enhance awareness of the problems faced in combining NLP with biomedical ontologies, along with the potential benefits; facilitate discussions within the ICBO community which we hope will advance the field; and foster new collaborations.

This half-day workshop will consist of paper presentations followed by an open discussion session on the issue of combining NLP and biomedical ontology. We invite and encourage submissions by researchers who make combined use of biomedical ontologies and NLP.

Topics include, but are not limited to:

• Novel uses of ontologies in NLP tasks, tools, or frameworks.
• Novel uses of NLP in ontology construction, evaluation, or use.
• Challenges in using NLP and ontology cooperatively, along with potential solutions
• Use of ontologies for automatic semantic indexing of text, including the coordination of multiple ontologies for this task.
• Ontologies and NLP for data infrastructure: reporting services, cohort discovery, and data warehousing.
• Ontologies and NLP supporting analyses of textual data in large EHR systems.

Submission Details

We invite submission of both full papers (5-10 pages) and short papers (2 pages) discussing work that combines these technologies. Papers will be evaluated by the scientific program committee based on their appropriateness to the workshop, scientific merit, and novelty. Short papers are expected to cover late-breaking or preliminary work along with presentations. We aim to have presented papers published in peer-reviewed proceedings.

Submissions should be formatted using the ICBO 2019 paper template, and submitted via EasyChair at https://easychair.org/conferences/?conf=icbonlp2019

Important Dates

Workshop papers due: May 1, 2019 May 15, 2019

Notification of acceptance: May 30, 2019

Workshop: July29, 2019 (tentative)

Organizers

• Jonathan P. Bona (University of Arkansas for Medical Sciences)
• Peter L. Elkin (University at Buffalo)
• Daniel R. Schlegel (SUNY Oswego)

Contact: icbo.nlp.2019@gmail.com

Program Committee

• Mathias Brochhausen (University of Arkansas for Medical Sciences)
• Paul M. Heider (The Medical University of South Carolina)
• Amanda Hicks (University of Florida)
• Hongfang Liu (Mayo Clinic)
• Danielle Mowery (University of Pennsylvania)