4th International Workshop on Vaccine and Drug Ontology Studies


Cui Tao, PhD, University of Texas, Health Science Center at Houston
Luca Toldo, PhD, Information Services Merck
Yongqun “Oliver” He, DVM, PhD, University of Michigan Medical School
Sivaram Arabandi, MD, MS Ontopro LLC Houston, TX

Vaccines and drugs have contributed to dramatic improvements in public health worldwide. There have been efforts from various areas in the biomedical ontology community that extend existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, and MedDRA), vernacular medical terminologies, and their applications to research and clinical data associated with vaccines and drugs.

This workshop will provide a platform for showcasing and discussing innovative solutions and challenges in the development and applications of biomedical ontologies to represent and analyze vaccines and drugs, their administration, immune responses induced, adverse events, and similar topics.

The workshop will cover two main areas: (i) ontology representation of vaccines/drugs and related domains, and (ii) ontology applications in real world situations. Examples of biomedical subject matter in the scope of this workshop: drug components (e.g., drug active ingredients, vaccine antigens and adjuvants), administration details (e.g., dosage, administration route, and frequency), gene immune responses and pathways, drug-drug or drug-food interactions, and adverse events. Both research and clinical subjects will be covered. We will also focus on computational methods used to study these, for example, literature mining of vaccine/drug-related literature and social media mining, retrieval and analysis of vaccine/drug-gene

Third International Workshop on Definitions in Ontologies


Selja Seppälä, University at Buffalo
Alan Ruttenberg, University at Buffalo
patric Ray, University at Buffalo
Barry Smith, University at Buffalo

This half-day event is the third workshop in the series on Definitions in Ontologies. The first two such workshops (DO 2013 and IWOOD 2014) were held in conjunction with ICBO 2013 and ICBO 2014.

Definitions of terms in ontologies serve a number of purposes. Logical definitions allow reasoners to assist in the process of classification and to verify the results, thereby lessening the development burden. Natural language definitions help ameliorate low inter-annotator agreement. Good definitions make it possible for non-experts and experts in adjacent disciplines to understand unfamiliar terms, thereby making it possible for them to reuse terms in external ontologies. In this way definitions can help to facilitate integration of data.

The goals of this workshop are: to raise awareness of the importance of well-constructed definitions; to bring together interested researchers and developers to explore issues relating to definitions and enable cross-fertilization leading to new approaches; to share case studies that expose difficulties arising in definition construction, evaluation, interpretation, and revision; to encourage evaluation of definitions by readers from different domains in order to surface potential difficulties in interpretation; to encourage participants to bring practices back to their projects that benefit the quality of their ontologies.


Genomics data standards - hackathon


Melanie Courtot
Pelin Yilmaz
Lynn Schriml
Elvira Mitraka
Jie Zheng
Joao Andre Carrico
Emma Griffiths
Pier Luigi Buttigieg

Next generation sequencing has produced large amount of genomic data at increasing ease and speed. Genomic Epidemiology relies on the combination of high-resolution genomics data and epidemiological techniques. To advance genomic epidemiology and allow meaningful genomic comparisons, it is critical to have adequate tools to annotate genomes archives in terms of metadata describing collection and sequencing of samples. Critical fields pertaining to sequencing/annotation/analysis methodology, source attribution, exposure, biochemical and typing testing, and patient identifiers will be highlighted. Better standardization of these fields will provide improved querying and correlation of laboratory and epidemiological data for faster and more efficient outbreak investigation and response.

This hackathon builds on the expertise on organizers and participants we will invite to contribute, as well as existing resources. Its goal is to foster discussions and exchanges, as well as improve and consolidate the subset of resources considered.


Tawny-OWL: re-purposing software engineering for ontology building


Phillip Lord, School of Computing Science, Newcastle University

Tawny-OWL addresses the need for a programmatic tool for the construction of Ontologies. With an increase in their size and complexity, programmatic access enables developers to modify and extend ontologies rapidly, to abstract, enforce consistency in patterns and to enable maintainable change.

Tawny-OWL combines an attractive and simple syntax, with the power of a rich programming language. It enables us to exploit a rich ecosystem of programming tools and apply them to ontology development. Rich IDEs and all the tools of the programmer come for free. It is R to Protege’s Excel. It is built on the OWL API, however, so also integrates with the existing ecosystem of ontology-specific tools.

Participants will finish with a clear understanding of ontology construction using Tawny-OWL, how to exploit its programmatic facilities and environment, and the current and future applications for it.

Basic Formal Ontology (BFO)


Barry Smith, University at Buffalo

The tutorial will fall into two parts. Part 1 is for beginners, and provides a simple introduction to the rationale and principles underlying BFO, a brief guide to the history of the ontology, of its relations to other candidate upper ontologies, and of its principal applications, culminating in some examples of how BFO is used to initiate ontology development. The introduction to BFO described at will be released in advance of the meeting.

Part 2 will provide a guide to the current state of BFO and specifically of the proposed BFO version 2, and of the state of work along the three parallel tracks of (i) English-language specification, (ii) OWL and (iii) FOL formalization. 2.0 will be released in draft form for public comment in advance of the tutorial. It will also describe how BFO 2.0 is being used in current work on the Information Artifact Ontology (IAO).

OBO Tutorial: Best Practices for Ontology Use


James A. Overton,
Alan Ruttenberg, University at Buffalo School of Dental Medicine
Barry Smith, University at Buffalo Department of Philosophy
Jie Zheng, University of Pennsylvania

The Open Biological and Biomedical Ontologies (OBO) provide a suite of interoperable ontologies for biology and medicine. Ontology users and developers benefit from close collaboration and shared best practices, and they benefit most when they are familiar with a range of shared tools and techniques. In this interactive tutorial we present a range of real-world examples focused on OBO Foundry and Library ontologies, building on our online tutorial. In the first half of this three hour session we will cover: (1) an overview of OBO; (2) finding the right ontologies and terms; (3) assessing ontologies and terms for reuse. In the second half we will cover: (4) building an application ontology; (5) working with instance data; and (6) filing effective term requests and bug reports.

Tutorial on the Biological Pathway Exchange (BioPAX) Ontology and Pathway Commons Database


Augustin Luna, Memorial Sloan Kettering Cancer Center
Emek Kemir, Memorial Sloan Kettering Cancer Center

The BioPAX ontology is a community standard for the description of biological pathways. It aims the facilitate the integration, exchange, and analysis of pathway data. In collaboration with many groups, we have developed a related resource Pathway Commons to act as a convenient access point for the pathway data represented in BioPAX and collected from many public databases, simplifying search, visualization and download of this data. This tutorial will help participants understand how to use the BioPAX ontology for their own data and make use of the expansive Pathway Commons dataset in their research projects. This tutorial will cover several topics: 1) a basic understanding of the BioPAX ontology and its usage, 2) an introduction to Paxtools, a Java library for BioPAX, 3) accessing the Pathway Commons web service, and 4) visualization of BioPAX data.