2018 Meeting - Chicago

Bio-Ontologies (#bioontologies; http://www.bio-ontologies.org.uk/) is an ISMB Community of Special Interest (COSI) that covers the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Join our mailing list and our slack team!  Have something to say? Tweet to @bioontologies or send an email to the organizers - bioontologies@gmail.com .

Bio-Ontologies will be in its 21th year at ISMB 2018, which will be held in Chicago, USA on July 6-10. It continues to provide a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The informal nature of the COSI offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA) and the W3C’s Healthcare and Life Sciences Community Group (HCLSCG), thereby increasing impact through broader dissemination and enabling new and exceptional collaborations. This year's event will be integrated into the main conference and will feature papers accepted for the ISMB proceedings.

Selected papers will be invited to submit an extended version of their manuscript to the bio-ontologies theme in the Journal of Biomedical Semantics.

Key Dates

 Submission Deadline

 April 5, 2018 (for poster, short talk abstracts)

 April 13, 2018 (for short papers)

 Late Poster Deadline: May 1, 2018

 Acceptance Notification: May 3, 2018

 Late Poster Notification: May 22, 2018

 Early Bird Registration: June 7, 2018

 Program Information: June 17, 2018

 Bio-Ontologies track @ ISMB: July 9-10, 2018

 Special Issue deadline: October 1, 2018


The use of existing and new ontologies in African biomedical research

Prof Nicola Mulder

African scientists have joined the genomics revolution, and large-scale projects to study the genetic and environmental determinants of diseases are underway across the continent. These have been made possible through initiatives such as the Human Heredity and Health in Africa (H3Africa), which is funding research projects, large collaborative centres, bioepositories and a bioinformatics network. H3ABioNet is the NIH funded bioinformatics network, composed of 27 institutions across 16 African countries, which is developing capacity for genomics research. One of the roles of the network is to facilitate data harmonization and submission to public repositories, such as the EGA. Data from the H3Africa projects is being collected for over 100,000 participants on multiple communicable and non-communicable diseases, and includes phenotype, genomic and other kinds of experimental data. H3ABioNet is working with the projects to harmonize the data and map to ontologies. In doing so, we identified a few gaps in existing ontologies, including those for the description of ethnolinguistic groups and for African specific diseases such as Sickle Cell Disease. To address these we extended existing terms for ethnolinguistic groups and developed a Sickle Cell Disease Ontology. This talk will describe some of this work and other challenges encountered in harmonizing the data.    

Bio: Prof Mulder heads the Computational Biology Division at the University of Cape Town (UCT), and leads H3ABioNet, a large Pan African Bioinformatics Network of 27 institutions in 16 African countries. H3ABioNet aims to develop bioinformatics capacity to enable genomic data analysis on the continent by developing and providing access to skills and computing infrastructure for data analysis. Prior to her position at UCT, she worked for nearly 9 years at the European Bioinformatics Institute (EBI) in Cambridge, as Team Leader for InterPro and the Gene Ontology Annotation project. At UCT her research focuses on genetic determinants of susceptibility to disease, African genome variation, microbiomes, microbial genomics and infectious diseases from both the host and pathogen perspectives. Her group also provides bioinformatics services for the local researchers, through which they develop visualization and analysis tools for high-throughput biology. Her team has also been involved in the development of new and improved algorithms for the analysis of complex African genetic data as well as for downstream analysis and interpretation of GWAS data. Prof Mulder is actively involved in training and education as well as curriculum development in bioinformatics and genomic medicine. 

Deep X: Deep Learning with Deep Knowledge

Prof Volker Tresp

Labeled graphs can describe states and events at a cognitive abstraction level, representing facts as subject-predicate-object triples.  A prominent and very successful example is the Google Knowledge Graph, representing on the order of 100B facts. Labeled graphs can be represented as adjacency tensors which can serve as inputs for prediction and decision making, and from which tensor models can be derived to generalize to unseen facts.  We show how these ideas can be used, together with deep recurrent networks, for clinical decision support by predicting orders and outcomes.  Following Goethe’s proverb, “you only see what you know”, we show how background knowledge can dramatically improve information extraction from images by deep convolutional networks and how tensor train models can be used for the efficient classification of videos. We discuss potential links to the memory and perceptual systems of the human brain.  We conclude that tensor models, in connection with deep learning, can be the basis for many technical solutions requiring memory and perception, and might be a basis for modern AI.

Bio: Volker Tresp received a Diploma degree from the University of Goettingen, Germany, in 1984 and the M.Sc. and Ph.D. degrees from Yale University, New Haven, CT, in 1986 and 1989 respectively. Since 1989 he is the head of various research teams in machine learning at Siemens, Research and Technology.  He filed more than 70 patent applications and was inventor of the year of Siemens in 1996. He has published more than 150 scientific articles and administered over 20 Ph.D. theses. The company Panoratio is a spin-off out of his team.  His research focus in recent years has been „Machine Learning in Information Networks“ for modelling Knowledge Graphs, medical decision processes and sensor networks. He is the coordinator of one of the first nationally funded Big Data projects for the realization of „Precision Medicine“.   Since 2011 he is also a Professor at the Ludwig Maximilian University of Munich where he teaches an annual course on Machine Learning.

Program: Available from ISMB site.

Call for Submissions

We invite the submission of short papers, flash updates and posters for presentation at the Bio-Ontologies. Papers are invited in the following three areas:

1. The development of biological and biomedical ontologies to represent and structure knowledge.

2. Ontology-focused tools and methods (e.g. ontology engineering, ontology alignment, biocuration, information extraction, text mining, data integration) featuring biological use cases.

3. Biological applications of ontologies (e.g. ontologies use in data mining, machine learning, visualization, knowledge graphs, semantic query answering)

Deadlines and Presentation Length

We welcome short research papers (4 pages), flash updates (1 page) and poster abstracts (1 page) as a PDF using the Bio-ontologies template for papers (https://goo.gl/KD7Bmi) or updates/posters (https://goo.gl/1OkQSH). Submissions can be made on the easychair site (https://easychair.org/conferences/?conf=ismb2018abstracts). Please note that accepted submissions require that one author present the work. The research presentations are normally allocated between 20 minutes while flash updates are presented in 5-10 minutes. The presenter must register and pay to attend the conference and the presenter should identify themselves as the corresponding author during the submission process.

Review Criteria

Organizing Committee


Have suggestions for this year? We'd love to hear from you at bioontologies@gmail.com