Bio-Ontologies (#bioontologies) 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.

Bio-Ontologies is celebrating its 20th year at ISMB in 2017, which will be held in Prague, Czech Republic on July 24 and July 25, 2017. 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 interest group (HCLSIG), 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.

Key Dates

  • ISMB Proceedings Abstract Submission: January 3, 2017
  • Submissions Deadline: April 13, 2017 April 20, 2017
  • Acceptance Notification: May 10, 2017 May 15, 2017
  • Poster Deadline: May 15, 2017
  • Early Bird Registration: June 15, 2017
  • Program Information: June 17, 2017
  • Bio-Ontologies: July 24-25, 2017


Monday July 24, 2017

Session I: Chair: Robert Hoehndorf

10:00 - 10:10 Welcoming Remarks [PDF]

10:10 - 11:10 Keynote: Ontologies: Necessary, but not sufficient Robert Stevens.

11:10 - 12:00 Panel: 20 Years of Bio-Ontologies @ ISMB w/ Mark Musen, Catia Pesquita, Lars Juhl Jensen, and Judith Blake. [PDF]

12:00 - 2:00 Lunch

Session II: Chair: Ian Harrow

2:00 - 2:30 Deep Learning with Word Embeddings improves Biomedical Named Entity Recognition. Maryam Habibi, Leon Weber, Mariana Neves, David Luis Wiegandt and Ulf Leser. Proceedings 

2:30 - 2:45 EXTRACT 2.0: text-mining-assisted interactive annotation of bio-medical named entities and ontology termsEvangelos Pafilis, Rūdolfs Bērziņš and Lars Juhl JensenFlash Update. [PDF]

2:45 - 3:00 A Text Mining Approach Characterizes Fusion Proteins and Their Interactions From PubMed PublicationsSomnath Tagore, Milana Frenkel-Morgenstern, Alessandro Gorohovski and Lars Juhl Jensen. Flash Update. [PDF]

3:00 - 4:00 Keynote: Sense and similarity: making sense of similarity for ontologies. Catia Pesquita

4:00 - 4:45 Coffee Break

Session III: Chair: Kevin Cohen

4:45 - 5:00 Classification and analysis of a large collection of in vivo assay descriptionsMagdalena Zwierzyna and John Overington. Flash Update. [PDF]

5:00 - 5:15 Onassis: Ontology Annotation and Semantic Similarity SoftwareEugenia Galeota and Mattia Pelizzola. Flash Update. [PDF]

5:15 - 6:00 Paper Writing: Accomplishments, Challenges and Opportunities in Bio-Ontologies. [working docs]

6:00 - 7:00 Poster Presentations [ list of posters ]

Tuesday July 25, 2017

Session IV: Chair: Robert Hoehndorf

8:30 - 9:30 Keynote: Mining the Ultimate Phenome Repository. Nigam Shah.

9:30 - 10:30 Coffee Break

10:30 - 11:00 A Machine-Compiled Database of Genome-Wide Association StudiesVolodymyr Kuleshov, Jialin Ding, Braden Hancock, Alexander Ratner, Christopher Re, Serafim Batzoglou and Michael Snyder. Short Paper. [PDF]

11:00 - 11:15 MetaCrowd: Crowdsourcing Biomedical Metadata Quality AssessmentAmrapali Zaveri and Michel Dumontier. Flash Update. [PDF]

11:15 - 11:30 Enabling community editing of assay terms in OBI while ensuring consistent use of design patterns with spreadsheet templatesJames A. Overton, Randi Vita, Bjoern Peters and OBI Consortium. Flash Update. [PDF]

11:30 - 11:45 Assessing the quality of manually curated drug indication and usage information via ontology term mappingsKody Moodley, Michel Dumontier, Linda Rieswijk and Tudor Oprea. Flash Update. [PDF]

11:45 - 12:00 1 minute madness!

12:00 - 2:00 Lunch & Poster Presentations [ list of posters ]

Session V - Chair: Philippe Rocca-Serra

2:00 - 2:30 BIOSSES: A Semantic Sentence Similarity Estimation System for the Biomedical Domain. Gizem Sogancioglu, Hakime Öztürk and Arzucan Ozgur. Proceedings.

2:30 - 2:45 Using ontologies to find and correct errors in database content. Randi Vita, James A. Overton and Bjoern Peters. Flash Update. [PDF]

2:45 - 3:00 EFO 3: “Your” experimental factor ontology. Sirarat Sarntivijai, Danielle Welter, Simon Jupp and Helen Parkinson. Flash Update. [PDF] 

3:00 - 3:15 Conventions to make ontology term labels predictable and unique. Bjoern Peters, Chris Mungall, James A. Overton, Randi Vita and Obo Operations Committee. Flash Update. [PDF]

3:15 - 3:45 Enhancing evidence from literature in Open Targets – a platform for drug target validationSenay Kafkas, Ian Dunham and Johanna McEntyre. Short Paper. [PDF]

3:45 - 4:00 Closing Remarks [slides]

Keynote Speakers

Nigam Shah: Mining the Ultimate Phenome Repository
Controlled terms are widely used to annotate gene products and literature abstracts. Subsequent analysis of the resulting annotations enable significant insights that advance molecular biology. In this presentation we will review how the use of ontologies in annotating, and analyzing, Electronic Health Records (EHR) make it possible to examine the outcomes of decisions made by doctors during clinical practice to generate evidence from the collective experience of millions of patients. I will describe the role that bio-ontologies play in supporting the Informatics Consult service at Stanford, and in enabling an advanced search engine that build cohorts of patients with specific phenotypes in sub-second response times.

Nigam Shah is associate professor of Medicine (Biomedical Informatics) at Stanford University, Assistant Director of the Center for Biomedical Informatics Research, and a core member of the Biomedical Informatics Graduate Program. Dr. Shah's research focuses on combining machine learning and prior knowledge in medical ontologies to enable use cases of the learning health system. Dr. Shah received the AMIA New Investigator Award for 2013, was elected into the American College of Medical Informatics (ACMI) in 2015 and is inducted into the American Society for Clinical Investigation (ASCI) in 2016. He holds an MBBS from Baroda Medical College, India, a PhD from Penn State University and completed postdoctoral training at Stanford University. More at:

Catia Pesquita: Sense and similarity: making sense of similarity for ontologies

Judging the similarity between things allows us to understand the world. Similar things tend to behave similarly, which supports inference. In the life sciences, knowledge can seldom be reduced to mathematical form, so calculating similarity is not trivial. Ontologies provide the scaffolding to compute similarity between entities based on their semantic annotations. However, biomedical entities can be annotated under multiple ontologies to cover distinct domains or due to fragmentation issues. Therefore, an accurate measure of the similarity between biomedical entities depends on the creation of meaningful links between related ontologies.  I will discuss the challenges and the evolutions of the last decade in computing the similarity between concepts from different bio-ontologies (ontology matching), and the similarity between bio-ontology annotated entities (semantic similarity), and their interconnectedness. I will look into applications in biological and clinical domains, namely for data mining and semantic data integration.

Catia Pesquita is an Assistant Professor at the Computer Science department at Faculdade de Ciências, Universidade de Lisboa. She is also a senior researcher at the Large Scale Information Systems Research Lab (LASIGE) where she leads research projects dedicated to several areas including the development of novel semantics based approaches to knowledge engineering and data mining, particularly in the biomedical and clinical domains. She has made significant contributions to the areas of ontology matching and ontology-based semantic similarity. Catia Pesquita has a degree in Biology, an MSc in Bioinformatics and a PhD in Computer Science, awarded by Universidade de Lisboa. She was the recipient of a research award from the Luso-American Foundation for Development. Together with her research team she has also won several awards and competitions in ontology matching. 

Robert StevensOntologies: Necessary, but not sufficient

The past twenty years of the Bio-Ontologies meeting have seen great advances in the use of ontologies within the domain of biology. The bio-ontology community has produced a broad range of ontologies that capture a wide variety of biological phenomena. At their heart, ontologies allow us  to `know what we are talking about', affording consistent annotation and thus querying of biological phenomena across species. This drive towards a common, shared understanding of the entities of the domain has its successes, but despite the successes we see in coverage and use in annotation, there are limitations in how we develop and use ontologies; there is more we can do.  Over the next twenty years, these limitations may cease to become inconveniences , and grow to become a block in the uptake of ontologies, and ontological technologies. To avoid this, we must accept that ontologies are necessary for exploiting knowledge computationally within biology, but they are not sufficient to do so. In this talk I will describe where I think the bio-ontologies community is, where it needs to go and how it should do so. Along the way, I will elucidate some of the  other necessary conditions for exploiting knowledge in biology. If we achieve these conditions, ontologies will still be used in another 20 years time and, by then, will have contributed significantly to our understanding of biology.

Robert Stevens is a professor of computer science at the University of Manchester. He has a Ph.D. in human computer interaction and a degree in biochemistry. he has used this background to drive a very cross-disciplinary research agenda. His main research interests are in how we develop, interact with and use logic based ontologies to describe, manage and analyse biological data. Along the way he has also  done work in workflows in bioinformatics, extracting and representing methods used in analysing biological data and how humans interact with complex information.  Robert has long been an advocate of description logic based ontologies and has established the "Pizza Tutorial" as one of the most widely used OWL tutorials. He was co-chair of the Bio-Ontologies SIG at ISMB for eight years, a co-chair of the ontologies and databases track at ISMB, co-chair of the International biomedical Ontology conference in 2012 and co-chair of SWAT4LS  in 2015.

Call for Submissions

We invite the submission of short papers, flash updates and posters for presentation at the Bio-Ontologies SIG. Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to):

  • Collaborative Ontology Authoring
  • Ontologies in Data and Metadata Standards
  • Machine-driven ontology development
  • Semantic Web Enabled Applications
  • Bio-Ontologies in the Learning Health System
  • Intelligent systems for accurate phenotyping 
  • Machine and Deep learning with Ontologies
  • Platforms for Biocuration
  • Automated Annotation Pipelines
  • Knowledge representation and knowledge discovery for biomedical data
  • Use of semantic technologies in text mining
  • Ontology growth, mapping and repair
  • Efforts to generate and assess FAIR data
  • Social, moral and technical issues in publishing and consuming biomedical and life sciences data.
  • Research in Ontology Engineering and Ontology Evaluation
  • Flash updates on Newly Developed or Existing Bio-Ontologies

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 ( or updates/posters ( Submissions can be made on the easychair site ( Please note that accepted submissions require that one author present the work. The research presentations are normally allocated between 20-25 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

  1. Relevance, interest, and value of the topic to conference attendees.
  2. Significance of the problem, such that reviewers understand the potential for impact.
  3. Novelty of the approach, including suitable treatment of related work.
  4. Soundness and potential for reproducibility of the proposed method.
  5. Quality of writing, including readability and clearly stated contribution(s)

Program Committee

coming soon

Previous Meetings

Orlando (2016), Dublin (2015), Boston (2014), Berlin (2013), Long Beach (2012), Vienna (2011), Boston (2010), Stockholm (2009), Toronto (2008), Vienna (2007), Fortaleza (2006), Detroit (2005), Glasgow (2004), Brisbane (2003), Edmonton (2002), Copenhagen (2001), San Diego (2000), Heidelberg (1999), Montreal (1998).


Have suggestions for this year? We'd love to hear from you at