A contingent of Phenotype RCN participants recently attended the 7th International Conference on Biological Ontology (ICBO) and BioCreative 2016 held over a stretch of pleasantly sunny days on the campus of Oregon State University in Corvallis, Oregon (August 1-4, 2016). The theme of the meeting was Food, Nutrition, Health, and Environment for the 9 billion and the meeting brought together folks interested in applying ontologies to innovative research in diverse domains including environment, biodiversity, biomedical sciences, plant biology, and agriculture.
The conference started off with a day of workshops covering text-mining, visualization, medicine, and tutorials on tools, techniques and standards. (Links to the program and abstracts are available here: http://icbo.cgrb.oregonstate.edu/program). Talks and posters during subsequent sessions included a diverse mix of topics such as sustainability, obstetrics and neonatal health, trauma centers, social science, infection disease, and biodiversity. Although wide-ranging in scope, a thread of common challenges emerged in working with ontology-based data, including the need for data harmonization/standardization, promoting shared resources, representation challenges for temporal or spatial reasoning, and improving descriptors/terminology.
The meeting ended with a panel discussion in which the question “Have ontologies reached their peak?” was discussed. This question was prompted by a noticeable decline since 2014 in Pubmed papers matching the word “ontology” (and a marked increase in those matching “data mining”). Consensus of the panel was that while the publication of new ontologies in Pubmed may have slowed, their use in biology was far from peaking. Rather, the community may have a more refined understanding of what an ontology is, which means fewer papers are being published that claim to be about ontologies.
Of particular interest to the phenotype community, here are the presentations given by recent RCN phenotypers:
- James Balhoff, Wasila Dahdul, Prashanti Manda, and the Phenoscape team: The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms
- Pier-Luigi Buttigieg: Sustainable food systems and food in ecosystems
- Pier-Luigi Buttigieg, Mark Jensen, Ramona Walls, Chris Mungall: Environmental semantics for sustainable development in an interconnected biosphere
- Brian Stucky, Ramona Walls, Robert Guralnick: The Plant Phenology Ontology for Phenological Data Integration
- Suzanna Lewis: Telling a genome’s story graphically
- Prashanti Manda, Jim Balhoff, Todd Vision: Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles
- Chris Mungall, M Jensen, M-A Laporte, P. Buttigieg. A sustainable approach to knowledge representation in the domain of sustainability: bridging SKOS and OWL
- N Vasilevsky, M Engelstad, E Foster, C Mungall, P Robinson, S Köhler, M Haendel: Enhancing the Human Phenotype Ontology for Use by the Layperson
- Melanie Courtot, James Malone, Chris Mungall: Ten simple rules for biomedical ontology development
- Chelsea Specht: Evolution of Floral Form: The potential of ontologies across diverse plant lineages
- Ramona Walls: Defining and sustaining populations and communities
- Ramona Walls, Robert Guralnick: The Biological Collections Ontology for linking traditional and contemporary biodiversity data
We thank the Phenotype RCN for providing travel support to the meeting.
— Jim Balhoff, Pier-Luigi Buttigieg, Wasila Dahdul, Rob Guralnick, Suzi Lewis, Prashanti Manda, Chris Mungall, Chelsea Specht, Brian Stucky, and Ramona Walls