Evolutionary research has been revolutionized by the explosion of genetic information available, and ontologies must play a central crucial in relating this knowledge to observable diversity. Ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. The theme for this year’s course is “enrichment”. We aim to help participants enrich their research through the use of ontologies, to enrich existing ontologies with new content, and to bring new domain expertise to the ontology community.

The course will start with introduction to ontology development and design (using OWL, Protege), including best practices for community interoperability. We will explore, explain, and demonstrate how ontologies are being used within the field of evolutionary biology. We will then focus on providing new material for and conceptual links between key existing ontologies and biodiversity informatics. Specifics will include strategies for ontology integration, mash-up of data using different ontologies, visualization tools, data stores leveraging ontologies, limits to ontological expression, and ontology manipulation tools and tricks. Following the introductory materials, we will apply what we have learned in the context of individual research projects and participants should come prepared with a research problem that they would like to use ontologies to help address.

This course seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Students will be required to complete some software installation and preliminary online exercises prior to the course.

Instructors

Melissa Haendel is currently lead ontologist for the eagle-i project, designed to collect and disseminate information about scientific resources. Dr. Haendel has a Ph.D. in neuroscience, where she studied early development in mouse, chick and zebrafish. Dr. Haendel has co-lead several anatomy ontology workshops and has participated in development of development of standards for anatomy ontologies. She has participated in development of the Common Anatomy Reference Ontology (CARO) and taxonspecific anatomy ontologies such as the zebrafish anatomy ontology (ZFA), the the teleost ontology (TAO), and the vertebrate skeletal ontology (VAO). Most recently, she has been working to facilitate cross-species anatomy interoperability (Uberon). Her interest is in using anatomy ontologies as a nexus for linking many types of data - genomic, biomedical, evolutionary - using Semantic Web standards.

Matt Yoder is a lead researcher on the Hymenoptera Anatomy Ontology and a biodiversity informatician at the Illinois Natural History Survey. Matt contributes to the curation of the HAO and seeks to develop user-friendly tools that enable domain experts, who are not usually ontology experts as well, to employ phenotype ontologies as part of their descriptive work. Trained in Hymenoptera systematics and biodiversity informatics Matt has broad experience in phylogenetic reconstruction, with specific background in rRNA multiple sequence alignment analysis. He has worked on implementing informatics solutions across a wide range of taxa.

Guest instructors

• Jim Balhoff - Working on the Phenoscape and Hymenoptera Anatomy ontologies Jim is an expert in semantic phenotype and ontology meta-data modelling, inference, and ontology-based application development.
• Erik Segerdell - Erik is the course assistant and help with the hands-on exercises. He is also particularly familiar with multi-species amphibian ontologies.