From academy
The course covers a basic introduction to ontology design principles and usage, specific ontology considerations for anatomy, application of anatomy ontologies in the context of evolutionary phenotype comparison, and use of anatomy ontologies for image annotation in different taxa. There will be strong emphasis on hands-on exercises that will develop ontology skills and provide exposure to different software applications that are useful in variety of areas of evolutionary biology.
Dates
Monday July 30- Friday August 3, 2012 at the National Evolutionary Synthesis Center (http://nescent.org) in Durham, NC.
Costs
Tuition will be approximately $250. Participants are responsible for their own travel costs, including transportation and accommodation. A limited number of travel scholarships from NESCent and the Phenotype Ontology RCN are available for US-based participants. Preference will be given to participants from under-represented minorities.
Now accepting applications!
We will continue to accept applications until we reach course capacity. To apply, please fill out the online application form. The deadline to be considered for travel awards is Friday, April 6, 2012. If you have any questions about the application process, please contact academy@nescent.org.
Description
Evolutionary research has been revolutionized by the explosion of genetic information available, and anatomy ontologies must play a central crucial in relating this knowledge to observable diversity. Anatomy ontologies and vocabularies are widely used to index data and are critical for relating gene expression and phenotype data across taxa. Within a single species, anatomy ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. In order for anatomy ontologies to successfully serve all of these purposes, they must be constructed consistently so that they can be utilized and understood by both researcher and software alike. This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further 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).
See the course materials for a detailed syllabus.
Intended audience
Postgraduate researchers in evolutionary biology and informatics. The course is designed for newcomers to ontologies. Students, postdocs and and faculty are all welcome. There are no prerequisites though participants should have a laptop computer and will need to install software prior to the workshop. In addition, there will be a brief course reading list that is intended to provide technical background for biologists and evolutionary background for technologists. There will be a limited number of laptops available for participants who cannot bring their own machine.
Sponsors
This course is co-sponsored by the Phenotype Ontology Research Coordination Network and the National Center for Biomedical Ontology
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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 is the primary programmer for ‘mx’, a Ruby-on-Rails/MySQL content management system for revisionary systematics that includes both a collaborative ontology development component and the ability to apply semantic annotations on top of natural language character descriptions. 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.
- Chris Mungall - An expert in the use of ontologies for bioinformatics analyses, Chris will share his experiences in building systems for aggregating anatomical and phenotypic data, as well as tools for building interoperable ontologies.
- Erik Segerdell - Erik is the course assistant and help with the hands-on exercises. He is also particularly familiar with multi-species amphibian ontologies.
- Carlo Torniai - Has expertise in Semantic Web application development, OWL import strategies, SPARQL queries, and the use of various APIs for ontology integration.
