Computable evolutionary phenotype knowledge: a hands-on workshop

September 29, 2017

Call for Participation:

Computable evolutionary phenotype knowledge: a hands-on workshop

The Phenoscape project is hosting a hands-on workshop on Dec 11-14, 2017, at Duke University in Durham, North Carolina.

Evolutionary phenotype data that is amenable to computational data science, including computation-driven discovery, remains relatively new to science. Therefore use-cases and applications that effectively exploit these new capabilities are only beginning to emerge. If you are interested in discovering, linking to, recombining, or computing with machine-interpretable evolutionary phenotypes, this is the workshop for you!

The event will bring together a diverse group of people to collaboratively design and work hands-on on targets of their interest that take advantage and promote reuse of Phenoscape’s online evolutionary data resources and services. The event is designed as a hands-on unconference-style workshop. Participants will break into subgroups to collaboratively tackle self-selected
work targets.

The full Call for Participation, including motivation and scope, is posted here:

To apply to participate in the event, please fill out the application form by Oct 9, 2017. Travel sponsorship is available but limited, as is space.

ICBO 2011

August 11, 2011

Jim Balhoff and I recently attended the International Conference on Biomedical Ontology (ICBO) held 26-30 July in Buffalo, NY. The conference focused on the use and development of ontologies in the biological and biomedical domains. Of particular interest to Phenoscape were the workshops and tutorials held during the two days before the main conference. Topics included ontology integration, Common Logic, ontology development tools, and using OBO and OWL formats for ontology development and reasoning.

We presented talks at the Facilitating Anatomy Ontology Interoperability workshop. Jim’s talk was on representing taxa as individuals in OWL, an alternative to the common representation of taxa as classes, which facilitates annotation of phenotypic data involving polymorphism and evolutionary reversals.  I presented a lightning talk on the anatomy ontology synchronization requirements for linking evolutionary and model organism phenotypes.  Other presentations from the workshop are available here. We also presented a poster describing the reasoning used in the Phenoscape Knowledgebase.

The main conference included interesting talks on a broad range of topics including the application of ontologies to proteins, diseases, biological mechanisms, and electronic health records. Presentations can be downloaded here.

Joint Phenoscape and AmphibAnat Workshop at ASIH, July 25th in Portland, Oregon

May 28, 2009

ASIH 2009 workshop banner

Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Read the rest of this entry »