Phenotype RCN announced

November 24, 2010

NSF has recently funded a Research Coordination Network for researchers who are interested in searching and comparing phenotypes across species and in developing the tools and methods needed in making this possible  (http://phenotypercn.org).  The representation of morphology, behavior and other phenotypic features using computational methods such as ontologies and controlled vocabularies is in its infancy.  Integrating phenotypes with data across all levels of the biological hierarchy, however, is possible if standards are co-developed and coordinated.

This RCN envisions building a broad base of community knowledge and resources so as to maximize the research potential of web-based data.  Funding for participation in meetings, presentations and laboratory exchanges for students, postdocs and faculty from ontology and taxonomic domains (initially plants, arthropods, and vertebrates) is available through the RCN (see http://phenotypercn.org/opportunities/.

We are eager to have you join us!  Please sign up for our participant and mailing lists for further information (http://phenotypercn.org/participants/add/) and feel free to contact one of the PIs (Paula Mabee, pmabee@usd.edu; Andy Deans, andy_deans@ncsu.edu; Eva Huala, huala@acoma.stanford.edu; and Suzanna Lewis, selewis@lbl.gov).


Lapp gives NCBO webinar for Phenoscape

November 17, 2010

Hilmar Lapp gave a great overview today of the ongoing work in the Phenoscape project to 29 participants in the NCBO Webinar series.  This series showcases new projects, technologies and ideas in biomedical ontology, many of which use ontologies for interoperability.  Hilmar presented the biological context (evolution, conservation, development, etc.) into which our work fits, and the challenges involved in representing phenotype.  A videorecording of his talk will be posted in case you missed it.

Update: The slides are also posted on Slideshare


Phenoscape and colleagues meet with PATO on ontology and phenotype representation issues, Sept. 25-27, 2010

November 12, 2010

At the end of September, members of Phenoscape (Mabee, Balhoff), the Hymenoptera Anatomy Ontology (HAO) project (Yoder, Deans, Seltmann) and TAIR (Huala) met with developers of the Phenotype and Trait Ontology (PATO) (Gkoutos, Mungall, Westerfield, Lewis) at the University of Oregon.   Our discussions were focused on finding solutions to problems that have arisen as a result of PATO ontology structure, and problems for representing phenotypes in the EQ model, which have arisen in the course of annotating comparative phenotype data from the fish and hymenoptera literature.  We prepared for this meeting by developing a list of common issues and importantly, specific examples, on a Google doc shared among participants.  We all co-edited this document during the meeting with notes, decisions and examples, and we ‘published’ this Google doc for you all to see.  A number of important changes to the PATO hierarchy were proposed and subsequently made.  We also clarified best practices for modelling some common but tricky phenotypic features. One additional outcome was the participants strong recommendation that a ‘shape jamboree’ be held to improve the usability of this branch of the PATO ontology. Read the rest of this entry »