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


Phenex paper is out

June 10, 2010

We’re happy to report that a paper describing the Phenex curation tool has just recently been published in PLoS ONE:

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, et al. (2010) Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5(5): e10500. doi:10.1371/journal.pone.0010500.

Abstract: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.  Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.  Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.


New article on the Teleost Anatomy Ontology published in Systematic Biology

March 30, 2010

We are pleased to announce the publication of the article “The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age” in Systematic Biology.  The paper describes how we developed this multispecies anatomy ontology for the annotation of systematic characters, and general solutions to various challenges in representing anatomical structures across a diverse clade of fishes.

Open access links to online versions of the paper are given below:

Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee.  2010.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.  Systematic Biology.  View full text or download PDF.


New fossil tells how piranhas got their teeth

August 16, 2009

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

click for full-zise image

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins. Read the rest of this entry »


Poster at the Evolution Meetings

April 30, 2008

Aside from the Evolutionary Biology and Ontologies Workshop that we organize together with the NCBO at the Evolution Meeting 2008 in Minneapolis, we will also be presenting a poster. For your advance pleasure, here is the abstract that we wrote, only to realize that registration for a poster presentation actually did not require or even offer any abstract submission.

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