Phenoscape

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.

Probably the most important branch of an anatomy ontology for vertebrates – at least from the standpoint of comparative morphologists, paleontologists, systematists – is the skeleton.  We invited a small group of bone and cartilage experts to come to a workshop at NESCent April 9-10, 2010, with the goal of reviewing, revising, and altogether enhancing the skeletal branch of the various vertebrate anatomy ontologies.  We had representation from the amphibian and teleost multispecies anatomy ontologies, the vertebrate model organism ontologies (zebrafish, Xenopus, mouse), and the cell ontology, as well as expert ontologists to advise on best representation (see our wiki page for their names and slides from their brief introductory presentations).  The workshop was productive beyond our expectations: we produced a ‘generic’ skeletal ontology that can be plugged into all vertebrate anatomy ontologies.  The files (including the useful cmap files) are under review by workshop participants at the moment, and we will be posting the outcome as a Vertebrate Skeletal Ontology in the obo foundry within the month.  Let us know if you want to review some giant spreadsheets of bone terms and relationships in the next few weeks….

In mid March Phenoscape met at the Biodiversity Synthesis Center (BioSynC) at the Field Museum of Natural History to host an education and outreach workshop, gather feedback on new user interface mockups for the Phenoscape Knowledgebase, and hold a project meeting. We sent announcements out to the Chicago morphologists, systematists, and developmental biologists. Because we are designing tools to address the general needs of the systematics and evo-devo community, we were delighted that about 20 people attended our day-long meeting. The  input was very useful, and we translated it into specifications for a better user interface (in the works right now). Big thanks to Mark Westneat and staff at the BioSynC for their help in organizing this workshop as well as Lance Grande for the superb behind-the-scenes tour. Please see our wiki page about this workshop for the list of speakers and their slides.