Phenoscape

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.