Phenex 1.0.2 released

January 20, 2010

Phenex 1.0.2 is now available.  This is a minor update which fixes an interface problem caused by a recent Mac OS X Java update.  It also fixes a file loading bug which occurred on specific older versions of Mac OS X.  Phenex can be downloaded from its homepage on the Phenoscape wiki.

Phenoscape solicits feedback on new interfaces at AmphibAnat Kansas City meeting

December 4, 2009

In early November Wasila and I attended the AmphibAnat workshop in Kansas City, MO (Nov. 5-8) that was organized by Anne Maglia. As you may know, Phenoscape has a close relationship with this group, not only because they work on herps (ichthyologists and herpetologists have a long tradition of working together…), but because they are also developing ontologies to annotate the published comparative anatomical literature. I presented the status of our work in Phenoscape to the large group (~40) of amphibian development and anatomy experts who were present. As these folks added new terms, synonyms, and images to the amphibian ontologies over the course of the next few days, we solicited comments on the prototypes of three new interfaces for the Phenoscape Knowledgebase. Using both images and paper copies of these prototypes, we invited people to sit down with us on a one-on-one basis and describe in detail what worked and what was missing or unclear. The feedback was extremely useful, and we appreciated the AmphibAnat time. We have now gone over all the comments within Phenoscape and logged them individually to FogBugz, our internal tracking system. We’ll be generating new versions of these prototypes through early February, when we plan a formal round of usability testing.

Beta release of the Phenoscape Knowledgebase

October 12, 2009

We are pleased to announce the beta release of the Phenoscape Knowledgebase (KB) at and would like to solicit feedback.

Phenoscape KB integrates phenotypic data from genetic studies of zebrafish with evolutionarily variable phenotypes from the literature of fishes. It currently contains 333,987 phenotype statements about 2,310 taxa (mainly ostariophysan fishes), from 51 publications, and 11,267 phenotype statements about 2,953 genes retrieved from ZFIN ( You can explore these data by searching for anatomical terms, taxa (by Latin name), or genes (by ZFIN gene symbol). Read the rest of this entry »

Our summer of code project

August 27, 2009

Phenoscape has mentored, under the auspices of NESCent, another Google Summer of Code student this year.  Kasia Hayden developed a plugin package for Mesquite that allows users to view character matrices and EQ (ontology-based) annotations produced using the Phenex tool.  The primary purpose was to allow curators to share their annotation work with others in the context of a more familiar tool.  Users can select cells in a Mesquite character matrix and, using two new cell tools, see EQ annotations either as text in the bottom pane of the matrix window, or as a graph in a separate pop-up window. Read the rest of this entry »