Phenoscape

Winner of a competition among participants to illustrate the essence of Phenoscape, from Paul Sereno

It’s easy to get caught up in the details when developing infrastructure. You know it will be useful – because the grant application said so!  But there’s so much engineering to do. And no matter how thoughtful and deliberate a process you follow to anticipate the needs of your future users, once they have a complicated thing in their hands who knows how they will actually use it.

Enter the Phenoscape Knowledgebase.  After a heroic data collection push this winter, our next release of the Knowledgebase will contain millions of evolutionary phenotypes from throughout the vertebrates, linked to genetic phenotypes from human, mouse, Xenopus, and zebrafish, and a particularly rich set of annotations for skeletal features of fins and limbs.  The Knowledgebase is far from comprehensive, and annotations do not capture the full richness of the original characters in the evolutionary literature, but we think it’s a pretty useful resource.

So, it’s time to see what capabilities our users are excited by and what limitations frustrate them. To that end, we brought a small group of experts who look at phenotypes in a variety of different ways (e.g. genetics, systematics, evo-devo, clinical biomedicine, paleontology, even zooarchaeology) to the California Academy of Sciences in February, and we asked them what questions they’d most like to address using the KB as it exists today.

To help us in tapping into the assembled brainpower, we enlisted KnowInnovation, facilitation pioneers that specialize in helping researchers self-organize into teams to tackle creative research challenges. This they did with amazing resourcefulness, milking ideas out of us that we wouldn’t have imagined we even had.  The workshop was no ordinary parade of PowerPoints. We did speed-dating to toss research ideas off of each other, generated a  staggering number of post-it notes, sculpted creatures and skeletal parts out of clay and engaged in a host of other seemingly contrived but strangely liberating activities.  We watched in amazement as Karl Gude took visual minutes.

And we came up with some great collaborative ideas for research that take leverage the Knowledgebase to ask questions that would have been difficult to impossible to answer without it, including questions about genetic convergence and parallelism, global comparisons of intra and interspecific phenotypic variation, and the evolution of phenotypes affected by duplicated genes. These projects will now serve as driving applications for Phenoscape so that we know better what our users really need the Knowledgebase to do for them.  We look forward to reporting on the outcome of those in due course.

A big thank you to David Blackburn and the Cal Academy for providing such an inspiring venue, being exquisite hosts, and for conveniently having an open museum night during our workshop.  Thanks also to a great group of participants and facilitators, and to to NSF for a supplemental award that helped to make the workshop a success.