California Dreaming

March 27, 2013

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.

Knowledgebase tutorial now available

October 4, 2012

The Phenoscape team has created a tutorial introduction to the Knowledgebase. The tutorial is designed to introduce users to exploring phenotypic data in the Phenoscape Knowledgebase, starting with searching for anatomical terms, browsing data using faceted browsing, and performing searches using the query panel. Let us know if you find it helpful in getting started with the KB.

Link: Phenoscape Knowledgebase tutorial

Call for Participants: Workshop on New Tools for Studying Phenotype Evolution in the Vertebrates

July 23, 2012

What new research opportunities are opened up by the power to compute over phenotype information from thousands of species of vertebrates, particularly when that information is combined with phenotype and expression information for thousands of genes in multiple model organisms? The Phenoscape project invites you to be among the pioneers in opening up this research.

The first release of the Phenoscape Knowledgebase includes over 500K species phenotypes linked to 4,000+ genes from zebrafish, and is currently being extended to capture phenotype data from other vertebrates and linked to phenotype and expression data for other model organisms (including mouse and Xenopus).

We are looking for participants for a small, 3-day workshop, February 8-10 (to be held at the California Academy of Sciences, San Francisco) who are interested in engaging in creative problem-solving directed at this outstanding problem and initiating collaborations. The outcome is expected to be several collaborative projects whose goals would drive the development of the Phenoscape tool set/interface and would present new and creative ways to deepen understanding of phenotypic evolution. Phenoscape aims to support the initial steps in these activities. We are particularly interested in a broad approach to this problem and welcome interest from scientists with backgrounds in computational and systems biology, mathematics, development, genomics, and evolution.

If you are interested, please contact Paula Mabee or Todd Vision.

Phenoscape goes mobile

July 9, 2012

Previous layout of the KB faceted browsing page on the iPhone. Text is tiny and must be zoomed and panned.

The NESCent Informatics group periodically holds “hack days”, one day mini-hackathons where we take a break from our usual schedule and push forward on a specific topic of interest. Most recently, the topic was support for the mobile web. I took a look at the Phenoscape Knowledgebase layout on the iPad and iPhone. In general the site did not adapt well to small screen sizes.

In order to avoid serving different layouts to specific devices, I applied techniques from the Responsive Web Design approach, which uses new functionality from CSS 3 to dynamically adjust the page layout based on the size of the browser window. In the new layout, when the window is small, controls move from the side to the top, allowing both the controls and the content table to use the full screen width.

Using responsive web design, the controls and content become stacked on small screens.

The new layout works across most of the pages on the Knowledgebase site. In general, it is a big improvement on mobile devices. However, there are a few remaining glitches to address, such as controls that appear upon mouse hover: difficult to use on a touchscreen device, where there is no mouse.

Third beta release of Phenoscape Knowledgebase 2.0

February 7, 2011

Phenoscape Knowledgebase 2.0 beta release 3 is now available at This version includes an enhanced publication info interface [example] which displays the original character matrix, as well as a list of taxa including the taxonomic names and museum specimens used in the dataset. Other recent developments in the KB are global term info popups and hierarchical browsing of ontology terms on their info pages [example].

We have also improved our software and data release processes so that the public Knowledgebase can easily keep up with new developments and the latest data updates from our curators. Looking forward, the next major feature to be added to the Knowledgebase is a faceted browsing interface which is currently under development. This interface should help provide an overview of how the data are organized within the various ontologies used in the Knowledgebase.

Matching Phenotypes

December 17, 2010

An important goal for the Phenoscape project is to be able to suggest candidate genes that may have contributed to evolutionary change.  The way that we have proposed to do this is to search for changes in phenotype that appear as the result of mutations in model organisms and also appear as phenotype changes on an evolutionary tree.  There are several challenges in designing this search, apart from simply recognizing similar phenotypes, that we have been working on during the past few months.

The first issue is that we are interested in changes in phenotype, not simply matching phenotypes.  For phenotypes associated with mutants of model organism mutants, it is understood that they vary with respect to the wild type.  For taxa, however, this means looking for taxonomic nodes where variation in a phenotype is observed among the children of the node.  For example, there are nine species within the genus Aspidoras with annotations for the shape of the opercle bone.  Of these, eight exhibit opercle bones with round shape, but the ninth (A. pauciradiatus) is annotated with a triangular opercle.  In contrast, all three annotated species of the related Hoplosternum are annotated with a triangular opercle.  Thus there is detectable variation in opercle shape within the children of Aspidoras, but not within  Hoplosternum – suggesting that change in opercle shape has occurred somewhere among the descendants of  Aspidoras. For our analysis, identifying variation among descendants is important.

Thus, our search for shared variation in phenotypes focuses on matching phenotypes associated with genes with phenotypes of taxa showing variation.  However we are looking for matches at a larger scale than single phenotypes; we are looking for matches across the set of phenotypes affected by a gene or the set of features that have changed among the descendants of a taxonomic node.   We refer to these sets of phenotypes as the ‘phenotypic profile’ of a gene or taxon, following a seminal paper by Washington et al. 2009.  Washington et al. propose four metrics (three based on ‘information content’) to score matches between the sets of phenotypes in a pair of profiles.

In the course of developing the search, we have encountered several important differences in curation approach between ZFIN and Phenoscape.  In some cases tehre are different uses of PATO to model the same phenotype, for example the absence of an entity.  In other cases ZFIN uses a quality ‘abnormal’ that applies to mutants, but not in a taxonomic, comparative sense, which means these phenotypes will be inaccessible to us.  Thus, implementing this search is helping us to better understand our data and our choices in modeling the data and how it interoperates with other ontology-based data.  Such reflection would have been difficult or impossible without the use of ontologies to represent the phenotypes.

Phenotype RCN announced

November 24, 2010

NSF has recently funded a Research Coordination Network for researchers who are interested in searching and comparing phenotypes across species and in developing the tools and methods needed in making this possible  (  The representation of morphology, behavior and other phenotypic features using computational methods such as ontologies and controlled vocabularies is in its infancy.  Integrating phenotypes with data across all levels of the biological hierarchy, however, is possible if standards are co-developed and coordinated.

This RCN envisions building a broad base of community knowledge and resources so as to maximize the research potential of web-based data.  Funding for participation in meetings, presentations and laboratory exchanges for students, postdocs and faculty from ontology and taxonomic domains (initially plants, arthropods, and vertebrates) is available through the RCN (see

We are eager to have you join us!  Please sign up for our participant and mailing lists for further information ( and feel free to contact one of the PIs (Paula Mabee,; Andy Deans,; Eva Huala,; and Suzanna Lewis,