Phenoscape

While working to describe two species of lizardfish (Synodus) with Carole Baldwin at the Smithsonian National Museum of Natural History, she received an email from Paula Mabee asking if she knew or had any students interested in working on the Phenoscape Project. I had realized that with advances in technology and communication, evolutionary biology and all science was headed towards a future of large-scale interdisciplinary collaborations to help address big questions and make tools and data readily available. Therefore, I immediately jumped on the opportunity to work on Phenoscape!

With the support of funding from DeepFin, I started my internship with Phenoscape at the National Evolutionary Synthesis Center (NESCent) in August 2011. My three months here at NESCent have flown by and even though it is my last day, I am just as excited about the project as the day I started! Working with Wasial Dahdul, Peter Midford and Jim Balhoff has enabled me to learn and understand a great deal about databases, collaboration and morphology. Phenoscape has completely changed the way I think about phenotypic characters. Breaking them down into logical statements in Phenex really allows you to understand a character as it fits in the bigger picture. I was able to work with Wasila in forging interdisciplinary ties by contributing to other ontologies and databases, such as PATO and PaleoDB. Additionally, working to assist in the expansion of Phenoscape to incorporate all vertebrates taught me a lot about the origins of vertebrates and the plethora of prehistoric life I did not realize existed- including my new personal favorite prehistoric fish, Jagorina!

NESCent is an amazing place. Being one of the few people here without a higher degree or a long list of publications under their belt, I was initially a little intimidated. However, the informatics group, post-docs and professors have been great and pushed me to participate in seminars and intellectual discussion. This is a stimulating environment that facilitates thinking outside the box and looking at bigger picture issues in evolutionary biology.

I am excited to continue my work on Phenoscape offsite back at the Smithsonian and I hope to contribute throughout my graduate career in Dr. Brian Sidlauskas’s (former NESCentian and Phenoscape tester and contributor) lab at Oregon State University.

Ben Frable
Graduate Student, Oregon State University
Student Researcher, Smithsonian National Museum of Natural History

We seek a postdoctoral researcher in computational biology for Phenoscape.  This person will contribute to two important research strands within the project:

1. Development of computational and statistical methodology for measuring semantic similarity between sets of phenotypes, in order to support searches within extremely large phenotype datasets.
2. Development and testing of methods for automatically generating ontologically based phenotype expressions from structured excerpts of natural language.

The position is based in the informatics group at the National Evolutionary Synthesis Center (NESCent), and will be administered through the University of North Carolina at Chapel Hill (UNC-CH) under the supervision of Hilmar Lapp at NESCent and Dr. Todd Vision at UNC-CH.   The research will be in collaboration with Dr. Chris Mungall at Lawrence Berkeley National Lab and Dr. Hong Cui at the University of Arizona.  The project also includes biologists and bioinformaticists from the University of South Dakota, the University of Chicago, the University of Kansas, in addition to the model organism databases for mouse (MGD), zebrafish (ZFIN), and Xenopus (Xenbase).

Applicants should have a PhD in bioinformatics, computational biology or a related field. Prior experience with machine reasoning using ontologies is strongly preferred. The position is for two years, pending satisfactory performance and availability of funds.  To apply, please provide a cover letter, CV, and contact information for three references.  Inquiries and applications may be sent to Hilmar Lapp at hlapp@nescent.org.  The post is open immediately and will remain open until filled.

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  (http://phenotypercn.org).  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 http://phenotypercn.org/opportunities/.

We are eager to have you join us!  Please sign up for our participant and mailing lists for further information (http://phenotypercn.org/participants/add/) and feel free to contact one of the PIs (Paula Mabee, pmabee@usd.edu; Andy Deans, andy_deans@ncsu.edu; Eva Huala, huala@acoma.stanford.edu; and Suzanna Lewis, selewis@lbl.gov).

Hilmar Lapp gave a great overview today of the ongoing work in the Phenoscape project to 29 participants in the NCBO Webinar series.  This series showcases new projects, technologies and ideas in biomedical ontology, many of which use ontologies for interoperability.  Hilmar presented the biological context (evolution, conservation, development, etc.) into which our work fits, and the challenges involved in representing phenotype.  A videorecording of his talk will be posted in case you missed it.

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.