Apr 042016
 
a group of people smiling and standing in front of sculpture at Biosphere 2

Participants at the fifth and final summit meeting of the Phenotype RCN. Photo by Andy Deans (CC BY 2.0).

The Phenotype Research Coordination Network hosted its fifth and final summit meeting at the end of February at Biosphere 2, with 66(!) people in attendance. The focus was on data integration, and we were fortunate to have the FuturePhy project join us. Our program was packed, with a mix of panels, talks (we have links to slideshows), and breakout sessions that focused on proposal ideas. One frequent topic for discussion was the need to keep this network going, as there remains a clear need for outreach and mechanisms that foster collaborations on phenotype data. Several working groups also focused on large, international collaborations that would make phenotype tools, like ontologies, and phenotype data more accessible and sustainable—imagine something like GenBank but for phenotypes.

Another successful and compelling component of this meeting was the inclusion of many early career researchers and graduate students, who formed a cohesive network themselves. Their discussions and reports to the larger group identified broad needs and informed our collective ideas for future outreach directions.

The Phenotype RCN has been productive, impactful, and and incredibly rewarding. We thank all who have been involved, especially meeting participants and our advisory board. While this phase—i.e., our original NSF-funded schedule—may be winding down, the network is robust and active. Stay tuned for further developments!

 Posted by on April 4, 2016 at 4:45 pm
Apr 012013
 

The Phenotype RCN has the means to facilitate collaborations among network participants (2 per year at $1500 each). Students, postdocs, faculty, or small working groups can apply for travel funds to support collaborations related to one or more of our aims:

  • Developing anatomical reference ontologies.
  • Aligning and synchronizing anatomy ontologies using homology and other similarity.
  • Defining anatomy ontology development best practices and standards.
  • Reaching out to ancillary phenotype groups to share with them common concepts and practices.
  • Educating the community about the methods for developing ontologies and their importance and utility in research.

Already the RCN has contributed funding and support for collaborations relating to neural crest representation, head and neck musculo-skeletal anatomy ontology development, and the chick anatomy ontology.

Do you have a great idea for a research exchange? Consider submitting an application. Any questions about opportunities offered by the Phenotype RCN may be directed to Paula Mabee (Paula.Mabee@usd.edu), Eva Huala (huala@acoma.stanford.edu), or Andy Deans (adeans@gmail.com).

Mar 192012
 


The second annual summit meeting of the Phenotype RCN was held February 23-25, 2012 at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina.  It included 61 participants, 12 of whom were from countries outside the USA, including Canada, France, Germany, UK, Switzerland, and Venezuela.  NESCent generously opened its doors to us once again, and our big and happy group made use of the entire facility including the large auditorium downstairs and all the breakout rooms and conversation areas.

We focused this meeting on the research and reasoning applications of phenotype ontologies, how to build them, and how to annotate phenotypic data.  Please see the slides from the excellent presentations from the meeting.  The desired outcome of the workshop was that people would take something tangible home with them: an idea, a method, or a collaboration that would help them with existing or new research.  Anticipating that almost half of the people attending were new to ontologies, we designed two hands-on exercises for the first day to give participants experience with ontology building (using Vue) and annotation (using a Phenote interface that was customized for the RCN meeting).  We met in small (4-5 person) groups and used images of dogs and humans to serve as a focus for the kinds of issues that arise, e.g., ‘What is a snout?’ and ‘Can the same anatomy ontology be used for dogs and humans?’.  On the second day of the workshop we focused on the kinds of discoveries that could be made with phenotypic data made computable with ontologies.  We broke out in challenge-centered groups (e.g., how to express complex and quantitative phenotypes?) as well as along taxonomic lines (plants, vertebrates, arthropods and now poriferans and fungi).  As documented in the working group reports, critical directions for new research were identified, and several collaborating groups were formed to moved ahead with prototyping or otherwise investigating opportunities for this work.

The RCN PIs (me, Eva, Andy, and Suzi) felt that this meeting was particularly successful, and that there was a palpable sense of momentum.  Participants departed with new colleagues and collaborations, and new ideas of how to interact effectively with ontologies and how using them can advance their science.  We are looking forward to our next chance to meet!  Let me know if you have any questions about this workshop or have interest in meeting with us in the future.  Please also consider applying for the new Anatomy Ontology course this summer.

Paula (pmabee@usd.ed)

 Posted by on March 19, 2012 at 3:09 pm
Dec 232011
 

We’ve been asked to potentially submit a phenotype workshop proposal for ICBO 201: http://www.kr-med.org/icbofois2012/

Submission requirements are quite straightforward (see http://kr-med.org/icbofois2012/icbows.htm, roughly a short abstract of the proposal and some explanations about its importance). I suspect that many of us, especially our European colleagues, would be interested in this topic will be attending ICBO in Graz at the end of July, and it may be far away enough from our Annual meeting to allow for some sort of follow-up. Submissions are due Dec 31st, so there isn’t very much time.

Alternately, there is the option for a 2hr informal meeting at ICBO, on July 21st (the first evening, between the 2 workshop days) from 6 to 8pm. The ICBO committee will review proposals and assign rooms space permitting, on a first come first serve basis. Deadline to submit an informal meeting proposal is April 15th.

Thoughts?

Happy holidays,

Melissa Haendel

Welcome to the Phenotype Ontology RCN!

 Announcements  Comments Off on Welcome to the Phenotype Ontology RCN!
Nov 232010
 

The Phenotype Ontology Research Coordination Network (RCN) was funded by NSF to establish a network of scientists who are interested in comparing phenotypes across species and in developing the tools and methods needed in making this possible.  The representation of morphology, behavior, and other phenotypic traits using ontologies 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 community that because of its domain expertise, sets the standards and best practices for the development of phenotype ontologies and a vision for their utility.  Please sign up as a participant and blog subscriber for further information and feel free to contact one of the PIs.  We look forward to this opportunity!

Paula Mabee, Andy Deans, Eva Huala, and Suzanna Lewis