Computable evolutionary phenotype knowledge: a hands-on workshop

 community, Informatics, Knowledge Base, knowledgebase, Outreach, Software, Workshops  Comments Off on Computable evolutionary phenotype knowledge: a hands-on workshop
Sep 302017
 

Call for Participation:

Computable evolutionary phenotype knowledge: a hands-on workshop

The Phenoscape project is hosting a hands-on workshop on Dec 11-14, 2017, at Duke University in Durham, North Carolina.

Evolutionary phenotype data that is amenable to computational data science, including computation-driven discovery, remains relatively new to science. Therefore use-cases and applications that effectively exploit these new capabilities are only beginning to emerge. If you are interested in discovering, linking to, recombining, or computing with machine-interpretable evolutionary phenotypes, this is the workshop for you!

The event will bring together a diverse group of people to collaboratively design and work hands-on on targets of their interest that take advantage and promote reuse of Phenoscape’s online evolutionary data resources and services. The event is designed as a hands-on unconference-style workshop. Participants will break into subgroups to collaboratively tackle self-selected
work targets.

The full Call for Participation, including motivation and scope, is posted here: https://hackmd.io/s/Sk6Xa7Eq-#

To apply to participate in the event, please fill out the application form by Oct 9, 2017. Travel sponsorship is available but limited, as is space.


Filed under: Informatics, Knowledge Base, Outreach, Workshops Tagged: community, knowledgebase, Software, Workshops
Sep 252014
 

[written by Matt Yoder. Posted by Andy Deans]

Regular RCN attendees Matt Yoder, István Mikó and Andy Deans attended ICIM3 in Berlin, Germany on August 3rd–7th. The congress brought together world leaders in invertebrate morphology for a week of presentations and discussion on the campus of the Humboldt University in Berlin. Logistics were flawless, with ample food and drink to wet interactions (e.g., endless beer and pretzels for the poster session!). The conference was truly a showcase of phenotypes and was fascinating from the standpoint of just seeing examples of life evolving. For those of us interested in semantically describing morphological diversity, the myriad approachs to representing morphology as data was extremely informative and indicative of the challenges we face.

people stand around, talking in a room full of posters

Morphologists talk phenotype, over endless pretzels and beer. Photo by Andy Deans (CC BY 2.0).

In addition to generally absorbing the goings on, Yoder and Deans participated in a eMorphology symposium led by Lars Vogt, one of the PIs of MorphDBase. Deans presented on the state of semantic phenotype representation, with particular attention to its role in taxonomy (Deans ICIM3 slideshow), a follow-up to a presentation and panel discussion from the last ICIM (Deans ICIM2 slideshow). Yoder delivered a talk (http://dx.doi.org/10.6084/m9.figshare.1127970) on behalf of Jim Balhoff et al., on presence/absence inference utilizing Phenoscape KB. Balhoff has written tools that utilize inference to expand the knowledge provided by curators into much larger datasets asserting the presence or absence of anatomical features across taxa. These tools also find logical inconsistencies with curator made statements, and are a great example of a practical approach to computing on phenotypes.

A meeting highlight was the opportunity to see the latest and greatest imaging technologies within a special symposium on advances in microscopy. Speakers highlighted advances in 3D and 4D imaging, with systems capable of generating massive datasets—easily rivaling the big-data world of genomics. Handling these data has become a science itself. It was great to see open-source software and hardware(!) initiatives leading the field in this regard. Stephen Saalfeld’s talk on image alignment was amazing, a presentation similar to that given at ICIM3 is available on Youtube. Pavel Tomancak’s description of light-sheet microscopy using OpenSpim was also inspirational.

non-hexapod pancrustaceans in vials of ethanol

Arthropod phenotypes on display in the halls. Ready access to specimens and hand-blown glass models (see below) catalyzed several discussions about the evolution of form and function in this phylum. Photo by Andy Deans (CC BY 2.0).

Finally, the meeting was flush with opportunities for developing longer term collaborations. The curators of MorphDBase and the recent initiative TaxonWorks spent significant time discussing the possibility of sharing a code-base and thus greatly extending their resources. We hope that this collaboration comes to fruition and that it becomes an important component of “phenotype-handling” in the future.

A special thanks to the Phenotype RCN PIs for supporting, in part, our attendance.

museum case full of boxes that contain glass models of organisms

Glass models of invertebrates, on display at the Humboldt University, in Berlin. Photo by Andy Deans (CC BY 2.0).

 Posted by on September 25, 2014 at 1:04 am

California Dreaming

 Evolution, Knowledge Base, Outreach, Science, Workshops  Comments Off on California Dreaming
Mar 282013
 

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.

clay1postitsspeed_dating2karl

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.


Filed under: Evolution, Knowledge Base, Outreach, Science, Workshops

Junior Biocurator

 Outreach, Training  Comments Off on Junior Biocurator
Sep 112012
 

This summer, with the help of non-profit organization Project Exploration (http://www.projectexploration.org/), we ran the Junior Biocurator program for the first time. This is the ‘outreach’ part of the Phenoscape project. The program content and structure was designed by Paul Sereno, Lauren Conroy, Nicole Ridgwell and myself. The program includes several lectures, covering topics as diverse as biocuration, comparative anatomy and photography techniques. Lectures were given by Lauren Conroy, Erin Fitzgerald, Nicole Ridgwell and myself. Nicole also supervised the day to day activities and labs. In their ‘hands on’ time the students acquired a whole array of impressive new skills, outlined below.

I was a little worried that the Jr Biocurators would find the curriculum to be too demanding and difficult, but the five students – Haley, Kyle, Hope, Michael and Kamal – really enjoyed their time and impressed everybody with their curiosity, enthusiasm and overall performance in the many exercises and other tasks they had to complete. The students learned how to put together vertebrate skeletons, how to organize biological information in an ontology, and how to take high quality photographs of vertebrate bones. They also learned how to manipulate these images in Photoshop, effectively creating publication quality image files. As if that was not enough, towards the end of the program, they learned how to use a laser scanner and visualized the bones in a whole new way. The images they created (photography and scanning) will be used by us – first in Protege and ultimately in the Phenoscape user interface. Our Jr Biocurators were extremely proud when they heard that their work would make a real, tangible contribution to a major NSF funded project.

While we were putting together the curriculum, I suggested we also offer the students opportunities to learn more about university life in general. Nicole took them to the University of Chicago admissions office, were they could ask all their questions, and they also went on a big campus tour and visited the Oriental Institute Museum (which is part of our university). This part of the curriculum was also extremely well received.

Running the program was a lot of work, but it was all worth it, considering that our Jr Biocurators all became good friends (and good young budding scientists!) and were genuinely sad when the program ended. I am looking forward to meeting the next Jr Biocurators in 2013 and am no longer worried about the degree of difficulty of the curriculum.

To find out more about the program and read some of the blog posts our Biocurators wrote visit:

http://www.projectexploration.org/blog/2012/07/18/two-day/

http://www.facebook.com/media/set/?set=a.10151007328856583.416729.91282556582&type=3

http://www.projectexploration.org/blog/2012/08/01/university-tour/

Nizar Ibrahim,

University of Chicago


Filed under: Outreach, Training