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
Jun 102015
 

Visualizing one or more trees/taxonomies with non-trivial number of characters and taxa is a challenge a number of projects is facing. The ETC project organized a workshop with information visualization experts, data providers (trees and characters), and end users to tackle the challenge together.
The meeting was organized by Hong Cui and hosted by Bertram Ludäscher in the National Center for Supercomputing Applications (NCSA), Urbana, IL, in May 11-13. Phenotype RCN participants Matt Yoder, Nico Franz and Martín Ramírez attended the meeting and posed vis challenges. Much of the workshop was devoted to brainstorm on the challenge of representing a large dataset together with some kind of mapping on a tree, and often on two trees simultaneously. This is a familiar challenge for anatomy ontologists, who are trying to represent the interaction of phylogenetic trees, matrices and ontologies:

Right, the level of anatomical data available for different parts of the fin and limb can be visualized for taxa along the fin to limb transition (figure from Dececchi et al. in press 2015, Systematic Biology, doi: 10.1093/sysbio/syv031). Left, a phylogeny of spiders colored according to anatomical complexity, derived from the ontology (figure from Ramírez & Michalik 2014, doi: 10.1111/cla.12075).

Right, the level of anatomical data available for different parts of the fin and limb can be visualized for taxa along the fin to limb transition (figure from Dececchi et al. in press 2015, Systematic Biology, doi: 10.1093/sysbio/syv031). Left, a phylogeny of spiders colored according to anatomical complexity, derived from the ontology (figure from Ramírez & Michalik 2014, doi: 10.1111/cla.12075).


The beautiful and clever examples presented by the vis experts were inspiring. How these gorgeous examples can help us represent or complex data in intuitive visualizations? Filters, sort controls, heat maps, zoom panes, collapsing, expanding, and more tools – all made in us two effects: Make some of our challenges look feasible, and refine our vague ideas into more precise challenges.
Hierarchical Circular Layouts, or HCL (Dang, Murray, and Forbes 2015), uses circular layouts on a hierarchical structure.

Hierarchical Circular Layouts, or HCL (Dang, Murray, and Forbes 2015), uses circular layouts on a hierarchical structure.


PathwayMatrix: Visualizing Binary Relationships between Proteins in Biological Pathways (Dang, Murray, and Forbes, 2015). PathwayMatrix can be used not only for biological pathway visualization, but also for character and taxon data.  See: http://biovis.net/year/2015/papers/pathwaymatrix-visualizing-binary-relationships-between-proteins-biological-pathways

PathwayMatrix: Visualizing Binary Relationships between Proteins in Biological Pathways (Dang, Murray, and Forbes, 2015). PathwayMatrix can be used not only for biological pathway visualization, but also for character and taxon data. See: http://biovis.net/year/2015/papers/pathwaymatrix-visualizing-binary-relationships-between-proteins-biological-pathways


The ETC project will implement a few promising techniques as part of ETC toolkit to invite comments and suggestions from broader communities. Stay tuned, and crunch your data into nice visualizations!
(post by Martin Ramírez)

May 272015
 

How do phenotypic data factor into the issues relating to integrating complex data? Three frequent phenotypers (Ramona Walls, Chris Mungall, and Maryann Martone) were supported by this RCN to participate with sixteen others in an ‘Integrating Complex Data’ workshop organized by the American Institute for Biological Sciences (AIBS) with NSF funding (EF-1450894), on March 30-31 at the Hyatt Regency Crystal City in Arlington, Virginia. The workshop was co-chaired by Paula Mabee, Corinna Gries, and Robert Gropp, facilitated by Kathy Joyce, and observed by various program officers and staff from NSF.

Complex data integration, defined as ‘bringing together data from two or more fields’, is required to address many fundamental scientific questions as well as understanding how to mitigate the challenges facing the planet. Participants (whose research interests ranged from genetics, genomics, metagenomics, systematics, taxonomy, and ecology, to bio/eco-informatics and cyberinfrastructure development) initially discussed specific use cases in which complex data integration was required. They then focused on the barriers that impede integration, recognizing domain silos as major problem at this scale. They illustrated with examples that data discovery and integration are currently hampered by lack of common standards, including those for IDs, representation, ontologies, data formats, data collection, and communication protocols.  The usefulness of ontologies in connecting phenotypic data to other data types across domains was described by Phenotype RCN participants.

Suggestions and next steps required to achieve better data integration were the focus of the second day of the workshop. Community coalescence around shared standards, rather than more standards, was considered key.  Participants advocated for interagency discussions about how to provide linkages across their data systems, thus making data from all sites more readily discoverable and distributing the financial burden.  Participants further recognized that the technical expertise required for complex data integration is high; they promoted cross-training in informatics for graduate students and a higher level of specialist ‘data scientist’ training.  They also felt that funding mechanisms to enable scientists to employ technical specialists for specific data integration tasks would enable complex data integration.  Particularly at this juncture, where cross-domain data analysis is required to address societal problems, participants stressed that it is important to try to solve the immediate problems while working toward long-range solutions.  A full report from this workshop is in preparation and a link will be posted when it is available.

 Posted by on May 27, 2015 at 11:55 pm
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
Mar 072014
 

Landscape at Catalina State Park, near Biosphere 2 in Arizona. A great place to observe arthropod phenotypes! Photo by Andy Deans (CC BY 2.0)

The Arthropod Working Group of the Phenotype RCN stayed an extra day at Biosphere 2, after the annual group summit meeting, so that we could take stock of our own progress and discuss future interactions. We’re a heterogeneous crowd, each working on a different taxon (non-Hexapod PancrustaceaAraneae, Hymenoptera, Coleoptera), often on different systems (integument, circulatory, neuroanatomy, etc.), and with different motivations (taxonomy, gene expression, evolutionary questions. etc.). Our annual meeting is a chance to catch each other up on progress in our systems but also to discuss limitations and possible solutions. We’re also charged with developing a common anatomy ontology that bridges disparate lineages, some of which are represented in existing anatomy ontologies (e.g., see Costa et al. 2013 and Yoder et al. 2010). In attendance this year:  (L to R in photo below): Lars Vogt (Universität Bonn, Germany), Peter Grobe (Stiftung Zoologisches Forschungsmuseum Alexander Koenig Bonn, Germany), István Mikó (Penn State, USA), Stefan Richter (Rostock University, Germany), Martín Ramírez (Museo Argentino de Ciencias Naturales), Matt Yoder (Speciesfile, University of Illinois, USA), and, behind the camera, Andy Deans (Penn State, USA).

Rogues gallery of arthropod fanatics. Photo by Andy Deans (CC BY 2.0)

Wisely, we mostly steered clear of anatomical discussions—what’s this part here, and how do we define it?—which freed us up to talk about tools, progress, future proposals, and other news. That is, we had fewer tangents (and shouting) and more constructive conversations about collaboration. We captured most of the dialog in a Google doc (needs synthesis, for sure, and likely doesn’t capture ALL of our discussions, especially complex ideas articulated on the easel), but here are a few quick hits:

  • The MorphDBase project (Grobe & Vogt) recently received funding for further development, and there is now a lot of potential to integrate ontologies. We discussed ideas for annotations, workflows, and how our projects could interact more with this resource.
  • We talked about anatomical complexity more generally, especially in the context of essentialistic classes vs. those classes that are not so easy to define (cluster class). Our aim should be to develop user-friendly tools that make it easier to employ ontologies (i.e., that don’t require morphologists and taxonomists to overthink annotations or burden them with excessive evidence gathering).
  • The spider ontology (SPD) is being used in an ongoing effort to extract characters from the literature (Ramírez). The group discussed tools that could help facilitate this process (e.g., CharaParser) and continued development of the SPD (especially Web-based tools, like mx, that facilitate rapid, community development of ontologies).
  • The TaxonWorks project (Yoder) is looking for feedback regarding ontology tools. Should they integrate an ontology builder, à la mx? Perhaps one that interacts easily with Protégé (and the reasoners therein)? What about templates for certain kinds of taxonomic and phylogenetic characters? The user would plug in the anatomy and the phenotype, and TaxonWorks would write the semantics.
  • Of course there was also some groupthink about how to make progress towards our mandate: to build a common anatomy ontology for arthropods. More on that later, but the consensus is that we should develop system-based pieces of it separately, forging links between them later. This ontology cloud would be synthesized in a future manuscript.

It was an intense, 12-hour, pizza-fueled, beverage-driven marathon in an inspiring location. After what we universally felt was forward progress, though, we’re excited for the next round! Perhaps in Argentina, Martín …?

As a side note, it was a bit cool in Arizona in February, for most arthropods anyway, but I did see two very cool critters: a Scolopendra centipede, which was way to fast for me to photograph, and a Hadrurus scorpion, which I forgot entirely to photograph. So here’s a great image from Flickr that illustrates them both:

A Hadrurus scorpion consumes a Scolopendra centipede at San Tan Regional Park (somewhat close to Biosphere 2). Photo by Jasper Nance (CC BY-NC-ND 2.0).

 Posted by on March 7, 2014 at 1:54 pm
Feb 212014
 

Dear all,

We are pleased to announce a Uberon workshop, satellite of the Biocuration2014 meeting, to be held in Toronto, Canada, on the 5th and 6th April 2014.

Uberon is an integrated cross-species anatomy ontology, representing a variety of entities classified according to traditional anatomical criteria such as structure, function, and developmental lineage. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference, allowing integration of model organism, human, and comparative morphology data.

This workshop will be user-oriented, and will be devoted to introducing and training participants to the use of Uberon. For more information and schedule, please see the workshop website:
http://edu.isb-sib.ch/course/view.php?id=167

Attendance is limited, and places will be allocated on a first come, first served basis. The estimated registration fee is C$200. The registration page is available at:
http://www.isb-sib.ch/edu/Registration/SIB_courses.php?id=234

For more information about the Biocuration conference, please see:
http://biocuration2014.events.oicr.on.ca/biocuration

Looking forward to meeting you in Toronto,

The organizers: Chris Mungall, Melissa Haendel, and Frederic Bastian

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

ICBO 2011

 Anatomy Ontology, Conference, Conferences, Workshops  Comments Off on ICBO 2011
Aug 122011
 

Jim Balhoff and I recently attended the International Conference on Biomedical Ontology (ICBO) held 26-30 July in Buffalo, NY. The conference focused on the use and development of ontologies in the biological and biomedical domains. Of particular interest to Phenoscape were the workshops and tutorials held during the two days before the main conference. Topics included ontology integration, Common Logic, ontology development tools, and using OBO and OWL formats for ontology development and reasoning.

We presented talks at the Facilitating Anatomy Ontology Interoperability workshop. Jim’s talk was on representing taxa as individuals in OWL, an alternative to the common representation of taxa as classes, which facilitates annotation of phenotypic data involving polymorphism and evolutionary reversals.  I presented a lightning talk on the anatomy ontology synchronization requirements for linking evolutionary and model organism phenotypes.  Other presentations from the workshop are available here. We also presented a poster describing the reasoning used in the Phenoscape Knowledgebase.

The main conference included interesting talks on a broad range of topics including the application of ontologies to proteins, diseases, biological mechanisms, and electronic health records. Presentations can be downloaded here.


Filed under: Conferences, Ontology, Uncategorized, Workshops Tagged: Anatomy Ontology, Conference, Ontology, Workshops