Andy Deans

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
Jan 202016
 

NBO-ABO Merger Workshop Smithsonian, DC 25Oct15-620

This post is a followup to our previous post about integrating the Animal Behavior Ontology (ABO) and the NeuroBehavior Ontology (NBO). This covers the second workshop, a conference call held in early December and the poster one of us (PM) presented at SICB 2016 on January 6.

With additional funding from the Phenotype RCN, on October 24–25, 2015 we held the second workshop to begin the process of merging the ABO and the NBO based on the first workshop’s recommendations. This workshop was held at the Smithsonian Museum in Washington. Attendees included Elissa Chesler, George Gkoutos, David Osumi-Sutherland, and Reid Rumelt (Cornell undergraduate working on media tagging-based research); and workshop organizers Anne Clark, Sue Margulis, Peter Midford, Cynthia Parr, and Katja Schultz (our Local Host). Melissa Haendel participated remotely.

We made good progress getting started on a use-case based paper for applications of a behavior ontology. We also have a real home for the ABO – we deposited the OWL rendering Peter Midford generated in 2006 as the initial commit in a GitHub repository (note that this is the same repository where NBO is maintained).

We started the process of merging the ABO and NBO, our central objective. One of ABO’s strengths is a clear division between observable behavior (acts, events, and processes) and functional interpretations (for example, running vs. fleeing from a predator). The NBO is organized rather differently and we would like the division in ABO to appear at least somewhere in NBO. NBO contains a sizable number of terms not relevant to the behavioral ecology community, just as ABO has terms that are not of current use to the model organism community. We identified a number of stakeholder projects who would be affected and could potentially benefit by the merger, including Virtual Fly Brain, Rat Genome Database, and the International Mouse Phenotype consortium and probably others.

Since the workshop we have had several conference calls with the NBO developers (George Gkoutos and Robert Hoehndorf) to refine the concerns of other stakeholders. Discussion made it clear that NBO is focussed on behavior phenotypes, rather than behavior processes. However, there was some interest in incorporating the ABO functional terms. The thought was that the remaining ABO terms (those referring to events, acts, and processes) should wind up in the Gene Ontology (GO). Several of us are working on the process of merging the functional terms into NBO, and separately, looking through the existing process terms in the GO. We may want to propose a behavior process ontology, at least as a parking place for terms that eventually are added to the GO.

Finally, we presented a poster at the SICB 2016 meeting in Portland, OR on January 6. We will continue to use opportunities like this to discuss the process and implications of this merger with the broader animal behavior and neuroscience communities. We are developing a set of case studies and have outlined a followup paper to highlight both the applications of the outcome of the merging process and lessons learned during that process.

 Posted by on January 20, 2016 at 4:40 pm
Dec 302015
 

Biosphere 2, the site of the final Phenotype RCN Summit meeting (February 2016). Photo (CC BY-NC 2.0) by pinkgranite. See original at https://flic.kr/p/52bMzk.

The Fifth Annual Summit of the Phenotype Ontology Research Coordination Network will be held at the University of Arizona’s Biosphere 2, about 40 miles north of Tucson, AZ, from February 26-28, 2016 (Friday through Sunday noon).

The theme of this meeting will be ‘Complex data integration with phenotypes’ with a focus on the integration of phenotype data with other data sets. We will summarize where our phenotype community is at with respect to integration with other data types, and we will highlight active projects. We will be looking to the future — what projects should be priorities for the future? Joining us this year will be folks from the newly funded ‘FuturePhy’ (futurephy.org), who are interested in how to integrate multiple data types, including phenotype, with phylogenetic trees.

We estimate that the costs for this meeting (transportation to meeting from airport, lodging, food) will be approximately $500, though we will be able to cover expenses for a small number of participants, particularly students and postdocs who have specific interests in using phenotypic data associated with environment in their research. Please contact one of us if you are interested in attending. It should be agreat meeting!

Paula Mabee; pmabee@usd.edu
Eva Huala; huala@acoma.stanford.edu
Andy Deans; adeans@psu.edu
Suzanna Lewis; suzi@berkeleybop.org

The Phenotype Ontology RCN (http://phenotypercn.org) was funded by the U.S. NSF to establish a network of scientists who are interested incomparing phenotypes across species and in developing the tools and methods needed to enable comparisons. In contrast to the many well-established efforts in the molecular community, the representation of phenotypic traits using ontologies is in its infancy. Phenotype ontologies, however, have the potential to integrate these data across all levels of the biological hierarchy and to the environment. This RCN is building a community that, because of its expertise, fosters communications across disciplines to enable co-development of interoperable community standards and best practices for phenotype.

 Posted by on December 30, 2015 at 1:50 am
Dec 212015
 

The following post is from Peter Midford. – Andy Deans

As you may recall, at a Spring 2013 meeting of the Phenotype RCN in Durham, NC, the Behavior Breakout group discussed the existence of multiple behavioral ontologies, including the gaps in existing ontologies (such as the Neuro Behavior Ontology, or NBO) that preclude their widespread use in behavioral ecology and other sub-disciplines in animal behavior. The group felt it could be possible to merge two existing behavioral ontologies – the NBO, developed to serve studies of animal models of human behavioral dysfunction, and the Animal Behavior Ontology or ABO, developed to serve the field of comparative animal behavior, including behavioral ecology and other sub-disciplines. If successful, the merger would facilitate the broader integration of behavioral studies: applied with basic, model organism with comparative investigations, mechanistic with evolutionary, and human with non-human animal questions. At the same time, it would also need to continue to serve the specialized needs of subfields.

In late summer 2014, a small group of animal behaviorists who were present at the 2013 meeting in Durham (Anne Clark, Sue Margulis, Peter Midford, Cynthia Parr) received NSF funding to hold two workshops to accomplish these goals.

Our first workshop, held August 2014 at Princeton University, convened over a dozen animal behaviorists with a broad range of expertise in comparative behavior to develop specific recommendations on how to integrate the basic terms and concepts of the two ontologies. Key outcomes included a list of proposed changes in parent-child relations in the NBO to emphasize function, and ABO term definition improvements that together could serve as the basis of integrating the two ontologies.

Our second workshop, supported in part by additional funding from the Phenotype RCN, was held at the Smithsonian’s National Museum of Natural History, Washington, DC, on October 24-25, 2015. Its specific goal was to start the process of merging the ABO and the NBO based on the first workshop’s recommendations. Attendees in addition to the four organizers, were our local host Katja Schultz (Encyclopedia of Life), Elissa Chesler (The Jackson Laboratory), George Gkoutos (NBO developer, University of Birmingham), David Osumi-Sutherland (European Bioinformatics Institute, Virtual Fly Brain), Melissa Haendel (Oregon Health and Science University), and Reid Rumelt (Cornell University undergraduate working with Macaulay Library and Encyclopedia of Life).

The workshop began with presentations about the histories of NBO and ABO. NBO had its roots in a phenotype vocabulary supporting the EUMORPHIA project (see http://empress.har.mrc.ac.uk/ and http://www.europhenome.org/). Behavior terms were initially included in the Gene Ontology, but also maps to phenotype ontologies, such as the Mammalian Phenotype ontology (MP) and Human Phenotype Ontology so as enable the integration of data. The Neuro Behavior Ontology was created to concentrate effort specifically on behavior.

Slide03

ABO was one of the first accomplishments of the EthoSource project1, begun with an NSF-sponsored workshop in 2000 with the goal of developing integrated online resources for the discipline of Animal Behavior. Two NSF- sponsored Ontology Workshops followed in 2004-2005, at which an international group of animal behaviorists developed a basic metadata standard for the discipline, the ABO. The primary use of the ABO subsequent to 2005 was indexing an online ethogram repository, EthoSearch.org.

In our second blog post, we will summarize the progress we made in the October workshop, and outline our next steps.

1Martins, E. P. 2004. EthoSource: Storing, Sharing, and Combining Behavioral Data. BioScience 54 (10): 886. doi:10.1641/0006-3568(2004)054[0886:ESSACB]2.0.CO;2

 Posted by on December 21, 2015 at 3:49 pm
Dec 182015
 

The following post is from Anne Thessen, who originally published this news on her blog, The Data Detektiv. – Andy Deans

One of the fundamental goals of biology is understanding the interactions of environment and phenotype, but this is a surprisingly difficult topic to study – not because of the concepts, but because of the data. Observations about environment and phenotype occur in separate data sets and the terms used are far too idiosyncratic for automated integration. Several biological domains, including conservation and phylogenetics could be advanced if these two data types could be easily merged on a large scale.

I led a recent paper, published in PeerJ, which suggests that the use of ontologies to standardize and link data about phenotypes and environments can enable scientific breakthroughs by increasing the scale and flexibility of research. This paper was a product of a workshop facilitated by the Phenotype RCN and supported by the National Science Foundation. My co-authors and I give several domain-specific use cases describing how an ontology can help advance science in four biological sciences. We then discuss the challenges to be addressed, present some proof-of-concept analyses, and discuss existing ontologies. The summary contains three suggestions for increasing interoperability between phenotype and environment data.

graphical illustration of the paper described in this blog

Graphical abstract for Thessen et al. (2015) DOI: 10.7717/peerj.1470. Click to enlarge.

We hope this paper provides you with an overview of the landscape of ontologies available for integrating environmental data, and inspires you to use them in relation to your own data. For more information about ontologies and semantics, a good first read is Semantic Web for the Working Ontologist by Dean Allemang and Jim Hendler.

 Posted by on December 18, 2015 at 2:27 am
Jul 272015
 
prickly plant leaf

Succulent plant with interesting adaptive phenotypes. Photo taken at the Rancho Santa Ana Botanic Garden (RSABG) by Manicosity (CC BY-ND 2.0). Click for original.

Supported by a Phenotype RCN collaboration grant, Grant Godden and Pier Luigi Buttigieg met during May 2015 at the Rancho Santa Ana Botanic Garden (RSABG) in Claremont, CA, with the aim of enhancing the ontological representation of plant environments. Grant and Pier processed label data from more than one million plant specimen records hosted by iDigBio, using a combination of natural language processing and text-mining techniques to identify well-represented terms and phrases in “habitat” descriptions. Their interactions with RSABG collections staff, whose active work with specimen digitization and insights into the creation of records that populate repositories like iDigBio, greatly enhanced the project and helped create a workable corpus. The preliminary results of the analyses were immediately informative, revealing gaps in the current coverage of the Environment Ontology (ENVO; Buttigieg et al., 2013).

Further work is planned to refine their computational pipeline and corpus, and to extend ENVO’s coverage of environments which the botanical community frequently sample. A brief publication reporting the process, findings, and results is in preparation.

GG is affiliated with the Rancho Santa Ana Botanic Garden, Claremont, CA, USA. PLB is affiliated with the Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany.

 Posted by on July 27, 2015 at 5:33 pm
Jan 092015
 
journal.pbio.1002033.g001

Figure assembled by Anya Broverman-Wray (CC BY 2.0) doi: 10.1371/journal.pbio.1002033.g001

In case you missed it, our latest Phenotype RCN publication came out this week in PLoS Biology. In this perspective we argue for more investment in the infrastructure needed to make phenotypes more accessible. Check it out!

Abstract.—Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today’s data barriers and facilitate analytical reproducibility.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Helen Parkinson, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee PM. (2015) Finding our way through phenotypes. PLoS Biology 13(1): e1002033. DOI: 10.1371/journal.pbio.1002033

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
Jun 102014
 

Calling all Phenotype RCNer’s and anyone else who works with phenotype data – We want your name on a manuscript supporting a computable phenotypes future! (If you read and agree of course.)

Over the past four years of sponsoring meetings, courses, and exchanges, we have, with your help and participation, developed a comprehensive understanding of where the phenotype community is at, what is needed for integration of phenotypes with other data, and a vision of the science that could be achieved with this integration. In this article, we attempt to educate researchers, granting agencies, and policy makers on the current ‘non-computable’ state of phenotypic data across various life science domains, and we try to motivate them to use, develop, and advocate for semantic methods. Because of the relevance of this work to most areas of biological sciences and because it relates specifically to creating interdisciplinary knowledge—and especially because it is open access—PLoS Biology is our target journal.

  1. The link to manuscript is here: http://bit.ly/PhenotypeMS (Google doc). And a Word version (.docx) with line numbers is available if you prefer.
  2. The form to add your comments, suggestions, references, and especially your author information is here: http://bit.ly/PhenotypeComments

Please respond by 18 June 2014 (next Wednesday). We will post updates here on our blog.

‘Branching’ phenotypes are not easily recovered from free text (far right column), the format in which most organismal phenotypes are recorded. (top row) Bee setae are usually modified in a way that presumably facilitates pollen collection, a €153 billion ecosystem service. This relatively simple phenotype has been described in myriad ways. Photo of bumble bee covered in pollen by Thomas Bresson (source). Photo of seta interacting with pollen grain by István Mikó (source). (middle row) Plant trichomes take on many forms and likewise are described using many lexicons. Photo of Arabidopsis plants covered in hair-like structures (trichomes) by BlueRidgeKitties (source). Scanning electron micrograph of Arabidopsis trichome by Heiti Paves (source). (bottom) In zebrafish larvae, angiogenesis starts with vessels branching to form a network (right image) that is referred in disparate ways. Zebrafish embryo photo by MichianaSTEM (source). Zebrafish blood vessels image is Figure 5A from Alvarez et al. 2009.

 Posted by on June 10, 2014 at 2:46 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