Andy Deans

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
Jan 152014
 

[posted on behalf of István Mikó, Penn State University]

bat fly (Diptera: Nycteribiidae)

A bat fly (Diptera: Nycteribiidae) poses for the camera. It’s barely recognizable as a relative of the familiar Drosophila melanogaster (Diptera: Drosophilidae) and is radically different from the fish tongue-eating arthropod in the photo below. This photo by Gilles San Martin (CC BY-SA 2.0).

The Phenotype RCN Arthropod working group has focused mostly on the development and characterization of the Common Arthropod Anatomy Ontology (CAAO). Despite difficulties defining basic classes due to the immense differences in basic anatomical concepts—there are, after all, more than a million known species of arthropods, with almost as many different forms (see photos above and below)—we made progress in the development of certain portions of CAAO. During 2013 the group established the basis of classes and relationships referring anatomical structures of the arthropod the integument. Establishing this system is especially crucial for disciplines targeting world species diversity, such as arthropod taxonomy and phylogenetics, where more than 90% of the applied characters are related to the outer layer of the integument, the cuticle. Efforts have also been made on the development of the arthropod nervous system portion by the adoption of the relatively recently published relation system by Richter et al. (2010).
The development of CAAO is ongoing, but the focus of the working group has shifted a bit towards the establishment of outreach strategies for the better utilization of available ontologies by the domain experts and to establish tighter collaborations between research group members. We’re especially interested in seeding research that will become the basis new funding. The main subjects of this new directions are:

  1. Cooperation between working group members who develop tools that enhance ontology development and usage for domain expert communities [e.g., mx (Yoder 2014) and Morph·D·Base (Vogt and Grobe 2010)].
  2. Making more widely accessible and understandable the ideas developed by individual working group members on applications of ontologies to different areas of arthropod research [e.g. ontology based measure of structural complexity for phylogenies (Ramirez 2013); demarcating and differentiating basic categories of anatomical entities (Vogt 2010) and application of semantic models in species descriptions (Balhoff et al. 2013)].
  3. To define the role and place of homology concepts in arthropod ontologies [e.g. Szucsich and Wirkner 2007, Franz 2013].

During 2013 some members of the Arthropod-working group were able to meet during two Arthropod specific meetings organized in Germany: Willi Hennig Society meeting in Rostock August 3rd-7th and the 6th Dresden Meeting on Insect Phylogeny in Dresden September 27-29. Although it was possible at these meetings to start cooperation on the above mentioned areas and outline future directions of the working group, it was also accepted that further meetings with more participants of the working group is needed in terms of establishing the planned collaborations. The annual RCN summit meeting on 21-23 February 2014 will be attended by most of the key personnels and hopefully help the working group to assure a workflow to reach the new directions.

Fish tongue-eating isopod (Isopoda: Cymothoidae), with radically different anatomy and phenotypes than the bat fly above. Photo by Andy Heyward (CC BY-NC-SA 2.0).

References

  • Balhoff J, Mikó I, Yoder M, Mullins P, Deans AR (2013) A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62 (5): 639–659 doi: 10.1093/sysbio/syt028.
  • Franz N (2013) Anatomy of cladistic analysis. Cladistics 2013: 1–28 doi: 10.1111/cla.12042
  • Ramirez (2013) An ontology-based measure of structural complexity for phylogenies. XXXII Meeting of the Willi Hennig Society. August 2013.
  • Richter S, Roesel R, Purschke G, Schmidt-Rhaesa A, Scholtz G, Stach T, Vogt L, Andreas W, Brenneis G, Döring C, Faller S, Fritsch M, Grobe P, Heuer CM, Kaul S, Møller OS, Müller CH, Rieger V, Rothe BH, Stegner ME, Harzsch S (2010) Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Frontiers in Zoology 7:1-49. doi: 10.1186/1742-9994-7-29
  • Szucsich MU, Wirkner C (2007) Homology: a synthetic concept of evolutionary robustness of patterns. Zoologica Scripta 36: 281–289. doi: 10.1111/j.1463-6409.2007.00275.x
  • Yoder MJ (2014) “mx” Web-based content management system for biodiversity informatics. http://mx.phenomix.org
  • Vogt L (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11: 289. doi: 10.1186/1471-2105-11-289
  • Vogt L. and Grobe P (2010) Morph·D·Base – Eine online Datenbank für morphologische Daten und Metadaten. GfBS Newsletter 24: 29–34. https://www.morphdbase.de/
Mar 012013
 

 

We’re looking for a few good interns! Photo by Gilles San Martin. (CC BY-SA 2.0)

The Frost Entomological Museum at Penn State seeks undergraduate summer (2013) interns to assist with projects related to insect phenotype data, especially in the context of systematics and evolution. Interns will be exposed to a broad array of biodiversity informatics tools, including ontologies, and will learn aspects of specimen collection, handling, and curation. Applications are due March 20, 2013. More information is available at http://bit.ly/FrostInterns

Nov 202012
 

Asilomar State Beach, Monterey, California, USA. The beach served as our chairs, and the rocks were our whiteboard.

We had a short but highly successful meeting a couple weeks ago, at the Asilomar State Beach conference center in beautiful Monterey, California. Our working group, the AAO, met in parallel with the vertebrate anatomy (with a twist of anthropology), plant anatomy, sponge morphology, and informatics working groups, which allowed for a few useful group exchanges and productive collaboration. (And the setting was difficult to beat! See above.) The AAO set several ambitious goals for this meeting, and we made substantial progress towards a first draft of a common Arthropod Anatomy Ontology. Arthropod group accomplishments from this meeting include:

  1. We moved closer to a general common understanding of how we need to build a broadly useful common arthropod anatomy ontology. It can be difficult to reach consensus and understand through Skype and email. The opportunity for a face-to-face was invaluable for our group as we move forward in this effort, especially since our group includes experts from multiple disciplines (primarily genomics, comparative morphology, and systematics) and is prone to unintentionally talking past one another.
  2. We moved closer to having a shared environment to view, search, and safely edit a common ontology with integrated OWL reasoning. We had been developing two ontologies in parallel, one in Protégé and one in mx, and one goal of this working group meeting was to reconcile those ontologies and move to a single mechanism for ontology development. We’ll be moving forward with an extended version of mx (developed over the next several months, hopefully) that includes a continuous integration and testing environment and which will automate error checking and feed back inferred classifications to mx so that they are visible for viewing. Ideally this environment will be extended to allow queries.
  3. We made some headway towards recruiting more experts and raising awareness of our effort. We have a short list of other experts to target for face-to-face meetings and ideas for how to bring this project to potential consumers through meeting talks and/or symposia. Stay tuned for more details!
  4. First draft definitions for general classes of arthropod external anatomy and a first attempt at OWL formalization for them (our biggest accomplishment). We spent a lot of time on cuticular classes (e.g., sclerite, conjunctiva) and articulations, including the various parts of articulations—structures we’d call condyles, fossae, etc. Some classes were relatively uncontroversial, for example articular surface: A sclerite surface that makes movable direct contact with another articular surface, with the properties is_a sclerite surface and contacts articular surface. Other classes were much more challenging, and our discussion often veered into the term/class danger zone. ‘Joint’ was especially troublesome. See for example the ‘wing joint’ of pterygote insects, which is a highly complex anatomical entity (image below). Another controversial (reactive? radioactive?) class was ‘area’, from the Hymenoptera Anatomy Ontology (HAO): An anatomical structure that is delimited by material or immaterial anatomical entities. Is this class useful for Arthropoda (or even Hymenoptera)?

Proximal area of a sawfly forewing, where the wing meets the thorax. This is a highly complex region of the body, chock-o-block with sclerites, conjunctiva, muscles, etc. Is there a way to define ‘joint’ so that it satisfies this complex? Should it be called ‘joint’?

As mentioned above we currently have two draft arthropod anatomy ontologies—one built largely by David Osumi-Sutherland (FlyBase, Cambridge University) in OWL and the other built largely by István Mikó (HAO, Penn State) in mx as a generalized version of the HAO—which overlap substantially, especially in general classes for external anatomy. David has been reconciling these two versions in one OBO-format file, with the aim that this will be used to seed the common version in mx (see small test ontologies on GitHub if you’re interested).

We’re considering a couple slight changes in our approach going forward: 1) moving to multiple meetings a month, rather than just one, and 2) establishing semi-independent subgroups that share anatomical interests, which could lead to more substantial growth/refinement of relevant areas (e.g., the nervous system or circulatory system). Email me, Andy Deans (adeans@psu.edu), if you are interested in the latest developments or to find out how to contribute. Thanks to all who were part of this working group: Frank Friedrich, István Mikó, David Osumi-Sutherland, Aaron Smith, Shaun Winterton, and Matt Yoder!

Aug 202012
 

One of the many goals of the Phenotype RCN is to generate a common anatomy ontology for Arthropoda, the phylum that includes “segmented” organisms (more on that in another post), with “jointed” appendages (again, more later) and a rigid exoskeleton (and more on this later). We’re talking about spiders, scorpions, centipedes, crabs, shrimp, insects, etc., a lineage that includes numerous model organisms (e.g., Drosophila melanogaster) and which accounts for more than a million known species – more than 50% of all organisms! Given the diversity of body forms exhibited by these critters, not to mention the huge array of researcher communities, one can imagine the disparity of concepts and terms for their body parts.

Several arthropod-relevant, taxon-specific anatomy ontologies have been developed in the last 10 years: one each for Drosophila, mosquitoes (Diptera: Culicidae), ticks (Acari), spiders (Araneae), and Hymenoptera (Insecta). Each was developed more or less independently, with no coordination of common, higher-level classes. Yet each community of researchers—the arthropod-relevant anatomy ontology users—stands to benefit from a set of common set of shared, higher-level classes. Imagine connecting one’s observation of millipede antenna phenotype to the vast body of Drosophila mutant phenotype data and also to a scorpion species description, through a common, higher-level ‘appendage’ class. Several domain experts are now working on new arthropod-relevant anatomy ontologies, especially for Neuroptera (lacewings), Coleoptera (beetles), and, more specifically, Tribolium. Should they develop  their own ontologies, or should  their efforts benefit from the experience, standards, technology, workflow, philosophy, classes, etc. of existing efforts? Here’s where the RCN comes in.

Psychopsis insolens by Shaun Winterton
How can we connect this ant lion’s phenotypes (e.g., the fuzzy wings) to knowledge derived from model organisms (e.g., Drosophila and Tribolium)? Perhaps the AAO can facilitate these connections. Photo of Psychopsis insolens (Neuroptera: Myrmeleontidae) by Shaun Winterton.

We’ve formed an arthropod working group (AWG), whose mandate is to identify and define these common classes across major arthropod lineages. We met face-to-face once, last summer at the Google offices in Boulder, CO (notes here). We also met briefly during the last summit meeting (blog post here), where we got a bit more organized about how this effort should look. And finally, true to our word, the AWG has been and continues to engage in regular skype chats – 3rd Friday of every month at 5:00pm GMT – and they seem to be working quite well.

A few of our accomplishements so far:

  1. We have a wiki, which includes a list of relevant projects and current AAO contributors: http://aao.speciesfile.org/
  2. We have an email list: arthropod anatomy discussion
  3. And a term / concept request tracker: arthropod AO
  4. We also tackled several higher level concepts, including sclerite, appendage, appendage segmentsegment, tagma, and glands, and identified relatively uncontroversial areas of the ontology could grow without too many arguments.

The successes and failures of our first few group discussions have helped us refine our workflow, and we now have a plan for partitioning the effort more effectively. We anticipate substantial refinement of the current classes at our October working group meeting, as well as considerable growth in the depth of our ontology. We’ll report the results here! In the meantime please peruse our emerging resources and contact Andy Deans (adeans @ gmail . com) if you’d like to get more involved.

 Posted by on August 20, 2012 at 2:49 pm
Mar 052012
 

External male (left) and female (right) genitalia of ceraphronoid wasps, as visualized using laser confocal microscopy. Which parts of these anatomical complexes are true 'appendages' and why? How do we define an arthropod 'segment'?

It’s been just over a week since our grand Phenotype RCN summit meeting at NESCent, and now that the dust has settled it’s a good time to report on some progress and future directions of the Arthropod Working Group (AWG). The AWG is one of four somewhat loose-knit working groups, organized under the Phenotype RCN umbrella, and our primary goal is to develop a common anatomy ontology for Arthropoda (CAAO, for now). This summit meeting was the third opportunity for us arthroöntologists (pretty sure that wasn’t a real word, until now) to meet since the RCN began last year, and we capitalized on the positive vibe permeating through the greater meeting to discuss five main questions:

1) What resources do we have already to move this effort forward in an organized, robust way? We itemized the various communication and ontology development tools we have at our disposal: Arthropod Anatomy email list (not used much yet, but could blossom), an arthropod anatomy ontology Google Code site with issue tracker, ontology development tools (primarily Protégé and mx), and Skype (of course!)

2) Given these resources, how do we envision the workflow unfolding? We’ve been working in a somewhat piecemeal fashion for the last year, which made progress a bit … slow. Given the varied informatics expertise of our group we still need to discuss mechanisms that will allow everyone to contribute in a relatively flexible way – e.g., some people could checkout the ontology and refine it using Protégé, whereas others will want simply to send requests via email. This discussion is ongoing.

3) Ontology development should be guided by real use cases. What are ours? Our working group (n=17 so far) is populated by systematists, comparative morphologists, neuro-anatomists, and evolutionary developmental biologists. And our study organisms ranged from established models (Drosophila) to emerging models (Parhyale, Gryllus) to fossils. Accordingly, our use cases were quite diverse: connecting behavior to anatomy (For any given behavior, what structures are implicated in clades X and Y?), discovering homology across Arthropoda (e.g., topologically same structure but named differently in different clades), understanding the context of internal arthropod anatomy (in which clades are the ovaries dorsally located anterior to segment X?), standardizing descriptions of comparative anatomy results (making descriptions explicit and logical), query for data about homologous or similar anatomical structures in related species (e.g., gene expression, phenotype, electrophysiology data), make data collected in one domain available/queryable to all other relevant domains (e.g., from descriptive taxonomy to genome-phenome researchers).

4) Given these use cases, how do we prioritize ontology development or otherwise partition its development? This discussion is ongoing, but we tossed around options for recruiting more experts to contribute for certain high priority anatomical systems. E.g., if we see immediate payoff for implementing the CAAO in the context of ovarian phenotypes we could organize a push to recruit more arthropod ovary experts for a working group.

5) What are our action items? We definitely need to organize regular virtual meetings, either as Skype chats/calls or regular conference calls. We’re scheduling the first chat soon and will post here when we finalize the date/time!

So, that’s the quick summary of our working group meeting. Expect more news soon, right here on this blog. In the meantime, if you crave a more detailed report of the AWG activities so far, and you seek to get more involved, don’t hesitate to contact Andy Deans (adeans @ gmail . com) – especially if you think you know the answers to the questions highlighted in the image caption above!

 Posted by on March 5, 2012 at 8:30 pm

RCN working group meeting – Boulder, CO

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Aug 272011
 
Last June the Phenotype RCN organized a set of concurrent working group meetings—focused on arthropod anatomy, vertebrate anatomy, plant phenotypes, and the informatics associated with phenotype data and ontologies—that were very graciously hosted by by Google's office in Boulder, CO. The meeting agenda and subsequent notes are already posted on the Phenotype RCN website, though I noticed today that the arthropod anatomy working group summary never got posted!

The longer version is available as a Google doc. Here's the short version: We are working towards developing two higher-level anatomy ontologies, one for classes in common across Arthropoda and another for Insecta. We've identified a series of potential classes, proposed candidate definitions for notoriously difficult ones (what's a 'segment'?!), identified some tools we can use to facilitate communication (an email list, Dropbox, Google docs, Git), development (mx, Protégé) and visualization (C-Map, Vue), and identified several highly motivated people to collaborate with.

I'll also use this opportunity to thank our host at Google's Boulder office, John Day-Richter, for hosting what ended up being an inspirational, productive meeting! Our next group meeting is at the National Evolutionary Synthesis Center in Durham, NC. Watch for more details!