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
Mar 072014
 

B2With its research emphasis on understanding the impact of climate change on the environment, Biosphere2 turned out to be the perfect venue for our fourth annual Phenotype RCN meeting!  More than 60 students, postdocs, and professionals from 7 countries participated in this inspirational event, and our expertise was evenly split between biology and informatics.  We were particularly pleased to have the support and participation from the EDEN RCN (6 people), with their focus on understanding the impact of ecological factors on organismal development and evolution.  

The goals for this summit meeting were to (1) understand the bioinformatics landscape of environmental ontologies and vocabularies (What resources exist? What acquisitions and mergers should happen?); (2) find out how (and whether) environment is represented with respect to phenotype in projects and annotation data sets; and (3) determine research that would benefit from the integration of environment ontologies.  We frontloaded this work by initiating a group Google doc prior to the meeting, with the goal to refine it and publish it following the meeting.  Combined with presentations from meeting participants, this activity was surprisingly effective (!), and the manuscript is progressing quickly.  In short, we discovered that the ENVO ontology is likely to be the most widely used and supported, and though it needs to be provisioned with many concepts from the user community, participants felt that it would be sufficient for their needs.  It doesn’t seem that environment has been formally represented with respect to phenotypes outside of the microbial realm (where it is very important), but many interesting research questions could be addressed if it was.  Please let us know if you’d like to contribute to this doc.

Another huge accomplishment: Over a dozen new research collaborations were spawned by this meeting!  We’re still sorting these out, but the RCN hopes to support many of these activities through our Collaborative Exchange Opportunities mechanism.

On the social side, this meeting was very fun!  To the relief and immense enjoyment from those of us from the North, who haven’t seen warm weather in what seems like an eternity, most meals were held outside on the patio of B2. And one dinner was even inside the Biosphere itself.  Some of our participants enjoyed antics in B2, including one who managed to get locked in (briefly)….. The clean and cozy casitas made for great breakout spaces, the fantastic catering kept our minds sharp, the fun and beautiful setting inspired interaction, and the care and attention to every organizational detail (thanks to Kim Land at B2 and Judy Logue for the RCN) made this meeting possibly our best.  Thanks everyone!

 

 

 

 Posted by on March 7, 2014 at 1:07 am
Feb 222014
 

The Seventh International Biocuration Conference (ISB2014) will be held at the University of Toronto in Toronto, Canada, from April 6-9, 2014.

Hosted by the Ontario Institute for Cancer Research, this meeting will provide a forum for curators and developers of biological databases to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research. Participants from academia, government and industry interested in the methods and tools employed in curation of biological and medical data are encouraged to attend.

Early bird registration ends March 7, 2014

Registration ends March 24, 2014

The Conference will be preceded by a workshop on the practical use of Uberon, the integrated cross-species anatomy ontology.

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

Feb 172014
 

By Pier Luigi Buttigieg

We’re happy to announce that a description of the Environment Ontology (ENVO; www.environmentontology.org) has been published in the Biomedical Ontologies series of the Journal of Biomedical Semantics:
http://dx.doi.org/10.1186/2041-1480-4-43

Capturing the environmental context of biological and biomedical entities is key to fully understanding their qualities, behaviour, and composition. That being said, concisely but meaningfully describing an “environment” with a small number of ontology classes quickly becomes a complex undertaking. This is further complicated by variability in the understanding of the boundaries and parts of environments as well as their relations to other entities of interest, even within a single discipline.

ENVO aims to offer an approachable and easily applicable ontology of environments, with classes that capture key elements of a given environmental context. In particular, ENVO focuses on the environmental system an entity is embedded in, the environmental features that causally influence it, and the environmental material that surrounds it. These complementary perspectives provide a compact but informative contextualisation that can readily aid, for example, data discovery and comparative studies. Work is underway to represent entities such as habitats, niches, and environmental conditions in order to further tease apart and define aspects of the environment. Further, instances of ENVO classes are being linked to classes in the Gazetteer (GAZ) to support (among other efforts) environmental contextualisation of place names.

To promote interoperability across existing ontologies, ENVO is being developed towards compliance with the OBO Foundry Principals. Linking ENVO with phenotypic ontologies and data offers great potential in enabling biological investigation using ontological resources and we look forward to exploring this at Phenotype RCN 2014!

Feb 132014
 

Dear Phenotype Community,

We are heading into our annual meeting next week, where we will be prioritizing our next year’s activities with the help of the Phenotype RCN Advisory Board. If you have an idea for a workshop, working group or collaborative exchange, please send me an email and/or fill out a short application with your idea. See our blog for previous posts by folks who have been funded, and email me if you would like to discuss an idea before you propose. Please get these to us by February 19th.

Thanks! Paula (pmabee@usd.edu)

 Posted by on February 13, 2014 at 2:32 am
Feb 102014
 

Via http://phenoday2014.bio-lark.org/:

The Phenotype day [International Conference on Intelligent Systems for Molecular Biology] is an initiative developed jointly with the Bio-Ontologies and BioLINK Special Interest Groups.

The systematic description of phenotype variation has gained increasing importance since the discovery of the causal relationship between a genotype placed in a certain environment and a phenotype. It plays not only a role when accessing and mining medical records but also for the analysis of model organism data, genome sequence analysis and translation of knowledge across species. Accurate phenotyping has the potential to be the bridge between studies that aim to advance the science of medicine (such as a better understanding of the genomic basis of diseases), and studies that aim to advance the practice of medicine (such as phase IV surveillance of approved drugs).

Various research activities that attempt to understand the underlying domain knowledge exist, but they are rather restrictively applied and not very well synchronized. In this Phenotype Day we propose to trigger a comprehensive and coherent approach to studying (and ultimately facilitating) the process of knowledge acquisition and support for Deep Phenotyping by bringing together researchers and practitioners that include but are not limited to the following fields:

• biology as well as computational biology

• genomics, clinical genetics, pharmacogenomics, healthcare

• text/data mining and knowledge discovery

• knowledge representation and ontology engineering

For more information including paper submission deadlines and instructions, please go to http://phenoday2014.bio-lark.org/.

Jan 252014
 

Our paper describing the Vertebrate Taxonomy Ontology (VTO)  is published!  See: http://www.jbiomedsem.com/content/4/1/34 .

One primary objective for Phenoscape and similar projects is to aggregate phenotypic data from multiple studies to named taxa, which in many phylogenetic studies are species but also might be at higher taxonomic levels such as genera or families. While there are many widely used taxonomies that include rich sampling of species and higher taxa, for example Bill Eschmeyer’s widely used Catalog of Fishes, there are few vetted “bridging” taxonomies that allow for aggregating data across, say, fishes, amphibians, and mammals. This problem becomes even more acute when you consider integrating data for extinct taxa as well. As a first step towards addressing this issue for vertebrates, we created the Vertebrate Taxonomy Ontology (VTO) that brings together taxonomies from NCBI, AmphibiaWeb, the Catalog of Fishes (via the previously existing Teleost Taxonomy Ontology), and the Paleobiology Database. The resulting curated taxonomy contains more than 106,000 terms, more than 104,000 additional synonyms, and extensive cross-referencing to these existing taxonomies. The Phenoscape Knowledgebase will leverage this taxonomic ontology by allowing for phenotype statistics to be displayed by taxon, including coarse measures of the extent of annotation coverage and phenotypic variation. Though phenotypes may be annotated to a species, the use of an ontological framework for the taxonomic hierarchy facilitates aggregating phenotypes to higher levels, such as genera or families. In the future, we hope to be able to integrate other excellent and rich sources of taxon-specific taxonomies, such as that in the Reptile Database or the International Ornithologists’ Union Bird List. This is a work-in-progress and the Phenoscape team is certainly interested to integrate new taxonomic sources as well as explore different ways that such a resource can be used and developed by the larger community.

 


Filed under: Taxonomy Ontology, Vertebrates
Jan 162014
 

Last week, the Phenotype RCN hosted a cross-working group call featuring presentations by Ramona Walls on the Plant Ontology and Cross-Species Reasoning [pdf] and Laurel Cooper on Common Reference Ontologies for Plants.

Dr. Walls (The iPlant Collaborative, University of Arizona, and New York Botanical Garden) demonstrated how the PO defines anatomical terms in a way that they can be used across all green plant species. After an overview of the ontology, which can be searched and browsed at http://plantontology.org/, she discussed its evolution, main branches (“plant anatomical entity” and “plant structure developmental stage”), and characteristics shared with CARO (the Common Anatomy Reference Ontology). She talked about specific changes to the ontology that make it work better for all green plants and presented use cases concerning comparison of gene expression, traits, and phenotypes across species.

Dr. Cooper (Oregon State University) followed with a talk about the PO and cROP, the Common Reference Ontologies for Plants. She identified problems arising from free-text phenotype descriptions and scattered data resources, and demonstrated how the PO fits into the centralized cROP platform, where reference ontologies for plants will be used to access data sources for plant traits, phenotypes, diseases, genomes linked to gene expression and genetic diversity data across a wide range of plant species. The cROP Ontology Database may be accessed via its web portal, http://crop.cgrb.oregonstate.edu/.

Many thanks to Ramona and Laurel for their outstanding talks!

The Phenotype RCN plans to host monthly calls the first Monday of every month at 8 a.m. Pacific / 11 a.m. Eastern time. If you would like to receive invitations to join via WebEx, please email Erik Segerdell. Suggestions for topics and volunteers for presenters are welcome!

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/