At the end of October 2012, the working groups of the Phenotype Research Coordination Network (RCN) all met at the Asilomar Conference Center, in Pacific Grove, CA. One of the groups, the Vertebrate working group, made it their goal to discuss methods of representing phylogenetic and serial homology in anatomy ontologies, an issue that is central to Phenoscape as well. Though common ancestry is implicit in the semantics of many classes and subclass relationships (see for example the ‘homology_notes’ for digit in Uberon), most multispecies anatomy ontologies, including Uberon, VSAO, and TAO, do not assert homology relationships between anatomical entities. Nonetheless, homology is central to comparative biology, and therefore to enriching computations across data types, species, and evolutionary change.
On 15–16 February 2012, I visited NESCent to work with Peter Midford, Jim Balhoff, and, especially, Wasila Dahdul. The focus of my trip was to push forward on the continued development of the Amphibian Anatomical Ontology and the integration of phenotypic data for amphibians into the larger Phenoscape project.
With Peter Midford, I worked to make a significant update to the Amphibian Taxonomy Ontology based largely on a recent revision to the higher-level taxonomy used on AmphibiaWeb (for which I am part of the steering committee). AmphibiaWeb provides an excellent resource for Phenoscape and other related projects because it provides a list of currently recognized species of living amphibians and is updated daily.
The majority of my visit was spent working with Wasila Dahdul on issues related to the Amphibian Anatomy Ontology (AAO) and on curating our first evolutionary dataset related to the fin–limb transition (Ruta et al., 2003). During this work, we plowed through a significant portion of AAO terms lacking parent terms (either adding parents or synonymizing the terms with others in either VAO or AAO). We also evaluated whether to add terms to the AAO that are present in the Xenopus Anatomy Ontology (XAO; Xenopus is a genus of African frogs used as a model system) but absent in the AAO. In some cases, this led to recommending that those terms be removed from the XAO. As we have started to curate morphological characters related to the limbs from the study by Ruta et al. (2003), we encountered many terms not present in existing anatomy ontologies, such as AAO or the Vertebrate Anatomy Ontology. Some terms had been slated for inclusion in the Amniote Anatomy Ontology (AmAO) being developed by Nizar Ibrahim and Paul Sereno (University of Chicago). Because these terms are also present in non-amniotes, we are recommending that they be migrated from the AmAO to the higher-level VAO.
As we start to focus on curating phenotypes from the literature of vertebrate paleontology, a few issues are emerging. One important issue is that curation of data from paleontological studies will likely necessitate adding a field to our information for specimens to accommodate free text alongside museum abbreviations and catalog numbers. The reason for this is that paleontological studies can rely on a combination of materials, including both specimens and examination of literature. We will also need to add to and refine the collection of museum codes used to curate specimen data. These last points about accurately curating data related to specimens examined are important if we are to use the Phenoscape knowledgebase to point to records for those same specimens in on-line databases, or if databases (such as those for museum collections) want to point to records of specimens in the Phenoscape knowledgebase.
A summer course on anatomy ontologies is being offered for the first time through the NESCent Academy and the Phenotype Ontology Research Coordination Network. The intended audience is postgraduate researchers in evolutionary biology and informatics – including students, postdocs and faculty – who are relative newcomers to ontologies. It will be held from 30-Jul to 3-Aug 2012 in Durham, NC. Spread the word, and if you are interested be sure to apply before the deadline of 6-Apr. [Full disclosure: a number of long-time friends of Phenoscape are among the instructors].
From the course website:
Evolutionary research has been revolutionized by the explosion of genetic information available, and anatomy ontologies must play a central crucial in relating this knowledge to observable diversity. Anatomy ontologies and vocabularies are widely used to index data and are critical for relating gene expression and phenotype data across taxa. Within a single species, anatomy ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. In order for anatomy ontologies to successfully serve all of these purposes, they must be constructed consistently so that they can be utilized and understood by both researcher and software alike. This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).
The course covers a basic introduction to ontology design principles and usage, specific ontology considerations for anatomy, application of anatomy ontologies in the context of evolutionary phenotype comparison, and use of anatomy ontologies for image annotation in different taxa. There will be strong emphasis on hands-on exercises that will develop ontology skills and provide exposure to different software applications that are useful in variety of areas of evolutionary biology.
With the help of Phenoscape and DeepFin intern Ben Frable, I recently finished adding 117 French anatomical terms and synonyms from Chanet & Desoutter’s glossary publication  to the Teleost Anatomy Ontology (TAO). These authors spent many years defining and translating Paul Chabanaud’s anatomical analyses of flatfishes into modern French and English to help researchers understand his important publications. Adding these terms to the TAO takes their translation one step further, enabling computers to link Chabanaud’s unusual terms to an ontology ID for each anatomical ‘concept’, which in turn enables connections among all phenotypic and related data that reference this ID.
These synonyms can now be used in searches of the Phenoscape Knowledgebase. For example, you can see the French synonyms for ‘paired fin’. One can imagine ultimately being able to select a preferred language or term label when browsing the ontology in the Knowledgebase.
These were the first set of foreign terms to be added to the teleost ontology, and we had to tweak the Phenoscape Knowledgebase interface to display the diacritical marks correctly. We are ready to accept more! Please send me anything you’d like added or changed to the TAO term tracker.
 Chanet, B., & Desoutter-Meniger, M. (2008). French-English glossary of terms found in Chabanaud’s published works on Pleuronectiformes. Cybium, Electronic Publication no 1:1-23. PDF download
While working to describe two species of lizardfish (Synodus) with Carole Baldwin at the Smithsonian National Museum of Natural History, she received an email from Paula Mabee asking if she knew or had any students interested in working on the Phenoscape Project. I had realized that with advances in technology and communication, evolutionary biology and all science was headed towards a future of large-scale interdisciplinary collaborations to help address big questions and make tools and data readily available. Therefore, I immediately jumped on the opportunity to work on Phenoscape!
With the support of funding from DeepFin, I started my internship with Phenoscape at the National Evolutionary Synthesis Center (NESCent) in August 2011. My three months here at NESCent have flown by and even though it is my last day, I am just as excited about the project as the day I started! Working with Wasial Dahdul, Peter Midford and Jim Balhoff has enabled me to learn and understand a great deal about databases, collaboration and morphology. Phenoscape has completely changed the way I think about phenotypic characters. Breaking them down into logical statements in Phenex really allows you to understand a character as it fits in the bigger picture. I was able to work with Wasila in forging interdisciplinary ties by contributing to other ontologies and databases, such as PATO and PaleoDB. Additionally, working to assist in the expansion of Phenoscape to incorporate all vertebrates taught me a lot about the origins of vertebrates and the plethora of prehistoric life I did not realize existed- including my new personal favorite prehistoric fish, Jagorina!
NESCent is an amazing place. Being one of the few people here without a higher degree or a long list of publications under their belt, I was initially a little intimidated. However, the informatics group, post-docs and professors have been great and pushed me to participate in seminars and intellectual discussion. This is a stimulating environment that facilitates thinking outside the box and looking at bigger picture issues in evolutionary biology.
I am excited to continue my work on Phenoscape offsite back at the Smithsonian and I hope to contribute throughout my graduate career in Dr. Brian Sidlauskas’s (former NESCentian and Phenoscape tester and contributor) lab at Oregon State University.
Graduate Student, Oregon State University
Student Researcher, Smithsonian National Museum of Natural History
Last month I visited Xenbase and Aaron Zorn’s lab at the Cincinnati Children’s Hospital for a couple of days (August 21-23, 2011) to work with Xenbase curators in preparing the Xenopus Anatomy Ontology (XAO) for its next big release. Xenbase curators Christina James Zorn and VG Ponferrada have been leading the effort, and Erik Segerdell, the ontology development coordinator for the Phenotype RCN and former Xenbase curator, was also visiting for the week and helping with the update. Erik and I provided training in ontology editing and synchronization tools. Read the rest of this entry »
The Vertebrate Anatomy Ontology (VAO) was recently developed as a high-level, bridging ontology for existing and future single species (e.g., zebrafish, mouse, Xenopus) and multispecies (teleosts, amphibians) vertebrate ontologies. We initiated VAO at a Phenoscape workshop held at NESCent in April 2010. VAO was developed to accommodate the various ways that biologists classify bones and cartilages, as distinct elements and tissue types, and based on developmental and locational criteria. After substantial review by experts in comparative anatomy, paleontology, systematics, and anatomy ontologies, VAO was submitted to the Open Biological and Biomedical Ontologies (OBO) Foundry and committed in December 2010. The ontology currently contains 127 defined terms and 63 synonyms for cells, tissues, skeletal elements, skeletal system parts, and biological processes. Cross references to several existing ontologies (Cell Type Ontology, Common Anatomy Reference Ontology, GO Biological Process) are included, thus connecting vertebrate ‘sub’ onotologies to a wealth of additional data. A mansucript detailing the VAO and evaluating the benefits of its use is in preparation.
Probably the most important branch of an anatomy ontology for vertebrates – at least from the standpoint of comparative morphologists, paleontologists, systematists – is the skeleton. We invited a small group of bone and cartilage experts to come to a workshop at NESCent April 9-10, 2010, with the goal of reviewing, revising, and altogether enhancing the skeletal branch of the various vertebrate anatomy ontologies. We had representation from the amphibian and teleost multispecies anatomy ontologies, the vertebrate model organism ontologies (zebrafish, Xenopus, mouse), and the cell ontology, as well as expert ontologists to advise on best representation (see our wiki page for their names and slides from their brief introductory presentations). The workshop was productive beyond our expectations: we produced a ‘generic’ skeletal ontology that can be plugged into all vertebrate anatomy ontologies. The files (including the useful cmap files) are under review by workshop participants at the moment, and we will be posting the outcome as a Vertebrate Skeletal Ontology in the obo foundry within the month. Let us know if you want to review some giant spreadsheets of bone terms and relationships in the next few weeks….
We are pleased to announce the publication of the article “The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age” in Systematic Biology. The paper describes how we developed this multispecies anatomy ontology for the annotation of systematic characters, and general solutions to various challenges in representing anatomical structures across a diverse clade of fishes.
Open access links to online versions of the paper are given below:
Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee. 2010. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology. View full text or download PDF.
In early November Wasila and I attended the AmphibAnat workshop in Kansas City, MO (Nov. 5-8) that was organized by Anne Maglia. As you may know, Phenoscape has a close relationship with this group, not only because they work on herps (ichthyologists and herpetologists have a long tradition of working together…), but because they are also developing ontologies to annotate the published comparative anatomical literature. I presented the status of our work in Phenoscape to the large group (~40) of amphibian development and anatomy experts who were present. As these folks added new terms, synonyms, and images to the amphibian ontologies over the course of the next few days, we solicited comments on the prototypes of three new interfaces for the Phenoscape Knowledgebase. Using both images and paper copies of these prototypes, we invited people to sit down with us on a one-on-one basis and describe in detail what worked and what was missing or unclear. The feedback was extremely useful, and we appreciated the AmphibAnat time. We have now gone over all the comments within Phenoscape and logged them individually to FogBugz, our internal tracking system. We’ll be generating new versions of these prototypes through early February, when we plan a formal round of usability testing.