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:

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:

For more information about the Biocuration conference, please see:

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:

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 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 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!

Nov 262013

A handful of new papers of interest are available at the Journal of Biomedical Semantics, which is publishing a collection of articles related to biomedical ontologies and ontology updates:

• P. E. Midford et al: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

• R. Nigam et al: Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD

• P. Ciccarese et al: PAV ontology: provenance, authoring and versioning

• K. M. Livingston et al: Representing annotation compositionality and provenance for the Semantic Web

Oct 222013

The Journal of Biomedical Semantics is publishing a collection of articles related to biomedical ontologies and ontology updates, including some that address phenotype representation. As of today, the following have been published and provisional PDFs are available at the JBMS website:

• The Drosophila anatomy ontology

• The Drosophila phenotype ontology

• Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

• Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP

• Function of dynamic models in systems biology: linking structure to behaviour

• Developing a semantically rich ontology for the biobank-administration domain

• Functional tissue units and their primary tissue motifs in multi-scale physiology

• Enrichment analysis applied to disease prognosis

• The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species

Oct 122013

On Monday, October 7, the Phenotype RCN hosted a cross-working group call featuring presentations by Pier Luigi Buttigieg on the Environment Ontology and by Matthew Brush on a workshop focused on genetic variation representation.

Dr. Buttigieg, a post-doctoral research associate at the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, gave an overview of the structure and applications of the Environment Ontology (EnvO), a community ontology for the concise, controlled description of environments. It contains terms at the levels of biomes, environmental features, and environmental material. He talked about EnvO’s sister project, GAZ, an open-source gazetteer built on ontological principles, and EnvO’s adoption by the Encyclopedia of Life (EOL) to provide environmental context to taxon information. EnvO is of particular interest to the RCN because we would like to further explore capturing environments in relation to phenotype.

Matthew Brush, a member of the Ontology Development Group at Oregon Health & Science University, reported on a RCN-sponsored workshop to align genetic variation representation across the Sequence Ontology and Monarch Initiative, in support of efforts to link phenotypes to genotype data. There will be more posted on the RCN blog soon about the workshop and its outcomes.

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!

An announcement for the next meeting, November 4, is coming soon.

Aug 062013

The final day of the course was presentation day, where we got to hear about everyone’s research questions and how they were going to use (or not!) ontologies for their work. We group brainstormed solutions and next steps for everyone’s projects. The group was very synergistic and we believe that we’ll see some nice contributions and connections being made in upcoming months in the ontology community. Highlights from the presentations are below:


Chris Sheil:

Developmental comparative morphology of the chondrocranium in turtles


Elise Larsen:

Developing a knowledge base of North American butterfly monitoring data


Ashleigh Smythe:

Comparative morphology of nematode anatomy and behavior


Mariangeles Arce:

Connectivity and function of cranial and ventral musculature in catfishes


Peter Uetz:

Representing diversity of form in The Reptile Database


Corrine Blank:

Phenomics of Prokaryota for Tree of Life


Jing Liu:

Use of CharaParser and ontologies to generate plant character matrices from publications


Maria Christina Diaz:

Development of the Porifera ontology to represent sponge comparative anatomy and biodiversity


Eric Chen:

Characterizing gene retention after whole genome duplication, triplication


John Wieczorek:

Semanticizing the Darwin Core


Laura Jackson:

Gene regulation of fin positioning in fishes


Steve Elliott:

Representing the semantic types in the Embryo Project


Anne Thessen:

Phenomics of Eukaryotic microbes


Aug 032013

We spent the entire Day 3 working on learning Protege and exploring the use of various OWL2 capabilities. The students worked at their own pace, but all made it to the light at the end of the tunnel. They are all now enlightened :-) (bearers_of some instance_of PATO:0001291). We had also converted the students VUE files into OWL, and some students were able to start work on their OWL files. Day 4 of the course was focused on developing skills around reuse of other ontologies and data interoperability. We learned techniques for performing OWL imports and the use of MIREOT (Minimum Information to Reference and External Ontology Term), which is basically a way to use a subset of another ontology in your own.

We saved a discussion of homology for the end of the last full day, knowing full well that a) the discussion would be vigorous, b) people would have to break for food at some time, and c) the conversation could continue into the evening. Kudos to our students, as they seemed to immediately understand our community’s general approach to this subject, to the degree that nobody even foamed at the mouth.