2010 Semantic Web Workshop

June 16, 2010

I recently attended the 2010 Semantic Web Workshop in Santa Fe, hosted by the SSWAP project and iPlant, at St. John’s College.  This was a two-day workshop, June 7-8, introducing semantic web technologies and applications to biological data and service integration.  The first day was scheduled to be a whirlwind overview of semantic web technologies, beginning with a lecture on the foundations of web logic and reasoning in classic formal logic and moving through RDF, RDFS, and OWL.  However, air travel problems led me to miss the entire first day of the workshop.  Fortunately Damian Gessler, the workshop organizer, provided me with all the slides for the first day upon my arrival, and I was able to somewhat catch up before day 2.  These slides are really a great overview of semantic web technologies and will be a useful resource.

The second day focused on applications to biological data and web services.  A discussion on “taxonomic intelligence” was particularly illuminating.  It provided an example of how different communities can share a set of identifiers for species, for example, yet provide their own set of statements about the taxonomy relating those species.  Each community can draw conclusions relevant to its preferred taxonomy using data associated with the same species.

The afternoon focused on the SSWAP project, led by Damian Gessler.  SSWAP is a protocol which uses OWL documents to describe the inputs and outputs relevant to a web service.  Interestingly, users of these web services would submit their input in the very same OWL model used for service descriptions.

In Phenoscape, we are using OBO ontologies rather than RDF and OWL and storing our ontological annotations in OBD, a datastore tailored for OBO technologies which provides its own very effective reasoner.  However, this workshop provided a great opportunity to stay up to date with semantic web standards and explore how to make our data compatible with and part of the global semantic web.  In addition, St. John’s College was a great meeting location – it is a small college with a wonderful natural landscape in the hills outside of Santa Fe.

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Posted by Jim

Phenex paper is out

June 10, 2010

We’re happy to report that a paper describing the Phenex curation tool has just recently been published in PLoS ONE:

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, et al. (2010) Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5(5): e10500. doi:10.1371/journal.pone.0010500.

Abstract: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.  Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.  Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

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Posted by tjvision