June 16, 2009
An NSF-funded postdoctoral position is available in the laboratory of Monte Westerfield (University of Oregon, Institute of Neuroscience) to study experimentally candidate genes for the diversification of skeletal architecture in fish species related to zebrafish.
The position is available through the Phenoscape project, a collaboration among evolutionary and model organism biologists (including Paula Mabee of the University of South Dakota, Monte Westerfield of the Zebrafish Information Network, and Todd Vision of the National Evolutionary Synthesis Center). Read the rest of this entry »
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Jobs | Tagged: Postdoc | 
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Posted by tjvision
May 28, 2009
Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Read the rest of this entry »
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Workshops | Tagged: AmphibAnat, ASIH, Outreach, Workshops | 
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Posted by tjvision
February 1, 2009
We are offering summer traineeships for graduate students and postdocs interested in gaining expertise in informatics and the application of ontologies to evolutionary, anatomical, developmental, and genetic data.
Opportunities are available to work as part of the Phenoscape team on data curation or open source software/database development. Participants would be located at the National Evolutionary Synthesis Center or the University of South Dakota. Stipends of $5,000 will be given to participants to cover travel, room and board for 10-12 weeks. Read the rest of this entry »
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Posted by tjvision
January 9, 2009
Our second “Evolutionary Biology & Ontologies Workshop” was held at the Society of Integrative and Comparative Biology (SICB) meetings in Boston (January 5, 2009). It was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). In our morning of talks, our speakers provided the audience with a solid introduction to ontologies, annotations, curation tools, databases, and examples of the integrative questions that can be answered using them. The speakers, titles, and slides for these talks are available through the links below, and they provide an instructive resource for the community. Read the rest of this entry »
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Posted by pmabee
October 24, 2008
“…where the buffalo roam and the data are rounded up-up all day….”
A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening. Read the rest of this entry »
1 Comment | Curation Tools, Data Curation, Informatics, Workshops | Tagged: Bison, Data Jamboree, Roundup | Permalink
Posted by pmabee
August 24, 2008
As we proposed in an earlier post, we have been developing an alternative to the traditional approach of representing taxonomy in ontologies. This alternative represents species (and currently higher taxa) as individuals in the ontology.
There is another phenoscape ontology that would benefit from the use of individuals: our ontology (ok, it’s really a vocabulary) of research collections of fish. Part of our process for curating anatomy papers involves constructing a list of all the specimens reported in the paper (generally the author includes this in the paper, but we enter it to facilitate annotation). The specimen lists consist of collection names and numbers. Although research collections are supposed to have standardize names and abbreviations, practice does not always reflect these standards: the same collection may be abbreviated in different ways by different authors, and collections occasionally merge and the smaller collections might disappear into larger ones or be renamed.
So we constructed a vocabulary of fish collections with their 4-5 letter abbreviations, longer name and possible synonyms. Now a research collection contains individual specimens, but these are parts of a collection, not subtypes of a particular collection, and therefore, the collection is best represented as an individual, not a class. So, the collections vocabulary, represented as an OBO ontology, should ideally use OBO instances (which exist to represent individuals), rather than terms for the collections.
Unfortunately, the current version of OBO-Edit, although it will read and save ontologies containing Individuals, provides no facility for either viewing or editing these individuals. Furthermore, although there are several OWL editors that would allow us to work with Individuals, there are no OBO<->OWL translators that understand what to do with OWL individuals, so they are just omitted in the OBO translation, even though the OBO file format, since version 1.2, has supported Instance ’stanzas.’ Read the rest of this entry »
Leave a Comment » | Collections Vocabulary, Ontology, Taxonomy Ontology | Permalink
Posted by pmidford
Posted by pmabee 
