Katie Chastain
Semantic eScience IS
Spring 2013
Summary of Semantic Use in the SVF
The Semantic Vernacular for Fungi strives to enrich the field of mycology by using semantic
technology to create a standardized and extensible vocabulary for identifying and discussing specimens.
Mushrooms are generally not easily identified on observable physical characteristics alone, with many
requiring microscopic or genetic analysis to determine the exact species. And when they are identified,
the complex Latinized scientific names can seem complex and inaccessible to amateur mycology
enthusiasts. By contrast, vernacular names often focus on observable qualitative features such as color,
shape, and where a specimen was found; however, there are instances of a one-to-many or many-toone mapping between vernacular names and scientific names. The SVF system also makes use of
semantic technology to represent these mappings.
On the Mushroom Observer website (http://mushroomobserver.org/), user can suggest new
vernacular names for specimens by identifying the observable characteristics that describe that
mushroom. A standard set of terms for describing fungus is important to the underlying ontology in this
regard, as it provides concrete terminology for the various structures and attributes common
throughout the fungus kingdom. Adding a specimen's specifics for the different structures such as shape
and color helps to build up a thorough description of that mushroom. This helps to identify the
particular species, by comparing the description of an unknown mushroom to those that exist in the
database, and provide the likely vernacular name. Or, if there is no similar mushroom in the database, a
mycologist can propose a new vernacular name. After review from other users, new vernacular names
can become working parts of the database, as well, allowing mycologists to actively expand their list of
names and increase their collective knowledge. The SVF papers describe safeguards in place to ensure
that no vernacular names are re-used, nor are specimens likely to be the same vernacular species
mistakenly given two different vernacular names without good reason. This helps to cut back on
redundancy that may lead to confusion – user submissions are allowed and encouraged, but there is
careful review by both the ontology and the other users of the Mushroom Observer site to control what
information becomes "official".
The ontology behind the Mushroom Observer site also works to map scientific names to
vernacular names. This can be difficult, as some single species of mushroom may produce fruits that
vary widely in appearance; or two different species may appear identical until their genetics are
Katie Chastain
Semantic eScience IS
Spring 2013
examined. The flexibility of ontology language allows these mappings that are not necessarily one-toone, which helps to preserve information, rather than forcing site users to generalize or oversimplify.
The one-to-many relationship is between scientific and vernacular names is also helpful because it
allows for vernacular names in several different languages, thereby helping mycological scientists and
enthusiasts who are not necessarily native English speakers to share their knowledge. In a way, this
brings some social science to the field of mycology as well, as users on the site are able to see and
discuss things like regional or linguistic differences in vernacular names.
I think the overall structure of the ontology of the SVF system could be expanded to other
kingdoms of life with appropriate modifications. Certain descriptors such as color and shape could apply
to features of the plant or animal kingdoms; for example, a section of ontology that unifies color names
from various languages could easily work in other similar classifying contexts. The idea of properties
listing the common features of fungus (eg, structural ones) would necessarily require a lot of extension
to apply to more complex life forms such as birds or trees, but I believe it is certainly possible. And
because the idea of what a fungus specimen "is" in a machine-readable sense exists, it would also be
easy to continue to extend the SVF system to include more and more spoken languages, as well.
Papers Summarized
Nathan Wilson, Kathryn M. Dunn, Han Wang, and Deborah L. McGuinness. "Application of Semantic
Technology to Define Names for Fungi".
Han Wang, Nathan Wilson, Kathryn M. Dunn, and Deborah L. McGuinness. "Semantic Vernacular System:
an Observation-based, Community-powered, and Semantics-enabled Naming System for
Organisms".
Nathan Wilson, Han Wang, and Deborah McGuinness. "Scientific Names and Descriptions for Organisms
on the Semantic Web".