Modeling Issues Encountered from Building a Taxonomy from a Biology Textbook A. Patrice Seyeda, John Pachecob, Andrew Goldenkranzb, and Vinay Chaudhrib aDepartment of Computer Science and Engineering, University at Buffalo, Buffalo, New York, bSRI International, Menlo Park, CA Introduction Linnaean Classification Entity/Process Dichotomy Subclass/Subevent • Task to create a taxonomy from an AP Biology • Biologists wanted to classify Light-Microscope textbook’s glossary terms (Campbell and • Biologists wanted to classify the under the subclass Technology Reece, 8th Edition) different kingdoms under the • Biologists also wanted to classify Technology • There was a strong initial class Kingdom under the subclass Inquiry tendency to use the Materials and Methods • However, there are 5 instances • These two uses of the term `Technology’ refer to hierarchy to organize sub- • Imported ~2400 glossary terms and definition of Kingdom two different senses parts or sub-processes strings from electronic glossary into • Glossary definition for Technology: “The • E.g., Telophase is a Collaborative Protégé in OWL format, as application of scientific knowledge for a specific purpose, often involving industry or commerce subclass of Mitosis, instead classes and comment strings but also including uses in basic research.” of a sub-process • Use of just the subclass-of relation • Biologists also wanted to relate the different levels of classification of the Linnaean Solution • Team consisted of biologists and KR specialists taxonomy to each other in the familiar • Move parts or sub-processes to appropriate • Biologists attempted initial classifications, where hierarchical way locations whenever they are found modeling issues were identified and solutions • However, an instance of Phylum is • In training sessions, reinforce the subclass of provided not an instance of Kingdom Solution relationship Results • In this case it was simple to notice the problem Solution and refactor the taxonomy Entity/Role Dichotomy • Built Linnaean taxonomy under organism • Some terms are polysemous Initial encoding of organic molecules included • Used common English names for simplicity • Definitions including “; also” are a classes defined by structure and classes defined warning sign • “Moss is a Plant” is clearer than “Moss Example: Wild Type is ``An individual by function is a Plantae” with the phenotype most commonly Proteins and steroids are defined by their observed in natural populations; also • Made the classes that represent the tiers in that chemical composition refers to the phenotype itself.’’ hierarchy into “Classification-Units” Hormones are defined by the function they perform There is an overlap between Steroid and Hormone Some hormones are steroids, others are proteins Solution Classifying Areas of Research • Hormones are defined as roles that certain chemicals play • Initial tendency to classify areas of Conclusions Potential Refinements research (Genetics, Anatomy, Ecology) • Initially, biologists relied on prior knowledge and • Steroid-Hormone is still a class in the under Inquiry taxonomy which represents a useful class • Add the latin-named classes as instances of their definitions for organizing class hierarchy, • Areas of research are complex, involving classes treated as organizational “buckets” of biologists’ intuitive thinking Classification-Unit research activities and educational Examples: institutions constituted of departments, • Ontological principles were applied to identify faculty members, programs and curricula. modeling issues and provide a foundation during • Animalia instance of Kingdom • However, the definitions of the terms for taxonomy building process • Plantae instance of Kingdom each area of research is prefixed by ``the • The biologists now have a much better sense for scientific study of’’ these types of modeling issues • Treat Classification Units as meta-classes • Given commitment to processes, • Animal would be an instance of the meta- classification under Inquiry is appropriate. Acknowledgements class Kingdom This work was funded by Vulcan Inc. • Animalia would be a synonym for that class References Campbell, N. A. and Reece, J. B. (2007). Biology: AP Edition. Pearson, 8th edition.
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