Udo Hahn, Jena University,

Language & Information Engineering (JULIE) Lab

What Do We Share? Conceptualizations of Biological Knowledge from the Viewpoints of Biology and Natural Language Processing

In this talk, two breeds of conceptual resources (ontologies) for biological knowledge will be compared. Those developed by biologists for the purpose of data curation, and those developed by NLP researchers for the purpose of information extraction and text mining. The gaps and misconceptions we encounter will give rise to proposals how we might improve interoperability among the products from both camps on a large(r) scale.

Suzanna Lewis,


The Joy of Ontology

In 1998, FlyBase announced that we intended to turn our personal collection of controlled vocabularies and techniques into an ontology. Ontology building would no longer remain a private passion for FlyBase. FlyBase was a celebrated model organism database that sensed that we were not alone in the need for a no-nonsense, practical resource in research. So, mustering what assets we (plus SGD, and MGI) had, we self-published The Gene Ontology: A Compilation of Reliable Terms with a Casual Textual Definitions. Out of these unlikely circumstances was born the most authoritative ontology in biology, the ontology your lab mate and mother probably learned to annotate from. To date it has annotated more than 200 thousand gene products. We, at the new National Center for Biomedical Ontology are updating the field with a series of All About ontology tutorials. With notes and techniques scattered throughout, along with helpful illustrations, we will continues our tradition of offering ontologies that take a reasonable amount of time to prepare but result in flexible, accurate, researcher-friendly ontologies that are beautiful enough to provide to anyone.