Toward principles for the design of ontologies used for knowledge sharing
International Journal of Human-Computer Studies - Special issue: the role of formal ontology in the information technology
Proceedings of the 1st international conference on Knowledge capture
The evolution of Protégé: an environment for knowledge-based systems development
International Journal of Human-Computer Studies
On carcinomas and other pathological entities: Research Articles
Comparative and Functional Genomics
From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies
Journal of Biomedical Informatics - Special issue: Biomedical ontologies
Desiderata for domain reference ontologies in biomedicine
Journal of Biomedical Informatics - Special issue: Biomedical ontologies
Ontology Design Principles and Normalization Techniques in the Web
DILS '08 Proceedings of the 5th international workshop on Data Integration in the Life Sciences
Applied Ontology - Towards a Metaontology for the Biomedical Domain
An overview of the CRAFT concept annotation guidelines
LAW IV '10 Proceedings of the Fourth Linguistic Annotation Workshop
Cross-product extensions of the Gene Ontology
Journal of Biomedical Informatics
Developing a robust part-of-speech tagger for biomedical text
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
IJCNLP'05 Proceedings of the Second international joint conference on Natural Language Processing
Guest Editorial: Ontologies for clinical and translational research: Introduction
Journal of Biomedical Informatics
Open-domain anatomical entity mention detection
ACL '12 Proceedings of the Workshop on Detecting Structure in Scholarly Discourse
Hi-index | 0.00 |
A wealth of knowledge valuable to the translational research scientist is contained within the vast biomedical literature, but this knowledge is typically in the form of natural language. Sophisticated natural-language-processing systems are needed to translate text into unambiguous formal representations grounded in high-quality consensus ontologies, and these systems in turn rely on gold-standard corpora of annotated documents for training and testing. To this end, we are constructing the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-text biomedical journal articles that are being manually annotated with the entire sets of terms from select vocabularies, predominantly from the Open Biomedical Ontologies (OBO) library. Our efforts in building this corpus has illuminated infelicities of these ontologies with respect to the semantic annotation of biomedical documents, and we propose desiderata whose implementation could substantially improve their utility in this task; these include the integration of overlapping terms across OBOs, the resolution of OBO-specific ambiguities, the integration of the BFO with the OBOs and the use of mid-level ontologies, the inclusion of noncanonical instances, and the expansion of relations and realizable entities.