Using reasoning to guide annotation with gene ontology terms in GOAT
ACM SIGMOD Record
Obol: integrating language and meaning in bio-ontologies: Conference Papers
Comparative and Functional Genomics
Metamodeling integration architecture for open biomedical ontologies: the GO extensions' case study
ER '07 Tutorials, posters, panels and industrial contributions at the 26th international conference on Conceptual modeling - Volume 83
Applied Ontology - Towards a Metaontology for the Biomedical Domain
Ontology learning from biomedical natural language documents using UMLS
Expert Systems with Applications: An International Journal
Applied Ontology - Towards a Metaontology for the Biomedical Domain
Enhancing semantic relation quality of UMLS knowledge sources
Proceedings of the International Conference on Management of Emergent Digital EcoSystems
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This paper describes a frame-based integration of the three GO subontologies, the Chemical Entities of Biological Interest ontology, and the Cell Type Ontology in which relationships are modeled in a way that better captures the semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions by identifying patterns in GO terms, mapping these patterns to new, specific relationships, and matching term substrings to concepts. Using this methodology, a predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid, resulting in an initial set of over 4000 assertions. Furthermore, this methodology programmatically integrates assertions into an ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels.