Ontology patterns for the representation of quality changes of cells in time.

Background: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical information from these data. This information can be used to develop process models of cellular dynamics.

Towards refactoring the Molecular Function Ontology with a UML profile for function modeling.

Background: Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies such as GO is generally far from being simple, as a whole as well as when focusing on certain aspects or fragments.

A top-level ontology of functions and its application in the Open Biomedical Ontologies.

Motivation: A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions.

Results: We present here a top-level ontological framework for representing knowledge about biological functions.