Conference Paper

Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes.

DOI: 10.1007/978-3-642-02879-3_7 Conference: Data Integration in the Life Sciences, 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009. Proceedings
Source: DBLP

ABSTRACT Ontology-based annotations associate objects, such as genes and proteins, with well-defined ontology concepts to semantically
and uniformly describe object properties. Such annotation mappings are utilized in different applications and analysis studies
whose results strongly depend on the quality of the used annotations. To study the quality of annotations we propose a generic
evaluation approach considering the annotation generation methods (provenance) as well as the evolution of ontologies, object
sources, and annotations. Thus, it facilitates the identification of reliable annotations, e.g., for use in analysis applications.
We evaluate our approach for functional protein annotations in Ensembl and Swiss-Prot using the Gene Ontology.

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    • "Annotations are frequently assigned a score, using a variety of methods. These approaches include assigning confidence scores to annotations based on their stability (Gross et al., 2009) or combining the breadth (coverage of gene product) and the depth (level of detail) for the terms in the Gene Ontology (GO) (Buza et al. 2008). However, while deeper nodes within an ontology are generally more specialized, these measures are problematic; first GO has three root domains and second an ontology, such as GO, is a graph not a tree, therefore depth is not necessarily meaningful. "
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