The rapidly increasing number of scientific documents available publicly on the Internet creates the challenge of efficiently organizing and indexing these documents. Due to the time consuming and tedious nature of manual classification and indexing, there is a need for better methods to automate this process. This thesis proposes an approach which leverages encyclopedic background knowledge for enriching domain-specific ontologies with textual and structural information about the semantic vicinity of the ontologies' concepts. The proposed approach aims to exploit this information for improving both ontology-based methods for classifying and indexing documents and methods based on supervised machine learning.
@cite_0: In this paper, we investigate strategies for automatically classifying documents in different languages thematically, geographically or according to other criteria. A novel linguistically motivated text representation scheme is presented that can be used with machine learning algorithms in order to learn classifications from pre-classified examples and then automatically classify documents that might be provided in entirely different languages. Our approach makes use of ontologies and lexical resources but goes beyond a simple mapping from terms to concepts by fully exploiting the external knowledge manifested in such resources and mapping to entire regions of concepts. For this, a graph traversal algorithm is used to explore related concepts that might be relevant. Extensive testing has shown that our methods lead to significant improvements compared to existing approaches.
@cite_5: The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata (www.bioontology.org). The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data.[1]
@cite_11: This paper gives an overview of the development of the field of Knowledge Engineering over the last 15 years. We discuss the paradigm shift from a transfer view to a modeling view and describe two approaches which considerably shaped research in Knowledge Engineering: Role-limiting Methods and Generic Tasks. To illustrate various concepts and methods which evolved in recent years we describe three modeling frameworks: CommonKADS, MIKE and PROTEGE-II. This description is supplemented by discussing some important methodological developments in more detail: specification languages for knowledge-based systems, problem-solving methods and ontologies. We conclude by outlining the relationship of Knowledge Engineering to Software Engineering, Information Integration and Knowledge Management.
An ontology is a @cite_11 Ontologies have been used as background knowledge for semantic annotation of documents (e.g. @cite_5 , @cite_0 ), mostly in the context of the Semantic Web. @cite_5 presented the Open Biomedical Annotator, which is an ontology-based Web service for annotating documents with biomedical ontology concepts. The annotation process consists of two main steps: The first step, produces direct annotations by matching textual meta-data of the documents to ontology concepts. In the second step, the set of direct annotations is by using semantic relations of the ontology and by using existing mappings to other ontologies. I plan to build upon and extend this approach by incorporating textual and structural encyclopedic background knowledge.