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.
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.
@cite_0 @cite_5 @cite_11
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The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of diverse resources such as datasets from GEO and ArrayExpress to annotate and index them with concepts from appropriate ontologies. This indexing requires the use of a concept-recognition tool to identify ontology concepts in the resource's textual metadata. In this paper, we present a comparison of two concept recognizers – NLM's MetaMap and the University of Michigan's Mgrep. We utilize a number of data sources and dictionaries to evaluate the concept recognizers in terms of precision, recall, speed of execution, scalability and customizability. Our evaluations demonstrate that Mgrep has a clear edge over MetaMap for large-scale service oriented applications. Based on our analysis we also suggest areas of potential improvements for Mgrep. We have subsequently used Mgrep to build the Open Biomedical Annotator service. The Annotator service has access to a large dictionary of biomedical terms derived from the United Medical Language System (UMLS) and NCBO ontologies. The Annotator also leverages the hierarchical structure of the ontologies and their mappings to expand annotations. The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data. 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] Team sports commentaries call for techniques that are able to select content and generate wordings to reflect the affinity of the targeted reader for one of the teams. The existing works tend to have in common that they either start from knowledge sources of limited size to whose structures then different ways of realization are explicitly assigned, or they work directly with linguistic corpora, without the use of a deep knowledge source. With the increasing availability of large-scale ontologies this is no longer satisfactory: techniques are needed that are applicable to general purpose ontologies, but which still take user preferences into account. We take the best of both worlds in that we use a two-layer ontology. The first layer is composed of raw domain data modelled in an application-independent base OWL ontology. The second layer contains a rich perspective generation-motivated domain communication knowledge ontology, inferred from the base ontology. The two-layer ontology allows us to take into account user perspective-oriented criteria at different stages of generation to generate perspective-oriented commentaries. We show how content selection, discourse structuring, information structure determination, and lexicalization are driven by these criteria and how stage after stage a truly user perspective-tailored summary is generated. The viability of our proposal has been evaluated for the generation of football match summaries of the First Spanish Football League. The reported outcome of the evaluation demonstrates that we are on the right track. Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http: bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.