Exploitation of ontological resources for scientific literature analysis: Searching genes and related diseases

Ontological resources such as controlled vocabularies, taxonomies and ontologies from the OBO foundry are used to represent biomedical domain knowledge. The development of such resources is a time consuming task. Once they are finished they contribute to standardization of information representation...

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Published in2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society Vol. 2009; pp. 7073 - 7078
Main Authors Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D.
Format Conference Proceeding Journal Article
LanguageEnglish
Published United States IEEE 01.01.2009
Subjects
Biomedical Engineering
Computational Biology
Data Mining - methods
Data Mining - statistics & numerical data
Database Management Systems
Databases, Factual
Diseases
Foundries
Genes
Humans
Information analysis
Information representation
Information retrieval
Information Storage and Retrieval - methods
Information Storage and Retrieval - statistics & numerical data
Ontologies
Standardization
Taxonomy
Text mining
Vocabulary
Vocabulary, Controlled
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Summary:Ontological resources such as controlled vocabularies, taxonomies and ontologies from the OBO foundry are used to represent biomedical domain knowledge. The development of such resources is a time consuming task. Once they are finished they contribute to standardization of information representation, interoperability of IT solutions, literature analysis and knowledge discovery. Text mining comprises IT solutions for information retrieval (IR) and information extraction (IE). IR technology exploits ontological resources to select documents that fit best to the processed query, for example, through indexing of the literature content with concept ids or through disambiguation of terms in the query. IE solutions make use of the ontological labels to identify concepts in the text. The text passages that denote conceptual entries are then used either to annotate named entities or to relate the named entities to each other. For knowledge discovery (KD) solutions the identified concepts in the scientific literature are used to relate entities to each other, e.g. to identify gene-disease relations based on shared molecular functions.
ISSN:1094-687X
1557-170X
1558-4615
DOI:10.1109/IEMBS.2009.5333359