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Design and Implementation of Platform for Parsing and Applying OBO Flat File

Author: WeiZuo
Tutor: LuQiang
School: Huazhong University of Science and Technology
Course: Bio - IT
Keywords: OBO Flat File Semantic Similarity Struts OWL Transformation
CLC: TP311.52
Type: Master's thesis
Year: 2007
Downloads: 57
Quote: 0
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Abstract


With the accomplishment of human genome project, bio-data has been growing at fantastic speed. Biologists are confronted with opportunity and challenge provided by the large scale bio-data. Bioinformatics is a rising area where computer is used to analyze the bio-data. As we know, with the continuous growing of bio-data, the problem of semantic disagreement emerges, which brings trouble in computer assisted analysis. Luckily, Semantic Web and ontology provide an effective method for solving semantic disagreement. The Open Biomedical Ontologies (OBO) is the most famous effort to cope with semantic disagreement of bio-data. It produces well-structured vocabularies for shared use across different biological and medical domains.To facilitate the application of Open Biomedical Ontologies, we developed a software platform, OBO-Parser. OBO-Parser, based on the struts construction, has the functions for parsing the OBO flat file submitted by users, computing semantic similarity between terms and transforming formats between OBO flat file and OWL file. OBO-Parser is built on J2EE B/S three tiers architecture, able to be accessed by browser, having good extensibility and reusability. To calculate the semantic similarity between terms, a model based semantic paths is implemented. In this paper, a use case is given, which proves OBO-Parser.

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CLC: > Industrial Technology > Automation technology,computer technology > Computing technology,computer technology > Computer software > Program design,software engineering > Software Engineering > Software Development
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