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An XML based semantic protein map

2004; WIT Press; Volume: 33; Linguagem: Inglês

10.2495/data040061

1746-4463

Amandeep S. Sidhu, Tharam S. Dillon, HT Setiawan,

Biomedical Text Mining and Ontologies

From the nature of the algorithms for data mining we note that an XML framework can be represented using graph matching algorithms. Various techniques currently exist for graph matching of data structures such as the Adjacency Matrix or Algebraic Representation of Graphs. The Graph Representation can be easily converted to a string representation. Both Graph and String Representations miss semantic relationships that exist in the data. These relationships can be captured by using semi-structured XML as a representation format. We already have an approach to integrate different data formats into a Unified Database. The technique is successfully applied to diverse Protein Databases in a Bioinformatics Domain. An XML representation of this comprehensive database preserving order and semantic relationships is already generated. In this paper we propose an approach to a Semantic Protein Map (PMAP) by building a shared ontology on our structured database model. This ontology can be used by various Bioinformatics researchers from one single site. This site will host mirrors of Protein Databases along with BIODB and have tools on Similarity Searching.