title: Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases.
abstract: BACKGROUND
  Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions.
  
  
  METHODS
  An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs.
  
  
  RESULTS
  When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF.
  
  
  CONCLUSIONS
  We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited.
authors.affiliation: Department of Industrial & Information Systems Engineering, Ajou University, Suwon 443-749, Korea.
authors.forename: Young Soo
authors.initials: YS
authors.lastname: Song
authors.forename: Chan Hee
authors.initials: CH
authors.lastname: Park
authors.forename: Hee-Joon
authors.initials: HJ
authors.lastname: Chung
authors.forename: Hyunjung
authors.initials: H
authors.lastname: Shin
authors.forename: Jihun
authors.initials: J
authors.lastname: Kim
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D046228:Microarray Analysis / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012660:Semantics