Research Center  for iBioSearch

iBioSearch: Integrated Biological Databases Search

Yuan An, Ph.D., Department of Computer Science, University of Toronto

The integrated biological databases search (iBioSearch) system is aimed at providing a unifying interface and advanced capability for searching various online biological databases. The iBioSearch system is an online search system which dynamically builds a biological database search ontology as the user interface. The ontology acting as a global schema connects to more than 1000 online biological databases. User's queries against the ontology are translated into queries against underlying online query interfaces. Query results returned from the underlying databases are consolidated, reconciled, and ranked by data cleansing and relevance computing algorithms.  Salient features of iBioSearch system includes dynamically updating biological databases repository and maintaining semantic mappings when base databases evolve.

keywords: Data Integration, Bioinformatics, Web Search, Meta Search, Web Information Systems, Schema Mapping,
Ontology-Based Information Integration, Reverse Engineering, Conceptual Modeling

Data Sets

  • The NAR Molecular Biology Database Collection: 2007 update
  • UMLS (Unified Medical Language System)
  • Open Biomedical Ontologies
  • A Library of information models (schemas) for biological collections
  • Molecular biology database list
  • GenBank
  • Structural Classification of Proteins
  • CATH protein structure classification
  • PDB protein Data Bank
  • SwissPort protein knowledgebase
  • OpenGalen
  • FRBR in RDF
  • GO ontology
  • MODS: Metadata object description schema
  • Con-way XML Schema library
  • Illinois Semantic Integration Archive
  • TPC Transaction Processing Performance Council
  • THALIA course testbed
  • MARC bibligraphic record
  • MDDL: market data definition language
  • Gene Expression Markup Language
  • GeneX
  • XML-based access to bioinformatics data
  • Standardization efforts for clinical data
  • HK Gov. XML Schemas
  • UK GOV talk schema library
  • Finance XML schemas
  • XML data repository UWashington
  • Springer A++ Book and Journal DTDs
  • Course testbed
  • BibTex ontology, LibDB etc.
  • Cim Schemas
  • Mark S. Fox about Enterprise Modelling
  • TAMBIS project
  • Drug schemas
  • OpenCyc
  • Sensus ontology
  • SUMO domain ontologies
  • Schemaweb ontologies
  • Protege ontologies
  • KSL stanford ontologies
  • KSL bibliographic-data ontology
  • oasis-open standard
  • xml.org resources
  • IM7.org medical records
  • Clinical Data Exchange
  • Genes db schema
  • Molecular biology database schema library
  • BCSL schema library
  • Ontologies for alignment test
  • Mondeca OWL ontologies
  • TPCH database

    Development tools

  • Bioinformatics.ca
  • Introduction to Ant, CVS, Eclipse and Tomcat