HCLSIG BioRDF Subgroup/Tasks/Ligand-Receptor Interaction, Molecular Interaction Networks, Ontology Evolution

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Converting the PDSP Ki Database and the BIND database to OWL while reusing and extending the existing BioPAX ontology. The Ki Database gives quantitative experimental data (Ki values) about the affinities of molecules to receptor molecules (mostly neuroreceptors).The task also includes the mapping of some database entries to Entrez Taxonomy and annotating receptors with the IUPHAR receptor code.

Task Objectives

  1. Extend existing BioPAX ontology to accommodate the data from the PDSP Ki database
  2. Write XQuery code for a XML to XML/RDF conversion, make manual mappings


This use case will demonstrate the automated conversions of existing databases with the XML query language XQuery. It will also demonstrate the basics of ontology re-use and decentralised ontology extension (‘ontology evolution’), which is probably one of the most unique (and arguably problematic) characteristics of the Semantic Web idea.


Matthias Samwald

Use case context

The resulting data will be most useful for basic research and pharmacological development. They could also be useful for clinical pharmacology in some cases.

Problem statement for this use case

This task demonstrates how existing ontologies that deal with qualitative data (BioPAX representing biological pathways) can be easily extended to accommodate additional, quantitative data (the Ki values from the PDSP Ki database).



  1. XQuery files for the conversion of existing formats (e.g. PSI-MI) to OWL
  2. Manual mappings of terms (e.g. between KiDB and Entrez Taxonomy and IUPHAR-DB)
  3. Data in OWL
  4. Extensions of existing ontologies

Related resources

  • PDSP KiDB [1]
  • BIND [2]
  • BioPAX [3]
  • IUPHAR receptor codes [4]

Tools and Services

  • XQuery
  • SAXON XQuery processor

Timeline for Task Completion

At the time (December 2006) most of the work has already been done. The BIND datasets need to be debugged.