Metrics Study

Introduction

We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

Download Metrics Files

• Ontology Metrics - metrics for all of the BioPortal ontologies taken on May 5, 2010.
• Annotation Metrics - metrics for the NCBO Resource Index taken on June 3, 2010.

Download Benchmark Ontologies

These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials such as source code for the tool will be forthcoming.

• Small
  • Small-Shallow (7, 1000000, 5, 6, 30)
  • Small-Mid (100, 1000000, 10, 4, 40)
  • Small-Deep (7, 1000000, 20, 2, 60)

• Medium
  • Medium-Shallow (7, 1000000, 5, 6, 30)
  • Medium-Mid (100, 1000000, 10, 4, 60)
  • Medium-Deep (7, 1000000, 20, 6, 28)

• Large
  • Large-Shallow (7, 1000000, 5, 11, 60)
  • Large-Mid (7, 1000000, 6, 40)
  • Large-Deep (7, 1000000, 20, 3, 52)