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Data Tools and Algorithms

  • Dipper: Dipper is a Python package to generate RDF triples from common scientific resources.
  • Biolink API: API integration layer for linked biological objects.
  • Exomiser: The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data in VCF 4 format.


  • Phenopacket: An open standard for sharing disease and phenotype information.

Monarch web

  • Analyze Phenotypes: The Phenotype Analysis Tool enables you search our database using the OwlSim Semantic Similarity analysis engine to find phenotypically similar diseases or genes in a variety of organisms, then visualize their overlap. Results will be displayed using Phenogrid, a Javascript component that visualizes semantic similarity calculations provided through APIs from the Monarch Initiative.
  • Text mining: Text Annotator provided by the SciGraph Annotation Service

Evaluation tools

  • Reusable Data Licensing Rubric: The (Re)usable Data Project created a rubric to evaluate resources on how well we believe a resource‚Äôs data may build upon, edited, modified, and redistributed.