Tools

Ontologies

• Mondo Disease Ontology
• Human Phenotype Ontology (HPO)
• Unified Phenotype Ontology (uPheno)
• Medical Action Ontology (MAxO)
• Environmental Exposure Ontology (ECTO)
• Uber Anatomy Ontology (Uberon)
• Cell Ontology
• GENO ontology
• Scientific Evidence and Provenance Information Ontology (SEPIO)
• Ontology of Biological Attributes (OBA)

Click here for ontology tutorials and resources

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.

Standards

• 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’s data may build upon, edited, modified, and redistributed.