How to prepare OBO Academy ontology overview

Overview

This 'how to' guide provides a template for an Ontology Overview for your ontology. Please create a markdown file using this template and share it in your ontology repository, either as part of your ReadMe file or as a separate document in your documentation. The Ontology Overview should include the following three sections:

1. Scope
2. Curation and governance workflows
3. How the ontology is used in practice

Scope

• Describe the domain and scope of ontology.
• For example, the Mondo ontology covers concepts in the area of diseases across species and integrates disease terminologies from several underlying sources.
• Include a figure of upper level terms (critical: give a list of all the high level terms that the ontology covers (1-2 levels). Eg Mondo: disease or disorder, disease susceptibility, disease characteristic).

• Include a figure with exemplary term (using OBO graph)

Curation and governance workflows

Ontology Curation

Describe the ontology level curation, ie how to add terms. For example, terms are added to the ontology via:

• Manual additions via Protege
• ROBOT templates
• DOSDP templates

Governance

• How do people request new terms or changes
• How do people contribute terms directly (ie ROBOT templates, etc) (if applicable)

Note: There is no need for details about QC, ODK unless it is related to curation (ie pipeline that automatically generates mappings, include that)

How the ontology used in practice

Include 1-3 actual use cases. Please provide concrete examples.

For example:

1. this group uses the ontology to annotate this data for this purpose
2. this group uses the ontology to compute phenotypic similarity for prediction of related diseases
3. The ontology is used for named entity recognition (NER) as a dictionary as a synonym source