How to prepare OBO Academy ontology 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:
- Curation and governance workflows
- How the ontology is used in practice
- 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¶
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
- 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.
- this group uses the ontology to annotate this data for this purpose
- this group uses the ontology to compute phenotypic similarity for prediction of related diseases
- The ontology is used for named entity recognition (NER) as a dictionary as a synonym source