Difference between revisions of "Ontology Change Requests"
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BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled: | BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled: | ||
| − | * [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology] | + | * [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)] |
| − | * [https://bioportal.bioontology.org/ontologies/GO Gene Ontology] | + | * [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)] |
| − | * [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology] | + | * [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)] |
| − | * [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology] | + | * [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)] |
| − | Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. | + | Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. |
| − | * Adding | + | == Supported change types == |
| − | * Removing | + | |
| − | * Marking a class obsolete | + | BioPortal supports several types of change requests including: |
| + | |||
| + | * Adding a synonym to a class | ||
| + | * Removing a synonym from a class | ||
| + | * Marking a class as obsolete | ||
* Renaming a class | * Renaming a class | ||
| − | + | Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few. | |
| + | |||
| + | All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations. | ||
| + | |||
| + | == How to enable change requests == | ||
| + | |||
| + | If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo. | ||
Revision as of 17:48, 22 May 2024
BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:
- Environment Ontology (ENVO)
- Gene Ontology (GO)
- Mondo Disease Ontology (MONDO)
- Uber Anatomy Ontology (UBERON)
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained.
Supported change types
BioPortal supports several types of change requests including:
- Adding a synonym to a class
- Removing a synonym from a class
- Marking a class as obsolete
- Renaming a class
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.
All of the change types that BioPortal supports are taken from the Knowledge Graph Change Language, a formal model for describing ontology change operations.
How to enable change requests
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the BioPortal support list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.