Becky Jackson
Becky Jackson
Some ontologies contain axioms that will not properly convert to OBO, and the OBO writer sometimes fails with no good information on how to fix the issue - see https://github.com/OBOFoundry/COB/issues/168...
Every time we load OBI now, we get the following error message: ``` 2021-02-22 18:43:34,590 ERROR org.obolibrary.robot.IOHelper - Input ontology contains 42 triple(s) that could not be parsed: - _:genid2147494670....
FP 2 - Common Format Automated checks: 1. The OWL PURL must resolve to RDF/XML Mechanism: We can ensure that the ontology properly loads in ROBOT, but this does not...
FP 3 - URI/Identifier Space Automated checks: 1. Core terms must follow `NAMESPACE_NUMID` format Mechanism: Any IRI that starts with `http://purl.obolibrary.org/obo/IDSPACE` must end with `_NUMID`. the `IDSPACE` comes from the...
FP 4 - Versioning Automated checks: 1. The ontology must have a version IRI 2. The version IRI must resolve 3. The versioning should follow the date system 3. The...
FP 5 - Scope Automated checks: 1. Does the ontology have a scope (domain)? 2. Is it orthogonal to other OBO Foundry ontologies? Mechanism: Some ontologies use the `domain` property...
FP 9 - Documented Plurality of Users Automated checks: 1. Is there a valid issue tracker? 2. Are there stated usages? Mechanism: We can pull the `tracker` value from the...
FP 11 - Locus of Authority Automated checks: 1. Does the contact have a name as `label`? 1. Does the contact have an email? 2. Does the contact have a...
FP 12 - Naming Conventions Automated checks: 1. All entities must have labels 2. No entities may share a label 3. No entity may have more than one label Mechanism:...
From @dosumis , migrated from https://github.com/ontodev/robot/issues/260 >I'd like to generate a JSON version of http://purl.obolibrary.org/obo/geno.owl (there doesn't appear to be a release with this conversion). JSON conversion works fine for...