Jim Balhoff

Translate value-specific annotation properties to xref

4

We should consider translating some annotation properties to xref annotations, such as ICD-O-3_Code, KEGG_ID, NCBI_Taxon_ID, USDA_ID, etc.

There will be two lists, one when negations are used within the basic NCIt transformation, and one when these are used with the Uberon/CL mappings.

problems with ontology IRI and version IRI

1

The OWL file at `http://purl.obolibrary.org/obo/ppo.owl` states its ontology IRI to be `https://raw.githubusercontent.com/PlantPhenoOntology/ppo/master/ppo.owl` and its version IRI to be `https://raw.githubusercontent.com/PlantPhenoOntology/ppo/master/releases/2018-10-26/ppo.owl`. Ideally these would be `http://purl.obolibrary.org/obo/ppo.owl` and `http://purl.obolibrary.org/obo/ppo/releases/2018-10-26/ppo.owl`.

Support contributors field

12

See https://github.com/INCATools/dead_simple_owl_design_patterns/pull/46

See https://github.com/INCATools/dead_simple_owl_design_patterns/pull/47

Improve error reporting for missing prefixes

2

See #17.

In some cases, the value for a field needs to be an ontology term. Since the value could be an arbitrary class expression, the simplest form for a name with...

Finding no value via readable_identifiers should probably cause a failure

1

If the ontology passed in doesn't have an annotation axiom that can provide a readable identifier with which to construct a label (for example), dosdp-tools can: 1. Default to IRI...