biolink / biolinkml

DEPRECATED: replaced by linkml

https://github.com/linkml/linkml

biolink/biolinkml Issues

THIS REPOSITORY IS CLOSING -- please post new isses at https://github.com/linkml/linkml
Updated 3 years ago
rdf generation from enums fails if the permissible value key includes a space
Closed 3 years ago
JSONLD Context needs `"@container": "@set"` for multivalued entries
Closed 3 years ago1
'@container' must be emitted for multivalued elements in JSON-LD Context
Closed 3 years ago1
`__post_init__` fails when presented with a pre-constructed object
Closed 3 years ago
gen-jsonld generates an incorrect @context
Closed 3 years ago1
Is `repr` property used?
Closed 3 years ago1
Mappings aren't listed in markdown
Closed 3 years ago
Empty list element not reported well
Closed 3 years ago
Relative import paths have one too many dots
Closed 3 years ago1
SchemaLoader line 101 -- commented out a couple of lines because loaded_file doesn't have a path while the comparison does
Closed 3 years ago
Should mappings.yaml include/be more SKOS-like?
Closed 3 years ago
default_range is not applied for slots defined within slot_usage
Closed 3 years ago
Update `__post_init__` signatures to match PyCharm IDE fix
Closed 3 years ago1
missing PATO prefix
Closed 3 years ago9
indentation of class hierarchy not working in generated index.md
Closed 3 years ago2
infer a simple data dictionary schema from a TSV
Closed 3 years ago
Biolink ML generation fails silently
Closed 3 years ago4
enums are not imported in generated python code
Closed 3 years ago
YAML generator isn't a command line option
Closed 3 years ago1
Boolean values don't include underlying python type
Closed 4 years ago1
SchemaLoader should be monotonic
Closed 4 years ago
gen-owl error(s)
Closed 4 years ago6
create gen-* modules as separate pip installs
Closed 4 years ago2
gen-owl error(s)
Closed 4 years ago2
alt_description not behaving as expected
Closed 4 years ago
Should `slot_usage` be allowed in `mixin` definitions?
Closed 4 years ago1
The `abstract: true` tag seems redundant for `mixin` components of schema
Closed 4 years ago1
Clarify semantics of inlined: True - dicts vs lists
Closed 4 years ago6
Slots, slot_usage and attributes
Closed 4 years ago6
Latest version of PyShEx causes an exception in biolinkml.
Closed 4 years ago5
biolinkml optional slots populated in object
Closed 4 years ago3
Markdown not generating output for non-owned slots
Closed 4 years ago
biolinkml None slots populated in object
Closed 4 years ago3
symmetry and inverse characteristics are not translated in OWL
Closed 4 years ago
Relative Imports base problem
Closed 4 years ago1
gen-owl failing in 1.5.3
Closed 4 years ago6
If you don't supply a default namespace, jsonldcontextgen.py errors out on line 50
Closed 4 years ago1
Mixins are not showing on diagrams that have the things they are mixed in to - see ResourceDescription as an example
Closed 4 years ago1
Broader, narrower, etc. mappings -- are they ALL in the metamodel? Should they be? Should their behavior be the same as generic mappings?
Closed 4 years ago1
gen-py-classes generating extra slot info
Closed 4 years ago2
gen-rdf doesn't work with a default context
Closed 4 years ago
Github actions force commit to the output directory is too forceful
Closed 4 years ago
Types URI is not generated correctly
Closed 4 years ago1
Slot_usage is not reflected in identifier class
Closed 4 years ago
Re-enable check_yaml section of `test_model_uris.py`
Closed 4 years ago
Edits on the __init__ file in the test directory should not be put-able
Closed 4 years ago
Integrate test output generation in github workflow
Closed 4 years ago1
Mixin slot missing in python generator
Closed 4 years ago
Need a way to test warning messages from logger
Closed 4 years ago1