ontology-access-kit

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If you create a `ValueSetExpander` without specifying a configuration, it will include a default config: ```python DEFAULT_CONFIG = ValueSetConfiguration(default_resolver=Resolver("", shorthand_prefix="sqlite:obo")) ... configuration: ValueSetConfiguration = field(default_factory=lambda: DEFAULT_CONFIG) ``` This is handy...

cmungall

Extended prefix map support

3

## Overview There doesn't seem to be much support yet for EPMs in OAK. ## Questions 1. Should there be a mirror issue for this in SemanticSQL? ## Additional info...

joeflack4

Hard coded CURIES in OAK code cause confusion when ontologies use different prefix maps

3

Having pieces of code like https://github.com/INCATools/ontology-access-kit/blob/d139e99fe7faa109e0b71840e20140852a8267d9/src/oaklib/utilities/lexical/lexical_indexer.py#L52, and I think just searching there are a number of cases in OAK where these are occur, seems dangerous to me. @joeflack4 just uncovered...

matentzn

`lexical_index_to_sssom()` EPM param

4

## Changes - Update: lexical_index_to_sssom(): Added param for extended prefix map ## Context I was working on this https://github.com/monarch-initiative/mondo-ingest/pull/394 and was getting errors in both `sssom-py` and `ontology-access-kit`. For `sssom-py`,...

joeflack4

Added additional documentation to why-predicates notebook

1

- Monarch tutorial for tomorrow - ignoring B027 (why did this start now?) - Adding info

cmungall

Support for reasoning

2

Strategies: - owlery #31 - owlapi interaction e.g via robot-python plugin - partial: https://github.com/INCATools/oakx-robot - async approach - separate process writes to common store - native python, or python wrapping...

cmungall

OAK Adapters vs. Invalid URI/CURIEs

5

(Possibly related: #499) It seems that any/many adapter methods are throwing errors/warnings about invalid URI/CURIEs: ``` ... ERROR:root:Skipping statements(subject=MONDO:8000018,predicate=skos:exactMatch,object=,value=None,datatype=None,language=None,); ValueError: is not a valid URI or CURIE ERROR:root:Skipping statements(subject=MONDO:8000019,predicate=skos:exactMatch,object=,value=None,datatype=None,language=None,); ValueError:...

glass-ships

`.entities()` typedef update

2

## Overview Currently, the return type definitions for `.entities()` methods are inaccurate. it says `Iterable[CURIE]`, but it is also possible for it to return "quoted URIs" (example: ``). ## Possible...

joeflack4

Document if and when to write plugins, and what the alternatives are

1

Currently we have docs on how to write plugins: https://incatools.github.io/ontology-access-kit/howtos/write-a-plugin.html From the docs: --- A plugin is a software component that adds a specific feature to an existing computer program....

cmungall

Define general patterns for CLI commands

2

I like how robot has a very predictable pattern for commands/operations, with most named as a single verb This is the current set of commands: |command|desc| |---|---| |add-taxon-constraints|Test candidate taxon...

cmungall