system requirements:

• go
• yamlfmt
• robot
• wget
• yq (Mike Farah/GO)

• try litellm instead of llm?
• extract Extensions with linkml-map instead of yq?

Ontology Access Kit operations

https://github.com/INCATools/ontology-access-kit/

These runoak commands fetch a SQLite version of EnvO from the clous (a BBOP S3 bucket?) if needed. They don't require downloading the EnvO RDF/XML OWL from GitHub CJM would create an alias like envo="runoak -i obo:sqlite:envo"

# for anything that uses the Bioportal endpoint
runoak set-apikey --endpoint bioportal <SECRET>

runoak --input bioportal: ontology-metadata envo
runoak --input bioportal: ontology-versions envo
runoak --input bioportal: search biome

runoak cache-ls # cache-clear if really necessary

# most useful for MIxS/EnvO subsetting tasks?
runoak --input sqlite:obo:envo relationships .desc//p=i ENVO:00000428 > biome-relationships.tsv # !!! pivot? include entailment? --include-entailed / --no-include-entailed; --non-redundant-entailed / --no-non-redundant-entailed
runoak --input sqlite:obo:envo term-metadata .desc//p=i ENVO:00000428 > biome-metadata.yaml # !!! try different formats? or predicate list?

runoak --input sqlite:obo:envo aliases 'biome'
runoak --input sqlite:obo:envo ancestors 'biome'
runoak --input sqlite:obo:envo definitions 'biome' 
runoak --input sqlite:obo:envo descendants 'biome' 
runoak --input sqlite:obo:envo info 'biome'
runoak --input sqlite:obo:envo labels 'biome' 
runoak --input sqlite:obo:envo languages
runoak --input sqlite:obo:envo leafs
runoak --input sqlite:obo:envo obsoletes
runoak --input sqlite:obo:envo prefixes
runoak --input sqlite:obo:envo siblings 'aquatic biome'
runoak --input sqlite:obo:envo terms
runoak --input sqlite:obo:envo tree  biome # up by default
runoak --input sqlite:obo:envo usages  biome

Needs followup

runoak --input envo.ofn axioms 'biome' # NotImplementedError requires OFN... but still getting ERROR:root:function AnnotationAssertion(oboInOwl:hasExactSynonym, obo:FOODON_00001014, yoghurt) TypeError: Type mismatch between en-br (type: <class 'str'> and [<class 'funowl.general_definitions.LanguageTag'>, <class 'NoneType'>]
runoak --input sqlite:obo:envo disjoints 'biome' --autolabel -O csv # biome is disjoint from both ecoregion and ecozone # additional single-blank-node disjoints?!
runoak --input sqlite:obo:envo paths  -p i,p biosphere 'polar biome' # reports results but then says no paths found
runoak --input sqlite:obo:envo roots # why are hail and CL:0000000 reported?
runoak --input sqlite:obo:envo singletons # do these results make sense?
runoak --input sqlite:obo:envo statistics # ERRORS
runoak --input sqlite:obo:envo subsets # output and ERRORS
runoak --input sqlite:obo:envo term-categories biome # nothing
runoak --input sqlite:obo:envo term-subsets biome # nothing```

Haven't goten these to work yet

May not be relevant for MIxS EnvO tasks

• cache-clear
• annotate
• apply
• apply-obsolete
• apply-taxon-constraints
• associations
• associations-counts
• associations-matrix
• diff
• diff-associations
• diff-terms
• diff-via-mappings
• dump
• enrichment
• expand-subsets # WARNING:root:Subset may be incorrectly encoded as value for envoPolar # subset term subset_termValueError: Subset envoPolar not found in ...
• EXTRACT
• fill-table
• generate-definitions
• generate-disjoints
• generate-lexical-replacements
• generate-logical-definitions
• generate-synonyms
• information-content
• lexmatch
• lint
• logical-definitions
• mappings
• migrate-curies
• normalize
• ontologies
• QUERY
• rollup
• similarity
• similarity-pair
• synonymize # Deprecated: use generate-synonyms
• taxon-constraints
• termset-similarity
• transform
• validate
• validate-definitions
• validate-mappings
• validate-multiple
• validate-synonyms