Initial commit

.claude-plugin/plugin.json

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+{
+  "name": "ontology-access-kit",
+  "description": "Skills for querying ontologies using the Ontology Access Kit (OAK)",
+  "version": "0.0.0-2025.11.28",
+  "author": {
+    "name": "Chris Mungall",
+    "email": "cjmungall@lbl.gov"
+  },
+  "skills": [
+    "./skills/ontology-access-kit"
+  ]
+}

README.md

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+# ontology-access-kit
+
+Skills for querying ontologies using the Ontology Access Kit (OAK)

plugin.lock.json

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skills/ontology-access-kit/SKILL.md

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+---
+name: ontology-access-kit
+description: Skills for querying ontologies using the Ontology Access Kit (OAK). This should only be used for complex ontology operations, for basic external ontology searching use the OLS MCP
+---
+
+# OAK Guide
+
+## Overview
+
+OAK is a powerful command line library for accessing ontologies. It can be installed via:
+
+- `uv add oaklib`
+- `pip install oaklib`
+
+The main command is `runoak`
+
+## When to use
+
+OAK is generally to be used for more complex operations.
+
+- if you want to do basic search over external ontologies, you should favor the OLS MCP over OAK
+- if you are working with local obo files, then hacky obo tools like `obo-grep.pl` may be better
+
+## Adapters
+
+You typically want to use the sqlite adapter. This gives you fast access to any ontology in OBO, plus a number of other commonly used ontologies, found in semantic-sql.
+
+Example:
+
+`runoak -i sqlite:obo:cl COMMAND COMMAND-OPTS ARGS`
+
+Note the `-i` comes (*before*) the command-specific opts
+
+You can also access any ontology in OLS or BioPortal:
+
+- `runoak -i bioportal:snomedct relationships SNOMEDCT:128351009`
+- `runoak -i bioportal:efo tree -p i EFO:0004200`
+
+But some OAK commands may not be implemented.
+
+With OLS or BioPortal you can also do searches over all ontologies:
+
+- `runoak -i bioportal: info l~NovaSeq`
+- `runoak -i ols: info l~NovaSeq`
+
+To work with local obo files:
+
+- `runoak -i impleobo:my_ont.obo info MY:1234 -O obo`
+
+## Common Operations
+
+You can find a list of all commands with `runoak --help`. oak is highly fully featured, and you are encouraged to
+explore to find the functionality you need. We provide some examples below.
+
+We use `info` for many examples, but note that many options and arguments work across different commands
+
+* Lookup
+   * By exact label: `runoak -i sqlite:obo:cl info neuron` (returns `CL:0000540 ! neuron`)
+   * By exact label (multiple): `runoak -i sqlite:obo:uberon info finger toe`
+   * Search (any match): `runoak -i sqlite:obo:cl info  'l~T cell'`
+   * Search (starts with): `runoak -i sqlite:obo:cl info l^neuron`
+* Fetching detailed info
+   * OBO format: `runoak -i sqlite:obo:cl info CL:0000540 -O obo`
+   * relationships: `runoak -i sqlite:obo:cl  relationships --direction both CL:0000540`
+   * mappings: `runoak -i sqlite:obo:mondo mappings 'Marfan syndrome'`
+   * tree (is-a only): `runoak -i sqlite:obo:cl tree -p i CL:0000540`
+   * metadata: `runoak -i sqlite:obo:chebi term-metdata CHEBI:35235`
+* Complex queries
+   * subclasses: `runoak -i sqlite:obo:cl info .sub CL:0000540 | head`
+   * disjunctions (OR): `runoak -i sqlite:obo:cl info .sub neuron .sub 'T cell' | tail`
+   * conjunctions: `runoak -i sqlite:obo:cl info .sub neuron .and .desc//p=i,p forebrain` (neurons and is-a/part-of the forebrain)
+   * minus: `runoak -i sqlite:obo:cl info .sub neuron .minus .desc//p=i,p forebrain` (neurons and NOT is-a/part-of the forebrain)
+* Visualization
+   * `cl viz -p i,p,RO:0002215 'dopaminergic neuron' -o /tmp/dn.png` - subgraph from a CL term.
+   * note that graphviz requires installing og2dot   
+* Subsets
+   * list subsets: `runoak -i sqlite:obo:go subsets` - list all subsets (goslim_prokaryote etc)
+   * terms in subsets: `runoak -i sqlite:obo:go info .in goslim_generic` - all terms in a subset
+   * terms in subsets: `runoak -i sqlite:obo:go info .in goslim_generic .minus .in goslim_prokaryote` - all terms in a subset not in another
+* Other
+   * `runoak lexmatch --help` for aligning ontologies
+   * `runoak statistics --help` for summary stats
+## Common Options and Idioms
+
+### Graphs
+
+OAK is very graph oriented, following ontologies like GO, CL
+
+Typically for graph operations you want to operate over only is-a and part-of, so use `-p i,p`
+
+You can also specify RO/BFO ids.
+
+E.g.
+
+```bash
+runoak -i sqlite:obo:ro info 'capable of'
+RO:0002215 ! capable of
+```
+
+```bash
+cl relationships -p RO:0002215 'dopaminergic neuron'
+subject	predicate	object	subject_label	predicate_label	object_label
+CL:0000700	RO:0002215	GO:0061527	dopaminergic neuron	capable of	dopamine secretion, neurotransmission
+```
+