BC ontology-term-resolution
Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistry, resolve compact identifiers via Identifiers.org, map lab shorthand with ZOOMA, and build Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "Zooma", "Bioregistry", "Identifiers.org", "Ontobee", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.
Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4).
As a process C 64/100 · Has gaps — weak spots: result and completion, inputs and preconditions, running it twice
What is at stake
Medium-severity findings: the skill is probably honest, but read what alarmed the scanner.
Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.
The skill asks for more than the task needs: broad tool access, credential environment variables, binaries. Every extra permission widens the damage from a mistake or a compromise.
Narrow allowed-tools and the variable list to the minimum; replace binaries with readable sources or scripts.
How to improve
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 1
✓ No critical or high findings
Medium and low: 1
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medium Broad scope
meta-broad-allowed-toolsSKILL.md:1Broad tool permissions pre-approved: Bashallowed-tools: Read Write Edit Bash
Files scanned: 12. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
- note
edit-residuethe text marks something as outdated (lines 77, 100, 148, 181): check that old rules are not kept next to new ones — the full check reads the text for contradictions
Process rating: all ten parameters 64/100
- 0Result and completion. Does not say what the result is
- 0Inputs and preconditions. Does not say what the process needs to start
- 30Running it twice. 4 mutating operations with no state check
- 50Failures and branches. 0 branches, has a failure section
- 70When it triggers. States when to use, but not when not to
- 100Tools and files. Tools declared in frontmatter
- 100Steps. 4 steps
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 2586 tokens
- 100Progress reporting. Reports progress
- low 12 top-level sections: this looks like several domains in one skill
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +4Description does not say when NOT to use the skill (false activations)
- +3Description length 999: 120–800 characters recommended
- +3Output format is not stated: the model decides each time
- -33 of 7 scripts are never mentioned in SKILL.md
- +2Single-language instructions
- +5Description quotes 10 example trigger phrases
- +4Structure: 13 headings
- +3Step-by-step instructions: 4 items
- +4Has examples (9 code blocks)
- +4Reference files are cited in the instructions (4 of 4)
- +1License stated
Quality base 70; lint remarks subtract, signals add up to 100. Result: 88.