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Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment.
Passed 3 of 8 test cases with the skill, and 6 of 8 without it.
1 fixed7 passed either way4 still failing10 broke
Tokens, turns and time describe resource use, not a dollar price.
A test case the skill fixed. Same model, same prompt, with and without the skill.
If an initial search for experiment raw files on ArrayExpress fails or shows files unavailable, what secondary repository or fallback note should be recorded in the profile?
| Checked | Without skill | With skill |
|---|---|---|
| The report notes BioStudies as a secondary fallback repository when primary files are unavailable. | Missed | Passed |
The instructions your model reads when the skill loads.
Retrieve gene expression experiments and multi-omics datasets with disambiguation and quality assessment.
IMPORTANT: Always use English terms in tool calls. Respond in the user's language.
LOOK UP DON'T GUESS: Never assume which datasets exist or their accessions. Always search to confirm.
Before retrieving, determine: organism, tissue, experimental design (case-control/time-series/dose-response). These affect which database to search and how to interpret results. RNA-seq provides wider dynamic range; microarray has extensive legacy data. Prioritize experiments with >=3 biological replicates, complete annotations, and both raw+processed data.
Phase 0: Clarify (if ambiguous) → Phase 1: Disambiguate → Phase 2: Search & Retrieve → Phase 3: Report
Ask ONLY if: gene name ambiguous, tissue/condition unclear, organism not specified. Skip for: specific accessions (E-MTAB-, E-GEOD-, S-BSST*), clear disease/tissue+organism, explicit platform requests.
Resolve official gene symbol (HGNC for human, MGI for mouse). Note common aliases for search expansion.
| User Query Type | Search Strategy |
|---|---|
| Specific accession | Direct retrieval |
| Gene + condition | "[gene] [condition]" + species filter |
| Disease only | "[disease]" + species filter |
| Technology-specific | Add platform keywords |
test cases passed, vs 6 / 8 without
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