mims-harvard ToolUniverse Tool Description Optimization
Optimize tool descriptions in ToolUniverse JSON configuration files to ensure they are clear, complete, and user-friendly.
When to Apply This Skill
Use when:
- Reviewing newly created tool descriptions
- User asks "are these tools easy to understand?"
- Improving existing tool documentation
- Adding new tools to ToolUniverse
- User mentions tool usability, clarity, or documentation
Quick Optimization Checklist
Tool Description Review:
- [ ] Prerequisites stated (packages, API keys, accounts)
- [ ] Critical abbreviations expanded on first use
- [ ] Required vs optional parameters clear
- [ ] Mutually exclusive options numbered/labeled
- [ ] Parameter guidance includes trade-offs
- [ ] Filter syntax shows available fields
- [ ] File size warnings where relevant
- [ ] Examples show realistic usage
Critical Improvements (Fix Immediately)
1. Clarify Required Input Requirements
Problem: Users don't know if they need ONE input or ALL inputs.
Fix: Use "Required: Provide ONE input type" for mutually exclusive options.
// Before
"description": "Process BED regions, motifs, or gene lists..."
// After
"description": "Process genomic data. **Required: Provide ONE input type** - (1) BED regions, (2) DNA motif, or (3) gene list. Analyzes..."
Number the options and use bold for "Required".
2. Add Prerequisites to First Tool
Problem: Users don't know what to install/configure before use.
Fix: Add prerequisites note to first tool in each family.
"description": "Query single-cell data. Prerequisites: Requires 'package-name' (install: pip install tooluniverse[extra]). Returns..."
Include:
- Package installation command
- API key requirements
- Account creation instructions
3. Expand Critical Abbreviations
Problem: New users don't understand technical terms.
Fix: Expand on first use with format: "Abbreviation (Full Name)".
Common abbreviations to expand:
- H5AD → HDF5-based AnnData
- RPM → Reads Per Million
- TSS → Transcription Start Site
- TAD → Topologically Associating Domain
- DRS → Data Repository Service
- API names (MACS2, IUPAC, etc.)
// Before
"description": "Download H5AD files..."
// After
"description": "Download H5AD (HDF5-based AnnData) files..."
High-Priority Improvements
4. Enhance Filter Parameter Descriptions
Problem: Users don't know what fields are available or what syntax to use.
Fix: List operators, common fields, and provide multiple examples.
"parameter_name": {
"type": "string",
"description": "Filter using SQL-like syntax. Format: 'field == \"value\"'. Operators: ==, !=, in, <, >, <=, >=. Combine with 'and'/'or'. Common fields: tissue, cell_type, disease, assay, sex, ethnicity. Examples: 'tissue == \"lung\"', 'disease == \"COVID-19\" and tissue == \"lung\"', 'cell_type in [\"T cell\", \"B cell\"]'."
}
Include:
- Syntax format
- Available operators
- List of 5-10 common fields
- 2-3 diverse examples
5. Improve Parameter Guidance
Problem: Users don't know which value to choose or what trade-offs exist.
Fix: Explain what each value means and provide recommendations.
// Before
"threshold": "Q-value threshold (05=1e-5, 10=1e-10, 20=1e-20)"
// After
"threshold": "Peak calling stringency. '05'=1e-5 (permissive, more peaks, broad features), '10'=1e-10 (moderate, balanced), '20'=1e-20 (strict, high confidence, narrow peaks). Default '05' suitable for most analyses. Higher values = fewer but more confident peaks."
For each parameter option, explain:
- What it means practically
- When to use it
- Trade-offs involved
- Recommended default
6. Number Mutually Exclusive Options
Problem: Users provide multiple options when only one is allowed.
Fix: Label options as "Option 1", "Option 2", etc.
"bed_data": {
"description": "**Option 1**: BED format regions (tab-separated: chr, start, end). Example: 'chr1\\t1000\\t2000'."
},
"motif": {
"description": "**Option 2**: DNA sequence motif in IUPAC notation. Use: A/T/G/C, W=A|T, S=G|C. Example: 'CANNTG'."
},
"gene_list": {
"description": "**Option 3**: Gene symbols as array. Example: ['TP53', 'MDM2']."
}
Medium-Priority Improvements
7. Add File Size Warnings
For tools that download or return large files:
"description": "Download contact matrices. Note: Files can be large (GBs), check file_size in metadata before downloading. Returns..."
8. Clarify Web Form vs API Results
When tool returns submission URL instead of direct results:
"description": "Perform enrichment analysis. Note: Returns submission URL (web form-based analysis). Analyzes..."
9. Explain File Type Differences
For tools with multiple format options:
"file_type": "File format. Common types: 'cooler' (multi-resolution contact matrices), 'pairs' (aligned read pairs), 'hic' (Juicer format), 'mcool' (multi-resolution cooler)."
Description Structure Template
{
"name": "Tool_operation_name",
"type": "ToolClassName",
"description": "[Action verb] to [purpose]. [Prerequisites if first tool]. [Key data/features]. [Required inputs if mutually exclusive]. [Note about limitations/requirements]. Use for: [use case 1], [use case 2], [use case 3].",
"parameter": {
"properties": {
"param_name": {
"type": "string",
"description": "[What it does]. [Format/syntax if applicable]. [Options with trade-offs]. [Examples]. [Recommendation if applicable]."
}
}
}
}
Description Quality Checklist
Clarity Checks
- Purpose clear in first sentence
- Technical terms expanded
- Prerequisites stated upfront
- Examples show realistic usage
- "Use for:" section lists 3-5 concrete use cases
Completeness Checks
- Required inputs clearly marked
- Parameter choices explained
- Limitations noted (file size, web form, etc.)
- Available fields listed for filters
- Default values recommended
Usability Checks
- New users can understand without external docs
- Users know what to provide
- Users can make informed parameter choices
- Error prevention (mutually exclusive options labeled)
Testing Description Quality
To verify description quality, ask:
Can a new user understand what the tool does?
- Read only the description (no docs)
- Should be clear within 30 seconds
Can a user provide correct inputs on first try?
- Required inputs obvious
- Format/syntax clear
- Mutually exclusive options labeled
Can a user choose appropriate parameters?
- Trade-offs explained
- Recommendations provided
- Defaults justified
Are prerequisites obvious?
- Installation instructions
- API keys/accounts
- File size warnings
Common Patterns by Tool Type
API Query Tools
"description": "Query [data type] from [source]. [Prerequisites]. Filter by [criteria]. Returns [output]. [Data scale]. Use for: [discovery], [analysis], [specific research tasks]."
Key elements:
- What you're querying
- How to filter
- What you get back
- Scale of data
- Prerequisites
Data Download Tools
"description": "Download [file types] from [source]. [Format details]. [File size warning]. [Authentication requirement]. Use for: [offline analysis], [custom processing], [integration]."
Key elements:
- File formats available
- Size warning
- Authentication needs
- What's in the files
Enrichment/Analysis Tools
"description": "Analyze [input type] to find [results]. **Required: Provide ONE input type** - (1) [option], (2) [option], (3) [option]. Compares against [database/background]. [Result format]. Use for: [identifying], [discovering], [predicting]."
Key elements:
- Input requirements clear
- Options numbered
- What gets compared
- What you learn
Validation Commands
After updating descriptions, validate JSON syntax:
# Validate all tool JSONs
python3 -m json.tool src/tooluniverse/data/your_tools.json > /dev/null && echo "✓ Valid"
# Check all tools in category
for f in src/tooluniverse/data/*_tools.json; do
python3 -m json.tool "$f" > /dev/null && echo "✓ $f valid" || echo "✗ $f invalid"
done
Example: Before and After
Before (Unclear):
{
"name": "Tool_enrichment",
"description": "Perform enrichment with tool to find factors.",
"parameter": {
"properties": {
"bed": {"description": "BED data"},
"motif": {"description": "Motif"},
"genes": {"description": "Genes"},
"threshold": {"description": "Threshold value"}
}
}
}
After (Clear):
{
"name": "Tool_enrichment_analysis",
"description": "Identify transcription factors enriched in your data. **Required: Provide ONE input type** - (1) BED genomic regions, (2) DNA sequence motif (IUPAC notation), or (3) gene symbol list. Compares against 400,000+ ChIP-seq experiments. Returns ranked proteins with enrichment scores. Note: Returns submission URL (web-based analysis). Use for: identifying regulators of regions, finding proteins bound to motifs, discovering transcription factors regulating genes.",
"parameter": {
"properties": {
"bed_data": {
"description": "**Option 1**: BED format regions (tab-separated: chr, start, end). For finding proteins bound to genomic regions. Example: 'chr1\\t1000\\t2000'."
},
"motif": {
"description": "**Option 2**: DNA motif in IUPAC notation (A/T/G/C, W=A|T, S=G|C, M=A|C, K=G|T, R=A|G, Y=C|T). Example: 'CANNTG' (E-box)."
},
"gene_list": {
"description": "**Option 3**: Gene symbols as array or single gene. Example: ['TP53', 'MDM2', 'CDKN1A']."
},
"threshold": {
"description": "Peak stringency. '05'=1e-5 (permissive, more peaks), '10'=1e-10 (moderate), '20'=1e-20 (strict, high confidence). Default '05' suitable for most analyses."
}
}
}
}
Summary
Priority order for optimization:
Critical (fix immediately):
- Clarify required inputs
- Add prerequisites
- Expand abbreviations
High (fix soon):
- Enhance filter descriptions
- Improve parameter guidance
- Number mutually exclusive options
Medium (nice to have):
- Add file size warnings
- Clarify web form vs API
- Explain file type differences
Expected impact: 50-75% reduction in user errors, 50-67% faster time to first successful use.