tooluniverse-clinical-guidelines

仓库: mims-harvard/tooluniverse
安装量: 104
排名: #8086

安装

npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-clinical-guidelines

Clinical Guidelines Search & Retrieval Search and retrieve evidence-based clinical practice guidelines from 12+ authoritative sources spanning 41 tools. Covers disease management guidelines, society recommendations, pharmacogenomics guidance, and patient resources. KEY PRINCIPLES : Multi-source search — Search ≥3 databases in parallel for comprehensive coverage Source-appropriate queries — Match query style to each database's strengths Condition + society specific — When user names a disease or society, use targeted tools English queries first — Use English medical terms in all tool calls; respond in user's language Cite sources — Every guideline result must include source organization and URL When to Use Apply when user asks: "What are the guidelines for [condition]?" "What does [ADA/AHA/NCCN/NICE/WHO] say about [topic]?" "Standard of care for [disease]?" "Drug-gene interactions for [drug/gene]?" (pharmacogenomics) "Screening recommendations for [condition]?" "Is there a guideline for [clinical question]?" "What do guidelines say about [treatment/drug]?" "Clinical recommendations for [oncology topic]?" Phase 0: Tool Verification (MANDATORY FIRST STEP) Before searching, verify tools load: from tooluniverse import ToolUniverse tu = ToolUniverse ( ) tu . load_tools ( ) assert hasattr ( tu . tools , 'NICE_Clinical_Guidelines_Search' ) Correct call pattern (use either approach):

Option A: direct attribute access

result

tu . tools . NICE_Clinical_Guidelines_Search ( query = 'diabetes' , limit = 5 )

Option B: run_one_function

result

tu
.
run_one_function
(
{
'name'
:
'NICE_Clinical_Guidelines_Search'
,
'arguments'
:
{
'query'
:
'diabetes'
,
'limit'
:
5
}
}
)
Phase 1: Identify Query Strategy
Determine which tools to use based on the user's question:
Query type
Primary tools
Secondary tools
General disease guideline
NICE, TRIP, GIN
PubMed, EuropePMC, CMA
Cardiology
AHA_ACC_search_guidelines, AHA_list_guidelines
NICE, TRIP
Oncology
NCCN_search_guidelines, NCCN_list_patient_guidelines
NICE, GIN
Diabetes / endocrinology
ADA_search_standards, ADA_list_standards_sections
NICE, SIGN
Pharmacogenomics
CPIC_get_gene_drug_pairs, CPIC_list_guidelines
CPIC_get_gene_info
Canadian guidelines
CMA_Guidelines_Search, CTFPHC_search_guidelines
—
Scottish/UK guidelines
SIGN_search_guidelines, NICE
CMA
International guidelines
GIN_Guidelines_Search
OpenAlex, EuropePMC
Living guidelines
MAGICapp_list_guidelines
GIN
Full-text retrieval
NICE_Guideline_Full_Text, WHO_Guideline_Full_Text, AHA_ACC_get_guideline
—
Phase 2: Multi-Source Search
2.1 General Search (Use ≥3 databases)
NICE_Clinical_Guidelines_Search
⭐ (Best general source)
Parameters:
query
(string, required),
limit
(integer, required)
Returns:
list
directly (NOT wrapped in dict) —
[{title, url, summary, content, date}, ...]
Handle:
result = tu.tools.NICE_Clinical_Guidelines_Search(...); isinstance(result, list)
Example:
NICE_Clinical_Guidelines_Search(query='type 2 diabetes management', limit=5)
GIN_Guidelines_Search
⭐ (Best multi-society aggregator)
Parameters:
query
(string, required),
limit
(integer, required)
Returns:
list
directly —
[{title, url, description, source, organization}, ...]
Example:
GIN_Guidelines_Search(query='colorectal cancer screening', limit=5)
TRIP_Database_Guidelines_Search
Parameters:
query
(string, required),
limit
(integer, required),
search_type
(string, required —
must be
'guidelines'
)
Returns:
list
directly —
[{title, url, description, content, publication}, ...]
Example:
TRIP_Database_Guidelines_Search(query='diabetes', limit=5, search_type='guidelines')
WHO_Guidelines_Search
⚠️ (Limited relevance)
Parameters:
query
(string, required),
limit
(integer, required)
Returns:
list
directly —
[{title, url, description, content, source}, ...]
LIMITATION
Does not reliably filter by topic. May return unrelated recent WHO publications.
Use for broad international queries; do not rely on for specific disease searches.
Example:
WHO_Guidelines_Search(query='diabetes', limit=5)
CMA_Guidelines_Search
(Canadian)
Parameters:
query
(string, required),
limit
(integer, required)
Returns:
list
directly —
[{title, url, description, content, date}, ...]
Example:
CMA_Guidelines_Search(query='diabetes', limit=5)
SIGN_search_guidelines
(Scottish/UK)
Parameters:
query
(string, required — NOT
q
),
limit
(integer, optional)
Returns:
list
directly —
[{number, title, topic, published, url}, ...]
Example:
SIGN_search_guidelines(query='diabetes', limit=5)
CTFPHC_search_guidelines
(Canadian prevention)
Parameters:
query
(string, required — NOT
q
),
limit
(integer, optional)
Returns:
list
directly —
[{title, url, year}, ...]
Example:
CTFPHC_search_guidelines(query='colorectal cancer', limit=5)
OpenAlex_Guidelines_Search
Parameters:
query
(string, required),
limit
(integer, required),
year_from
(integer,
optional
),
year_to
(integer,
optional
)
Returns:
list
directly —
[{title, authors, institutions, year, doi}, ...]
Example:
OpenAlex_Guidelines_Search(query='diabetes management', limit=5)
(year params optional)
With years:
OpenAlex_Guidelines_Search(query='diabetes management', limit=5, year_from=2020, year_to=2024)
EuropePMC_Guidelines_Search
Parameters:
query
(string, required),
limit
(integer, required)
Returns:
list
directly —
[{title, pmid, pmcid, doi, authors}, ...]
Note: May return loosely relevant results; use for literature discovery not definitive guidelines
Example:
EuropePMC_Guidelines_Search(query='diabetes guideline', limit=5)
PubMed_Guidelines_Search
Parameters:
query
(string, required),
limit
(integer, required),
api_key
(string,
optional
— use
''
for anonymous)
Returns:
list
directly —
[{title, pmid, pmcid, doi}, ...]
Example:
PubMed_Guidelines_Search(query='diabetes guideline', limit=5)
(api_key optional)
2.2 Society-Specific Search
ADA Standards of Care (Diabetes)
ADA_list_standards_sections()
— No parameters. Lists all 19 sections of ADA Standards of Care (2026).
Returns list of section titles with PMIDs
ADA_search_standards(query, limit)
— Search within ADA Standards.
Returns: list —
[{title, ...}]
Note
Uses PubMed corporate author filter. Use broad medical terms, not specific phrases.
✅ Works:
'glycemic targets'
,
'pharmacologic approaches'
,
'cardiovascular risk'
❌ May fail: very specific phrases like
'first-line medication metformin'
ADA_get_standards_section(section_number)
— Get metadata for a specific section.
Returns dict with section abstract (not full PMC text)
AHA/ACC Cardiology
AHA_ACC_search_guidelines(query, limit)
— Search AHA/ACC guidelines.
Returns:
list
directly —
[{title, ...}]
Example:
AHA_ACC_search_guidelines(query='heart failure management', limit=5)
AHA_list_guidelines(limit)
/
ACC_list_guidelines(limit)
— List recent guidelines.
AHA_ACC_get_guideline(pmid)
— Get full text of AHA/ACC guideline by PMID (via PMC).
Returns dict with full text
Example:
AHA_ACC_get_guideline(pmid='37952199')
NCCN Oncology
NCCN_list_patient_guidelines(limit)
— List all NCCN patient guideline resources (up to 74).
Returns:
list
directly —
[{cancer_type, url, category}, ...]
⚠️ Field is
cancer_type
, NOT
title
Use
r[i]['cancer_type']
to get the cancer name,
r[i]['url']
for URL
NCCN_search_guidelines(query, limit)
— Search NCCN publications.
Returns:
list
directly —
[{title, ...}]
Note: Returns PubMed abstracts of NCCN articles (JNCCN), not proprietary guideline text
NCCN_get_patient_guideline(url)
— Get full text of a patient guideline.
Parameter:
url
(string) — the full URL from NCCN_list_patient_guidelines
Example:
NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient-resources/guidelines-for-patients/guidelines-for-patients-details?patientGuidelineId=61')
⚠️ Do NOT pass an integer ID — pass the full URL string
MAGICapp Living Guidelines
MAGICapp_list_guidelines(limit)
— List living guidelines.
Returns:
dict wrapped
—
r.get('data', [])
gives the list
⚠️ Field is
name
, NOT
title
; use
item['name']
for guideline title
Use
item['guidelineId']
for follow-up calls
MAGICapp_get_guideline(guideline_id)
— Get full guideline details.
MAGICapp_get_recommendations(guideline_id)
— Get recommendations for a guideline.
MAGICapp_get_sections(guideline_id)
— Get sections.
NCI Resources
⚠️ (Research tools catalog, NOT clinical guidelines)
NCI_search_cancer_resources(q, size)
— Search NCI Research Resources for Researchers (R4R).
⚠️
This is a catalog of bioinformatics tools, datasets, and lab instruments — NOT a clinical guidelines database
Parameters:
q
(NOT
query
),
size
(NOT
limit
— use
size
for result count)
Returns: dict —
r.get('data', {}).get('results', [])
gives the list
Useful for: finding analysis tools, datasets, bioinformatics resources related to a cancer type
Example:
NCI_search_cancer_resources(q='colorectal cancer screening', size=5)
2.3 Pharmacogenomics Search (CPIC)
Recommended workflow for gene-drug queries:
Step 1: CPIC_get_gene_info(genesymbol='GENE') → gene overview
Step 2: CPIC_get_gene_drug_pairs(genesymbol='GENE') → all drug pairs + CPIC levels
Step 3: CPIC_list_guidelines(limit=50) → find guideline_id for gene+drug
Step 4: CPIC_get_recommendations(guideline_id=N) → specific dosing recommendations
Step 5: CPIC_get_alleles(genesymbol='GENE') → allele definitions
All CPIC tools return
dict-wrapped
use r.get('data', []) to access results. CPIC_get_gene_info(genesymbol) — Gene overview. Example: CPIC_get_gene_info(genesymbol='CYP2D6') CPIC_get_gene_drug_pairs(genesymbol, limit) — All gene-drug interactions with CPIC levels. Returns: data = list of {genesymbol, drugid, cpiclevel, pgkbcalevel, usedforrecommendation, ...} cpiclevel A/B/C/D: A = strongest evidence CPIC_list_guidelines(limit) — All CPIC guidelines. Returns: data = list of {name: 'GENE and Drug', guidelineId, url, ...} Use to find the guidelineId for a specific gene+drug pair CPIC_get_recommendations(guideline_id, limit) — Get dosing recommendations. ⚠️ Parameter is guideline_id (integer), NOT genesymbol Workflow: first find guideline_id from CPIC_list_guidelines , then call this Example: CPIC_get_recommendations(guideline_id=100416, limit=20) Returns duplicate records per allele combination — deduplicate by phenotype before presenting CPIC_get_alleles(genesymbol, limit) — Allele definitions. Use clinicalfunctionalstatus field (NOT functionalstatus which is always null) Example: CPIC_get_alleles(genesymbol='CYP2D6', limit=10) CPIC_get_drug_info(drugname) — Drug details. Example: CPIC_get_drug_info(drugname='codeine') CPIC_search_gene_drug_pairs(genesymbol, limit) — Search gene-drug pairs. ⚠️ Requires PostgREST filter syntax : genesymbol='eq.CYP2D6' (not just 'CYP2D6' ) Example: CPIC_search_gene_drug_pairs(genesymbol='eq.CYP2D6', limit=5) 2.4 Full-Text Retrieval NICE_Guideline_Full_Text(url) — Get NICE guideline text. Use URL from NICE_Clinical_Guidelines_Search results Returns dict (may have empty data for some guidelines; try chapter URLs like .../chapter/Recommendations ) WHO_Guideline_Full_Text(url) — Get WHO guideline text. Note: Most WHO T2D content is in PDFs; tool may return PDF link not full text AHA_ACC_get_guideline(pmid) — Get AHA/ACC guideline text via PMC. Phase 3: Synthesize Results 3.1 Report Structure

Clinical Guidelines: [Topic]

Summary

[2-3 sentence overview of what guidelines say]

Key Recommendations

[Source 1: NICE/ADA/NCCN/etc.]

[Key recommendations with evidence grade, URL]

[Source 2]

[Key recommendations]

Pharmacogenomics (if applicable)

[CPIC phenotype-to-recommendation table]

References

[All URLs cited]
3.2 Evidence Grading
Grade A
(ADA) /
Class I
(AHA) /
Strong
(SIGN) = high confidence
Grade B/C
= moderate confidence;
Grade D
/
Consensus
= expert opinion
CPIC Level A
= strongest PGx evidence;
B
= moderate;
C/D
= limited
Note recommendation year — guidelines vary in currency (SIGN 2025, ADA 2026, NICE Feb 2026)
3.3 CPIC Recommendation Deduplication
CPIC returns multiple records for the same phenotype (one per allele combination). Before presenting:
seen_phenotypes
=
set
(
)
unique_recs
=
[
]
for
rec
in
recs
:
phenotype
=
rec
.
get
(
'phenotype'
)
or
rec
.
get
(
'lookupkey'
,
''
)
if
phenotype
not
in
seen_phenotypes
:
seen_phenotypes
.
add
(
phenotype
)
unique_recs
.
append
(
rec
)
Phase 4: Decision Logic
General disease guideline:
NICE (
query
,
limit
) — UK, high quality
GIN (
query
,
limit
) — multi-society aggregator ⭐ best for breadth
TRIP (
query
,
limit
,
search_type='guidelines'
)
If cardiac → add AHA_ACC_search_guidelines
If cancer → add NCCN_search_guidelines + NCCN_list_patient_guidelines
If diabetes → add ADA_list_standards_sections + ADA_search_standards
Pharmacogenomics:
CPIC_get_gene_info(genesymbol)
→ overview
CPIC_get_gene_drug_pairs(genesymbol)
→ all drugs with CPIC levels
CPIC_list_guidelines(limit=50)
→ find guideline_id for target gene+drug
CPIC_get_recommendations(guideline_id=N)
→ specific recs (deduplicate by phenotype)
Full text retrieval:
Find guideline URL/PMID from search results
NICE URL → NICE_Guideline_Full_Text
AHA/ACC PMID → AHA_ACC_get_guideline
WHO URL → WHO_Guideline_Full_Text
NCCN patient guideline URL → NCCN_get_patient_guideline
Fallback strategy:
If NICE returns empty → try TRIP or GIN
If ADA returns 0 results → broaden query terms (e.g.,
'pharmacologic approaches'
instead of
'metformin first-line'
)
If WHO returns irrelevant results → skip WHO, use GIN or EuropePMC instead
If CPIC returns no recommendations → list gene-drug pairs with CPIC levels as a proxy
Critical Parameter Notes (Verified by Testing)
Tool
CORRECT
WRONG
NICE_Clinical_Guidelines_Search
query='...'
,
limit=N
(both required)
❌
q='...'
TRIP_Database_Guidelines_Search
search_type='guidelines'
required
❌ omitting search_type
OpenAlex_Guidelines_Search
year_from
/
year_to
are
optional
❌ treating as required
PubMed_Guidelines_Search
api_key
is
optional
(omit or use
''
)
❌ treating api_key as required
GIN_Guidelines_Search
limit=N
required
❌ omitting limit
CMA_Guidelines_Search
limit=N
required
❌ omitting limit
SIGN_search_guidelines
query='...'
(NOT
q
)
❌
q='...'
CTFPHC_search_guidelines
query='...'
(NOT
q
)
❌
q='...'
NCI_search_cancer_resources
q='...'
,
size=N
(NOT
limit
)
❌
query=...
or
limit=N
NCCN_list_patient_guidelines
field
cancer_type
(not
title
)
❌
.get('title')
NCCN_get_patient_guideline
url='https://...'
(full URL string)
❌ integer patientGuidelineId
MAGICapp_list_guidelines
r.get('data', [])
for list
❌ accessing
r
directly as list
MAGICapp_* items
field
name
(not
title
)
❌
.get('title')
CPIC_* tools
r.get('data', [])
for list
❌ accessing
r
directly
CPIC_get_recommendations
guideline_id=N
(integer)
❌
genesymbol='CYP2D6'
CPIC_search_gene_drug_pairs
genesymbol='eq.CYP2D6'
(PostgREST)
❌
genesymbol='CYP2D6'
CPIC_get_alleles
use
clinicalfunctionalstatus
field
❌
functionalstatus
(always null)
NCI_search_cancer_resources
r.get('data',{}).get('results',[])
❌
r.get('data', [])
Response Format Reference
Tool
Return type
Access pattern
NICE_Clinical_Guidelines_Search
list
(raw)
result[0]['title']
GIN_Guidelines_Search
list
(raw)
result[0]['title']
TRIP_Database_Guidelines_Search
list
(raw)
result[0]['title']
WHO_Guidelines_Search
list
(raw)
result[0]['title']
EuropePMC_Guidelines_Search
list
(raw)
result[0]['title']
PubMed_Guidelines_Search
list
(raw)
result[0]['title']
CMA_Guidelines_Search
list
(raw)
result[0]['title']
SIGN_search_guidelines
list
(raw)
result[0]['title']
CTFPHC_search_guidelines
list
(raw)
result[0]['title']
ADA_search_standards
list
(raw)
result[0]['title']
AHA_ACC_search_guidelines
list
(raw)
result[0]['title']
NCCN_search_guidelines
list
(raw)
result[0]['title']
NCCN_list_patient_guidelines
list
(raw)
result[0]['cancer_type']
OpenAlex_Guidelines_Search
list
(raw)
result[0]['title']
CPIC_list_guidelines
dict
→
data
r.get('data', [])[0]['name']
CPIC_get_gene_drug_pairs
dict
→
data
r.get('data', [])[0]['genesymbol']
CPIC_get_recommendations
dict
→
data
r.get('data', [])[0]
CPIC_get_gene_info
dict
→
data
r.get('data', {})
MAGICapp_list_guidelines
dict
→
data
r.get('data', [])[0]['name']
NCI_search_cancer_resources
dict
nested
r.get('data',{}).get('results',[])[0]['title']
Known Limitations
WHO_Guidelines_Search
Returns recently-published WHO docs regardless of query topic — results may be irrelevant for specific diseases. Supplement with GIN for international guidelines.
NCI_search_cancer_resources
Catalogs research tools/datasets, NOT clinical practice guidelines.
NICE_Guideline_Full_Text
Retrieves overview page only; recommendation sub-pages (
.../chapter/Recommendations
) may need direct URL
SIGN
No full-text tool; guideline text only available as PDFs
ADA_get_standards_section
Returns abstract only, not full PMC text
CPIC_get_recommendations
Returns many duplicate records per allele combination; deduplicate by phenotype
NCCN_search_guidelines
Returns PubMed/JNCCN abstracts, not proprietary NCCN guideline text
TRIP content
Some TRIP results link to PDF-gated URLs; content extraction may fail with 403 Missing Sources (Potential Future Tools) USPSTF (US Preventive Services Task Force) — primary US screening recommendations ACG (American College of Gastroenterology) — gastroenterology guidelines AGA (American Gastroenterological Association) Cochrane Reviews — systematic reviews on clinical interventions AHRQ — Agency for Healthcare Research and Quality
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