skills/structural-biology-drug-discovery/dailymed-database/SKILL.md
Query FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.
npx skillsauth add jaechang-hits/scicraft dailymed-databaseInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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DailyMed is the National Library of Medicine's official repository of FDA-approved drug labeling information, containing 140,000+ structured product labels (SPLs) for prescription drugs, OTC medications, biologics, and vaccines. The REST API (v2) provides structured JSON/XML access to the full label content including indications, dosage, warnings, contraindications, adverse reactions, and packaging data — with no authentication required.
fda-database instead; DailyMed contains label text, not post-market safety signalsddinter-database; DailyMed label text is unstructured for interactionsrequests, pandas, matplotlibtime.sleep(0.3) in batch loopspip install requests pandas matplotlib
import requests
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
# Search drug labels by name
r = requests.get(f"{BASE}/spls.json", params={"drug_name": "metformin", "pagesize": 5})
r.raise_for_status()
data = r.json()
print(f"Total labels found: {data['metadata']['total_elements']}")
for spl in data["data"][:3]:
print(f" {spl['title']!r:60s} setid={spl['setid']}")
Search for structured product labels (SPLs) using drug name. Returns paginated list of matching labels with set IDs.
import requests
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def search_spls(drug_name, pagesize=20, page=1):
"""Search DailyMed SPLs by drug name. Returns list of label summaries."""
r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": pagesize, "page": page},
timeout=15)
r.raise_for_status()
return r.json()
result = search_spls("atorvastatin", pagesize=10)
meta = result["metadata"]
print(f"Search: 'atorvastatin' → {meta['total_elements']} labels across {meta['total_pages']} pages")
df = pd.DataFrame(result["data"])
print(df[["setid", "title", "published_date"]].to_string(index=False))
# setid title published_date
# 8f6c7c7c-... ATORVASTATIN CALCIUM tablet 2024-03-15
# a4b7d3e1-... ATORVASTATIN CALCIUM tablet, film coated 2023-11-20
Fetch the complete structured product label for a specific drug using its set ID. Returns all label sections including indications, warnings, dosage, and adverse reactions.
import requests
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def get_spl(setid):
"""Retrieve full SPL document by set ID. Returns label metadata and XML/JSON."""
r = requests.get(f"{BASE}/spls/{setid}.json", timeout=20)
r.raise_for_status()
return r.json()
# Use a known set ID from search results
setid = "8f6c7c7c-1f7f-4f1a-af86-8b2eef2a8b2c" # example atorvastatin label
label = get_spl(setid)
data = label["data"]
print(f"Title: {data.get('title')}")
print(f"Set ID: {data.get('setid')}")
print(f"Published: {data.get('published_date')}")
print(f"Version: {data.get('version')}")
# Access structured sections
if "sections" in data:
sections = data["sections"]
print(f"\nLabel sections ({len(sections)} total):")
for sec in sections[:5]:
print(f" [{sec.get('loinc_code', 'N/A')}] {sec.get('title', 'Untitled')}")
Look up drug labels by National Drug Code (NDC) — useful when you have a product barcode or dispensing record.
import requests
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def search_by_ndc(ndc_code):
"""Find SPL by NDC code (formatted as XXXXX-XXXX-XX or without dashes)."""
r = requests.get(f"{BASE}/spls.json",
params={"ndc": ndc_code},
timeout=15)
r.raise_for_status()
return r.json()
# NDC for Lipitor 10mg (atorvastatin)
result = search_by_ndc("0071-0155-23")
if result["data"]:
spl = result["data"][0]
print(f"Drug: {spl['title']}")
print(f"Set ID: {spl['setid']}")
print(f"Published: {spl['published_date']}")
else:
print("No label found for this NDC")
Get detailed packaging data (NDC codes, package types, quantities) for a specific drug label by set ID.
import requests
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def get_packaging(setid):
"""Retrieve packaging information for a label (NDC codes, dosage forms, quantities)."""
r = requests.get(f"{BASE}/spls/{setid}/packaging.json", timeout=15)
r.raise_for_status()
return r.json()
setid = "8f6c7c7c-1f7f-4f1a-af86-8b2eef2a8b2c" # example setid
pkg = get_packaging(setid)
if pkg["data"]:
packages = pkg["data"]
print(f"Packaging variants: {len(packages)}")
df = pd.DataFrame(packages)
# Common fields: ndc, dosage_form, route, marketing_status
for col in ["ndc", "dosage_form", "route", "marketing_status"]:
if col in df.columns:
print(f"\n{col.upper()}:")
print(df[col].value_counts().head(5))
Retrieve drug labels using RxNorm Concept Unique Identifier (RxCUI) for integration with RxNorm-based clinical systems.
import requests
import time
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def get_spls_by_rxcui(rxcui):
"""Get all SPLs associated with an RxCUI. Returns list of set IDs and titles."""
r = requests.get(f"{BASE}/rxcuis/{rxcui}/spls.json", timeout=15)
r.raise_for_status()
return r.json()
# RxCUI for atorvastatin: 83367
rxcui = "83367"
result = get_spls_by_rxcui(rxcui)
print(f"SPLs for RxCUI {rxcui} (atorvastatin):")
for spl in result["data"][:5]:
print(f" {spl['setid']} | {spl['title'][:70]}")
print(f" Total: {result['metadata']['total_elements']} labels")
List all standardized drug names in DailyMed — useful for name normalization and autocomplete in drug lookup pipelines.
import requests
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def search_drug_names(query, pagesize=20):
"""Search the DailyMed drug name index for name normalization."""
r = requests.get(f"{BASE}/drugnames.json",
params={"drug_name": query, "pagesize": pagesize},
timeout=15)
r.raise_for_status()
return r.json()
result = search_drug_names("metformin")
print(f"Drug name matches for 'metformin': {result['metadata']['total_elements']}")
for entry in result["data"][:8]:
print(f" {entry['drug_name']}")
# METFORMIN HYDROCHLORIDE
# METFORMIN HYDROCHLORIDE AND SITAGLIPTIN PHOSPHATE
# METFORMIN HYDROCHLORIDE AND SAXAGLIPTIN
Extract specific label sections (e.g., indications, warnings) from multiple drug labels for comparative analysis.
import requests
import time
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
# LOINC codes for common SPL sections
SECTION_LOINC = {
"34067-9": "Indications and Usage",
"34068-7": "Dosage and Administration",
"34071-1": "Warnings",
"34084-4": "Adverse Reactions",
"34070-3": "Contraindications",
"43685-7": "Warnings and Precautions",
}
def get_label_sections(setid):
"""Extract structured sections from an SPL by set ID."""
r = requests.get(f"{BASE}/spls/{setid}.json", timeout=20)
r.raise_for_status()
data = r.json()["data"]
sections = {}
for sec in data.get("sections", []):
loinc = sec.get("loinc_code")
if loinc in SECTION_LOINC:
sections[SECTION_LOINC[loinc]] = sec.get("text", "")
return sections
# Get indications for two statin labels
statins = [
("Atorvastatin", "8f6c7c7c-1f7f-4f1a-af86-8b2eef2a8b2c"),
("Rosuvastatin", "a3b2c4d5-1234-5678-abcd-ef0123456789"), # example
]
records = []
for drug_name, setid in statins:
try:
sections = get_label_sections(setid)
records.append({"drug": drug_name, "indications_length": len(sections.get("Indications and Usage", ""))})
except Exception as e:
print(f"Warning: {drug_name} failed — {e}")
time.sleep(0.3)
df = pd.DataFrame(records)
print(df.to_string(index=False))
An SPL is the official FDA-approved drug label in XML format, structured using Health Level 7 (HL7) Clinical Document Architecture (CDA). Each unique drug product label has a globally unique set ID (UUID format). Multiple versions of the same label share the same set ID but have different version numbers. Always use the most recent published version for current prescribing information.
DailyMed SPLs use standardized LOINC codes to identify label sections, enabling consistent programmatic extraction across all labels:
| LOINC Code | Section Name |
|------------|-------------|
| 34067-9 | Indications and Usage |
| 34068-7 | Dosage and Administration |
| 34070-3 | Contraindications |
| 34071-1 | Warnings |
| 43685-7 | Warnings and Precautions |
| 34084-4 | Adverse Reactions |
| 34073-7 | Drug Interactions |
| 34076-0 | Patient Counseling Information |
| 42229-5 | Mechanism of Action |
| 34069-5 | How Supplied/Storage |
National Drug Codes (NDCs) identify drug products with a three-segment numeric format: labeler-product-package (e.g., 0071-0155-23). NDCs can also appear without dashes in some systems. DailyMed accepts both formats in API queries.
Goal: Retrieve and compare label content for all formulations of an active ingredient — useful for generic vs. brand name comparison.
import requests
import time
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def search_spls(drug_name, pagesize=50):
r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": pagesize},
timeout=15)
r.raise_for_status()
return r.json()
def get_packaging(setid):
r = requests.get(f"{BASE}/spls/{setid}/packaging.json", timeout=15)
r.raise_for_status()
return r.json()
# Search for all metformin labels
result = search_spls("metformin", pagesize=20)
labels = result["data"]
print(f"Found {len(labels)} metformin labels")
rows = []
for label in labels[:10]: # limit for demo
setid = label["setid"]
try:
pkg = get_packaging(setid)
for item in pkg["data"][:2]:
rows.append({
"title": label["title"][:60],
"setid": setid,
"ndc": item.get("ndc"),
"dosage_form": item.get("dosage_form"),
"route": item.get("route"),
"marketing_status": item.get("marketing_status"),
"published_date": label.get("published_date"),
})
except Exception as e:
print(f"Skipping {setid}: {e}")
time.sleep(0.3)
df = pd.DataFrame(rows)
print(f"\nFormulations with packaging data: {len(df)}")
print(df[["title", "dosage_form", "route", "marketing_status"]].drop_duplicates().to_string(index=False))
df.to_csv("metformin_formulations.csv", index=False)
print("\nSaved: metformin_formulations.csv")
Goal: Systematically extract structured warning and adverse reaction text from a set of drug labels for pharmacovigilance research.
import requests
import time
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
TARGET_SECTIONS = {
"34071-1": "Warnings",
"43685-7": "Warnings_and_Precautions",
"34084-4": "Adverse_Reactions",
"34070-3": "Contraindications",
}
def search_and_get_sections(drug_name, max_labels=5):
"""Search for labels and extract safety-relevant sections."""
search_r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": max_labels},
timeout=15)
search_r.raise_for_status()
labels = search_r.json()["data"][:max_labels]
records = []
for label in labels:
setid = label["setid"]
try:
label_r = requests.get(f"{BASE}/spls/{setid}.json", timeout=20)
label_r.raise_for_status()
spl_data = label_r.json()["data"]
row = {"drug_name": drug_name, "title": label["title"][:80], "setid": setid}
for loinc, col in TARGET_SECTIONS.items():
text = ""
for sec in spl_data.get("sections", []):
if sec.get("loinc_code") == loinc:
text = sec.get("text", "")[:500] # first 500 chars
break
row[col] = text
records.append(row)
except Exception as e:
print(f" Skipping {setid}: {e}")
time.sleep(0.3)
return pd.DataFrame(records)
# Compare safety sections across ACE inhibitor labels
drugs = ["lisinopril", "enalapril"]
all_records = []
for drug in drugs:
print(f"Processing: {drug}")
df = search_and_get_sections(drug, max_labels=3)
all_records.append(df)
combined = pd.concat(all_records, ignore_index=True)
print(f"\nExtracted safety sections: {len(combined)} labels")
print(combined[["drug_name", "title"]].to_string(index=False))
combined.to_csv("ace_inhibitor_safety_sections.csv", index=False)
print("Saved: ace_inhibitor_safety_sections.csv")
Goal: Query multiple drugs in a class, count their labeled formulations, and visualize the distribution.
import requests
import time
import pandas as pd
import matplotlib.pyplot as plt
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def count_labels(drug_name):
"""Return total SPL count for a drug name."""
r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": 1},
timeout=15)
r.raise_for_status()
return r.json()["metadata"]["total_elements"]
# Count labels for common statins
statins = {
"atorvastatin": "Atorvastatin",
"rosuvastatin": "Rosuvastatin",
"simvastatin": "Simvastatin",
"pravastatin": "Pravastatin",
"lovastatin": "Lovastatin",
"fluvastatin": "Fluvastatin",
"pitavastatin": "Pitavastatin",
}
counts = {}
for query, label in statins.items():
try:
counts[label] = count_labels(query)
print(f" {label}: {counts[label]} labels")
except Exception as e:
print(f" {label}: error — {e}")
time.sleep(0.3)
# Visualization
df = pd.DataFrame(list(counts.items()), columns=["Drug", "Label_Count"])
df = df.sort_values("Label_Count", ascending=True)
fig, ax = plt.subplots(figsize=(9, 5))
bars = ax.barh(df["Drug"], df["Label_Count"], color="#2196F3", edgecolor="white")
ax.bar_label(bars, fmt="%d", padding=4, fontsize=9)
ax.set_xlabel("Number of DailyMed SPL Entries")
ax.set_title("DailyMed: FDA Drug Label Count by Statin\n(includes brand + generic formulations)")
ax.set_xlim(0, df["Label_Count"].max() * 1.15)
plt.tight_layout()
plt.savefig("statin_label_counts.png", dpi=150, bbox_inches="tight")
print(f"Saved: statin_label_counts.png (total labels: {df['Label_Count'].sum()})")
| Parameter | Endpoint | Default | Range / Options | Effect |
|-----------|----------|---------|-----------------|--------|
| drug_name | /spls, /drugnames | — | any drug name string | Filter labels by drug name (partial match supported) |
| ndc | /spls | — | NDC code string | Filter labels by National Drug Code |
| pagesize | /spls, /drugnames | 20 | 1–100 | Results per page; max 100 |
| page | /spls, /drugnames | 1 | positive integer | Page number for pagination |
| setid | /spls/{setid}, /spls/{setid}/packaging | — | UUID string | Unique label identifier; required for direct access |
| rxcui | /rxcuis/{rxcui}/spls | — | RxNorm concept ID | Look up labels by RxCUI for clinical system integration |
| format | any endpoint | json | json, xml | Response format; JSON is default and preferred |
Resolve set IDs before batch processing: Use the /spls search to get set IDs, then fetch full labels by set ID. Do not construct set IDs from drug names — they are UUID identifiers assigned by FDA.
Add time.sleep(0.3) in batch loops: DailyMed has no published rate limits but is public NIH infrastructure. Polite delays prevent throttling.
import time
for drug in drug_list:
result = search_spls(drug)
time.sleep(0.3) # 200 requests/minute safe upper bound
Use LOINC codes for section extraction, not text parsing: Label sections are indexed by LOINC code, providing consistent section access across all SPL documents without brittle regex on section headers.
Pagination for comprehensive results: The default pagesize=20 may miss formulations. Use metadata["total_elements"] to detect if pagination is needed:
meta = result["metadata"]
total_pages = meta["total_pages"]
if total_pages > 1:
for p in range(2, total_pages + 1):
result = search_spls(drug_name, page=p)
Prefer RxCUI for clinical integration: When integrating with clinical systems (EHR, dispensing), use RxCUI-based lookups (/rxcuis/{rxcui}/spls) for standardized, unambiguous drug identification.
When to use: Quickly determine whether a drug carries the FDA's strongest warning level.
import requests
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
BLACK_BOX_LOINC = "34066-1"
def has_black_box_warning(setid):
"""Return True and warning text if drug label has a black box (boxed) warning."""
r = requests.get(f"{BASE}/spls/{setid}.json", timeout=20)
r.raise_for_status()
sections = r.json()["data"].get("sections", [])
for sec in sections:
if sec.get("loinc_code") == BLACK_BOX_LOINC:
return True, sec.get("text", "")[:300]
return False, ""
# Example: check warfarin label
setid = "8b7c3d4e-5678-90ab-cdef-1234567890ab" # example warfarin setid
has_warning, text = has_black_box_warning(setid)
print(f"Black box warning: {has_warning}")
if has_warning:
print(f"Warning text (first 300 chars): {text}")
When to use: Retrieve all matching labels for a drug when total count exceeds one page.
import requests
import time
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def search_all_spls(drug_name, pagesize=100, delay=0.3):
"""Retrieve all SPLs for a drug name across multiple pages."""
all_labels = []
page = 1
while True:
r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": pagesize, "page": page},
timeout=15)
r.raise_for_status()
data = r.json()
all_labels.extend(data["data"])
if page >= data["metadata"]["total_pages"]:
break
page += 1
time.sleep(delay)
return all_labels
labels = search_all_spls("ibuprofen")
print(f"Total ibuprofen labels: {len(labels)}")
When to use: Build a flat reference table of drug labels for offline analysis.
import requests
import pandas as pd
BASE = "https://dailymed.nlm.nih.gov/dailymed/services/v2"
def export_drug_labels(drug_name, pagesize=50):
"""Export label summaries for a drug name to DataFrame."""
r = requests.get(f"{BASE}/spls.json",
params={"drug_name": drug_name, "pagesize": pagesize},
timeout=15)
r.raise_for_status()
data = r.json()
df = pd.DataFrame(data["data"])
df["drug_query"] = drug_name
return df, data["metadata"]["total_elements"]
df, total = export_drug_labels("amoxicillin")
print(f"Retrieved {len(df)} of {total} amoxicillin labels")
df[["setid", "title", "published_date"]].to_csv("amoxicillin_labels.csv", index=False)
print(f"Saved: amoxicillin_labels.csv (columns: {list(df.columns[:5])})")
| Problem | Cause | Solution |
|---------|-------|----------|
| 404 Not Found on /spls/{setid} | Invalid or retired set ID | Re-search by drug name to get current set IDs |
| Empty data list from search | Drug name not matching any labels | Try shorter name (e.g., "metformin" not "metformin HCl tablets"); check spelling |
| Missing sections in SPL JSON | Older labels may not have all LOINC-coded sections | Check len(sections) before iterating; fall back to XML format for legacy labels |
| ConnectionError / timeout | DailyMed server overload | Retry with exponential backoff; increase timeout=30 |
| Pagination returning duplicates | Page boundary race condition | De-duplicate results by setid after all pages collected |
| Packaging endpoint returns empty | Label exists but has no packaging records | Some biologics and vaccines lack packaging data; use label data directly |
| RxCUI lookup returns no results | RxCUI not mapped in DailyMed | Verify RxCUI via RxNorm API before querying; some experimental drugs are not mapped |
fda-database — openFDA for adverse event reports (FAERS), drug recalls, and enforcement actionsddinter-database — drug-drug interaction severity and mechanisms from DDInterdrugbank-database-access — comprehensive drug information including targets, pathways, and chemical propertiesclinicaltrials-database-search — ClinicalTrials.gov for clinical trial data on drugstools
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