@wentorai/research-plugins 1.3.1 → 1.4.0

package/skills/domains/biomedical/enrichr-api/SKILL.md

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+---
+name: enrichr-api
+description: "Perform gene set enrichment analysis using the Enrichr API"
+metadata:
+  openclaw:
+    emoji: "🔬"
+    category: "domains"
+    subcategory: "biomedical"
+    keywords: ["gene set enrichment", "pathway analysis", "GO terms", "KEGG", "Enrichr", "functional analysis"]
+    source: "https://maayanlab.cloud/Enrichr"
+---
+
+# Enrichr Gene Set Enrichment Analysis API
+
+## Overview
+
+Enrichr is the most widely used gene set enrichment analysis tool, developed by the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai. It tests whether a user-supplied gene list is statistically over-represented in curated gene set libraries spanning pathways, ontologies, transcription factor targets, disease associations, and cell types. The API provides access to 225 background libraries covering over 500,000 annotated gene sets. Free, no authentication required.
+
+## Two-Step Workflow
+
+Enrichr uses a submit-then-query pattern:
+
+1. **POST gene list** to `/addList` -- returns a `userListId` token
+2. **GET enrichment** from `/enrich` using that token and a chosen library
+
+The `userListId` persists on the server, so you can run multiple library queries against the same submission without re-uploading.
+
+## Core Endpoints
+
+### Base URL
+
+```
+https://maayanlab.cloud/Enrichr
+```
+
+### Step 1: Submit Gene List
+
+```bash
+curl -X POST "https://maayanlab.cloud/Enrichr/addList" \
+  -F "list=BRCA1
+BRCA2
+TP53
+EGFR
+MYC
+PTEN
+AKT1
+KRAS
+PIK3CA
+RAF1" \
+  -F "description=cancer_genes"
+```
+
+**Response:**
+
+```json
+{
+  "shortId": "8619200cc78f1513ff1029a04af90ad7",
+  "userListId": 124544426
+}
+```
+
+Genes are newline-separated. The request must use `multipart/form-data` (the `-F` flag), not `application/x-www-form-urlencoded`.
+
+### Step 2: Retrieve Enrichment Results
+
+```bash
+curl "https://maayanlab.cloud/Enrichr/enrich?userListId=124544426&backgroundType=KEGG_2021_Human"
+```
+
+**Response (first 3 of 143 results):**
+
+```json
+{
+  "KEGG_2021_Human": [
+    [1, "Breast cancer", 3.37e-22, 198530.0, 9815800.25,
+     ["PIK3CA","MYC","PTEN","AKT1","KRAS","BRCA1","BRCA2","RAF1","TP53","EGFR"],
+     4.82e-20, 0, 0],
+    [2, "Endometrial cancer", 1.35e-19, 1595.2, 69306.12,
+     ["PIK3CA","MYC","PTEN","AKT1","KRAS","RAF1","TP53","EGFR"],
+     9.68e-18, 0, 0],
+    [3, "Central carbon metabolism in cancer", 6.66e-19, 1285.68, 53809.88,
+     ["PIK3CA","MYC","PTEN","AKT1","KRAS","RAF1","TP53","EGFR"],
+     3.17e-17, 0, 0]
+  ]
+}
+```
+
+Each result array contains: `[rank, term_name, p_value, z_score, combined_score, overlapping_genes, adjusted_p_value, old_p_value, old_adjusted_p_value]`.
+
+### View Submitted Gene List
+
+```bash
+curl "https://maayanlab.cloud/Enrichr/view?userListId=124544426"
+```
+
+```json
+{
+  "genes": ["PIK3CA","MYC","AKT1","PTEN","BRCA1","KRAS","BRCA2","EGFR","TP53","RAF1"],
+  "description": "cancer_genes"
+}
+```
+
+### Export Results as TSV
+
+```bash
+curl "https://maayanlab.cloud/Enrichr/export?userListId=124544426&backgroundType=KEGG_2021_Human&filename=results" \
+  -o enrichr_results.txt
+```
+
+### List Available Libraries
+
+```bash
+curl "https://maayanlab.cloud/Enrichr/datasetStatistics"
+```
+
+Returns metadata for all 225 libraries, each entry containing `libraryName`, `numTerms`, `geneCoverage`, and `genesPerTerm`.
+
+## Available Libraries (225 Total)
+
+### Pathway Databases
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| KEGG_2026 | 352 | 8,110 |
+| KEGG_2021_Human | 320 | 8,078 |
+| WikiPathways_2024_Human | 829 | 8,281 |
+| Reactome_Pathways_2024 | 2,105 | 11,671 |
+| BioCarta_2016 | 237 | 1,348 |
+
+### Gene Ontology
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| GO_Biological_Process_2025 | 5,343 | 14,674 |
+| GO_Molecular_Function_2025 | 1,174 | 11,484 |
+| GO_Cellular_Component_2025 | 468 | 11,501 |
+
+### Disease and Phenotype
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| DisGeNET | 9,828 | 17,464 |
+| GWAS_Catalog_2025 | 2,369 | 15,030 |
+| ClinVar_2025 | 609 | 3,481 |
+| OMIM_Disease | 90 | 1,759 |
+| Human_Phenotype_Ontology | 1,779 | 3,096 |
+
+### Transcription Factor and Epigenomics
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| ChEA_2022 | 757 | 18,365 |
+| ENCODE_TF_ChIP-seq_2015 | 816 | 26,382 |
+| JASPAR_PWM_Human_2025 | 675 | 18,518 |
+
+### Cell Type and Tissue
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| CellMarker_2024 | 1,692 | 12,642 |
+| ARCHS4_Tissues | 108 | 21,809 |
+| Human_Gene_Atlas | 84 | 13,373 |
+
+### Cancer and Drug
+
+| Library | Terms | Genes |
+|---------|-------|-------|
+| MSigDB_Hallmark_2020 | 50 | 4,383 |
+| MSigDB_Oncogenic_Signatures | 189 | 11,250 |
+| DGIdb_Drug_Targets_2024 | 659 | 2,513 |
+
+## Rate Limits
+
+- No authentication or API key required
+- No officially published rate limits, but automated queries should include reasonable delays (1-2 seconds between requests)
+- Very large gene lists (>3,000 genes) may time out on some libraries
+- The `userListId` persists server-side; avoid re-submitting the same list repeatedly
+
+## Academic Use Cases
+
+- **Differential expression follow-up**: Submit DEGs from RNA-seq to identify enriched pathways and GO terms
+- **GWAS hit annotation**: Map GWAS-significant genes to disease phenotypes via DisGeNET or GWAS_Catalog
+- **Drug target discovery**: Cross-reference gene signatures against DGIdb_Drug_Targets for druggable candidates
+- **Transcription factor analysis**: Identify upstream regulators via ChEA or ENCODE TF libraries
+
+## Python Usage
+
+```python
+import requests
+
+ENRICHR_URL = "https://maayanlab.cloud/Enrichr"
+
+
+def submit_gene_list(genes: list[str], description: str = "") -> int:
+    """Submit a gene list to Enrichr, return userListId."""
+    payload = {
+        "list": (None, "\n".join(genes)),
+        "description": (None, description),
+    }
+    resp = requests.post(f"{ENRICHR_URL}/addList", files=payload)
+    resp.raise_for_status()
+    return resp.json()["userListId"]
+
+
+def get_enrichment(user_list_id: int, library: str) -> list[dict]:
+    """Retrieve enrichment results for a given library."""
+    resp = requests.get(
+        f"{ENRICHR_URL}/enrich",
+        params={"userListId": user_list_id, "backgroundType": library},
+    )
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for entry in data.get(library, []):
+        results.append({
+            "rank": entry[0],
+            "term": entry[1],
+            "p_value": entry[2],
+            "z_score": entry[3],
+            "combined_score": entry[4],
+            "genes": entry[5],
+            "adj_p_value": entry[6],
+        })
+    return results
+
+
+def get_libraries() -> list[dict]:
+    """List all available Enrichr libraries."""
+    resp = requests.get(f"{ENRICHR_URL}/datasetStatistics")
+    resp.raise_for_status()
+    return resp.json()["statistics"]
+
+
+# Example: enrichment analysis of cancer-related genes
+genes = ["BRCA1", "BRCA2", "TP53", "EGFR", "MYC",
+         "PTEN", "AKT1", "KRAS", "PIK3CA", "RAF1"]
+
+list_id = submit_gene_list(genes, "cancer_genes")
+print(f"Submitted gene list, ID: {list_id}")
+
+# Query KEGG pathways
+kegg = get_enrichment(list_id, "KEGG_2021_Human")
+print(f"\nTop 5 KEGG pathways ({len(kegg)} total):")
+for r in kegg[:5]:
+    print(f"  {r['rank']}. {r['term']}")
+    print(f"     p={r['p_value']:.2e}, adj_p={r['adj_p_value']:.2e}, "
+          f"genes={','.join(r['genes'][:5])}...")
+
+# Query GO Biological Process
+go_bp = get_enrichment(list_id, "GO_Biological_Process_2023")
+print(f"\nTop 5 GO Biological Processes ({len(go_bp)} total):")
+for r in go_bp[:5]:
+    print(f"  {r['rank']}. {r['term']}")
+    print(f"     p={r['p_value']:.2e}, genes={','.join(r['genes'])}")
+```
+
+## References
+
+- [Enrichr Web App](https://maayanlab.cloud/Enrichr)
+- [Enrichr API Docs](https://maayanlab.cloud/Enrichr/help#api)
+- Chen, E.Y. et al. (2013). "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool." *BMC Bioinformatics* 14:128.
+- Kuleshov, M.V. et al. (2016). "Enrichr: a comprehensive gene set enrichment analysis web server 2016 update." *Nucleic Acids Res.* 44(W1).
+- Xie, Z. et al. (2021). "Gene Set Knowledge Discovery with Enrichr." *Current Protocols* 1(3):e90.

package/skills/domains/biomedical/ensembl-rest-api/SKILL.md

@@ -0,0 +1,204 @@
+---
+name: ensembl-rest-api
+description: "Query gene, sequence, and variant data via the Ensembl REST API"
+metadata:
+  openclaw:
+    emoji: "🧬"
+    category: "domains"
+    subcategory: "biomedical"
+    keywords: ["Ensembl", "gene lookup", "sequence retrieval", "genomics", "variant data", "bioinformatics"]
+    source: "https://rest.ensembl.org"
+---
+
+# Ensembl REST API Guide
+
+## Overview
+
+Ensembl is a genome browser and annotation system maintained by EMBL-EBI and the Wellcome Sanger Institute, providing reference assemblies, gene annotations, variant data, and comparative genomics for over 300 vertebrate genomes. It is the genomic reference underpinning gget, PyEnsembl, and BioMart.
+
+The REST API exposes Ensembl data via stateless HTTP. Researchers can look up genes by symbol or stable ID, retrieve genomic/cDNA/protein sequences, query variant annotations (rsIDs, clinical significance, consequences), access cross-references (HGNC, UniProt, RefSeq, OMIM), and obtain assembly metadata. Responses in JSON or XML.
+
+## Authentication
+
+No authentication required. All endpoints are publicly accessible. Users needing higher throughput can register for an API token.
+
+## Core Endpoints
+
+### lookup/symbol: Gene Lookup by Symbol
+
+Retrieve gene metadata: coordinates, biotype, canonical transcript.
+
+- **URL**: `GET https://rest.ensembl.org/lookup/symbol/{species}/{symbol}`
+- **Parameters**:
+
+| Parameter     | Type   | Required | Description                                      |
+|---------------|--------|----------|--------------------------------------------------|
+| species       | string | Yes      | Species name (e.g., `homo_sapiens`)              |
+| symbol        | string | Yes      | Gene symbol (e.g., `BRCA1`, `TP53`)              |
+| expand        | int    | No       | Set to 1 to include transcripts and translations |
+| content-type  | string | Yes      | `application/json` or `text/xml`                 |
+
+- **Example**:
+
+```bash
+curl "https://rest.ensembl.org/lookup/symbol/homo_sapiens/BRCA1?content-type=application/json"
+```
+
+- **Response** (actual):
+
+```json
+{
+  "display_name": "BRCA1",
+  "description": "BRCA1 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1100]",
+  "object_type": "Gene", "species": "homo_sapiens",
+  "assembly_name": "GRCh38", "biotype": "protein_coding",
+  "seq_region_name": "17", "start": 43044292, "end": 43170245, "strand": -1,
+  "id": "ENSG00000012048", "canonical_transcript": "ENST00000357654.9"
+}
+```
+
+### sequence/id: Sequence Retrieval
+
+Retrieve genomic, cDNA, CDS, or protein sequences by Ensembl stable ID.
+
+- **URL**: `GET https://rest.ensembl.org/sequence/id/{id}`
+- **Parameters**:
+
+| Parameter      | Type   | Required | Description                                           |
+|----------------|--------|----------|-------------------------------------------------------|
+| id             | string | Yes      | Ensembl stable ID (e.g., `ENSG00000012048`)           |
+| type           | string | No       | `genomic`, `cdna`, `cds`, or `protein`                |
+| expand_5prime  | int    | No       | Expand 5' flanking region by N bases                  |
+| expand_3prime  | int    | No       | Expand 3' flanking region by N bases                  |
+| content-type   | string | Yes      | `application/json` or `text/plain` (FASTA)            |
+
+- **Example**:
+
+```bash
+curl "https://rest.ensembl.org/sequence/id/ENSG00000012048?content-type=application/json&type=genomic"
+```
+
+- **Response** (actual, seq truncated):
+
+```json
+{
+  "id": "ENSG00000012048", "query": "ENSG00000012048",
+  "desc": "chromosome:GRCh38:17:43044292:43170245:-1",
+  "molecule": "DNA",
+  "seq": "AAAGCGTGGGAATTACAGATAAATTAAAACTGTGGAACCCCTTTCCTCGGCTGCCGCCAAGGTGTTCGG..."
+}
+```
+
+### xrefs/symbol: Cross-References
+
+Map a gene symbol to Ensembl stable IDs and external database identifiers.
+
+- **URL**: `GET https://rest.ensembl.org/xrefs/symbol/{species}/{symbol}`
+- **Key params**: `species` (required), `symbol` (required), `external_db` (optional filter, e.g., `UniProt`)
+- **Example**:
+
+```bash
+curl "https://rest.ensembl.org/xrefs/symbol/homo_sapiens/TP53?content-type=application/json"
+```
+
+- **Response** (actual): `[{"type":"gene","id":"ENSG00000141510"},{"type":"gene","id":"LRG_321"}]`
+
+Use `xrefs/id/{id}` to expand an Ensembl ID to all external cross-references (UniProt, HGNC, RefSeq, OMIM).
+
+### variation: Variant Annotation
+
+Retrieve variant data by rsID: mappings, alleles, consequence, clinical significance.
+
+- **URL**: `GET https://rest.ensembl.org/variation/{species}/{id}`
+- **Key params**: `species` (required), `id` (required, e.g., `rs699`)
+- **Example**:
+
+```bash
+curl "https://rest.ensembl.org/variation/homo_sapiens/rs699?content-type=application/json"
+```
+
+- **Response** (actual, synonyms truncated):
+
+```json
+{
+  "name": "rs699", "var_class": "SNP",
+  "most_severe_consequence": "missense_variant",
+  "clinical_significance": ["benign"],
+  "evidence": ["Frequency","1000Genomes","Cited","ESP","Phenotype_or_Disease","ExAC","TOPMed","gnomAD"],
+  "mappings": [{"location":"1:230710048-230710048","allele_string":"A/G","strand":1,"assembly_name":"GRCh38"}]
+}
+```
+
+### info/assembly: Assembly Metadata
+
+- **URL**: `GET https://rest.ensembl.org/info/assembly/{species}`
+- **Response** (actual): Returns `assembly_name` ("GRCh38.p14"), `assembly_date` ("2013-12"), `assembly_accession` ("GCA_000001405.29"), full `karyotype` array (1-22, X, Y, MT), and 347 `top_level_region` entries.
+
+## Rate Limits
+
+- **Without token**: 15 requests per second per IP.
+- **With token**: higher limits available upon registration.
+- **Response headers**: `X-RateLimit-Limit`, `X-RateLimit-Remaining`, `X-RateLimit-Reset` on every response.
+- **Batch POST endpoints** (`/lookup/id`, `/sequence/id`): accept up to 1000 IDs per request.
+- **GRCh37 mirror**: `https://grch37.rest.ensembl.org`
+
+## Academic Use Cases
+
+- **Gene annotation**: Look up coordinates and biotypes for HGNC symbols to annotate RNA-seq results.
+- **Variant interpretation**: Retrieve consequence types and clinical significance for GWAS rsIDs.
+- **ID mapping**: Map between Ensembl, UniProt, RefSeq, and HGNC identifiers.
+- **Primer design**: Fetch genomic sequences with flanking regions for PCR or CRISPR targeting.
+- **Comparative genomics**: Query homology endpoints for orthologs across species.
+
+## Code Examples (Python)
+
+### Gene Lookup and Sequence Retrieval
+
+```python
+import requests
+
+BASE = "https://rest.ensembl.org"
+HEADERS = {"Content-Type": "application/json"}
+
+gene = requests.get(f"{BASE}/lookup/symbol/homo_sapiens/BRCA1", headers=HEADERS).json()
+print(f"{gene['display_name']} ({gene['id']}) chr{gene['seq_region_name']}:{gene['start']}-{gene['end']}")
+
+seq = requests.get(f"{BASE}/sequence/id/{gene['id']}?type=cds", headers=HEADERS).json()
+print(f"CDS length: {len(seq['seq'])} bp")
+```
+
+### Batch ID Lookup (POST)
+
+```python
+import requests
+
+ids = ["ENSG00000012048", "ENSG00000141510", "ENSG00000157764"]  # BRCA1, TP53, BRAF
+resp = requests.post(
+    "https://rest.ensembl.org/lookup/id",
+    headers={"Content-Type": "application/json", "Accept": "application/json"},
+    json={"ids": ids}
+)
+for ens_id, info in resp.json().items():
+    print(f"{info['display_name']:10s} chr{info['seq_region_name']}:{info['start']}-{info['end']}")
+```
+
+### Variant Annotation Pipeline
+
+```python
+import requests
+
+for rsid in ["rs699", "rs1042522", "rs334"]:
+    v = requests.get(
+        f"https://rest.ensembl.org/variation/homo_sapiens/{rsid}",
+        headers={"Content-Type": "application/json"}
+    ).json()
+    loc = v["mappings"][0]["location"] if v.get("mappings") else "N/A"
+    print(f"{v['name']:12s} {v['var_class']:5s} {v['most_severe_consequence']:25s} {loc}")
+```
+
+## References
+
+- REST API docs: https://rest.ensembl.org/documentation
+- Ensembl browser: https://www.ensembl.org
+- gget toolkit (built on Ensembl REST): https://pachterlab.github.io/gget/
+- GRCh37 archive API: https://grch37.rest.ensembl.org

package/skills/domains/biomedical/epidemiology-guide/SKILL.md

@@ -3,7 +3,7 @@ name: epidemiology-guide
 description: "Epidemiological study designs, measures of association, and public health ana..."
 metadata:
   openclaw:
-    emoji: "microscope"
+    emoji: "🔬"
     category: "domains"
     subcategory: "biomedical"
     keywords: ["epidemiology", "public health", "evidence-based medicine", "clinical medicine", "disease surveillance"]

package/skills/domains/biomedical/genomics-analysis-guide/SKILL.md

@@ -3,7 +3,7 @@ name: genomics-analysis-guide
 description: "Workflows for RNA-seq, GWAS, and variant calling in genomic research"
 metadata:
   openclaw:
-    emoji: "microscope"
+    emoji: "🔬"
     category: "domains"
     subcategory: "biomedical"
     keywords: ["genomics", "RNA-seq", "GWAS", "molecular biology", "genetics", "bioinformatics"]

package/skills/domains/biomedical/medical-data-api/SKILL.md

@@ -0,0 +1,197 @@
+---
+name: medical-data-api
+description: "Access FDA drug data and WHO global health statistics for research"
+metadata:
+  openclaw:
+    emoji: "💊"
+    category: "domains"
+    subcategory: "biomedical"
+    keywords: ["FDA", "drug safety", "WHO", "global health", "adverse events", "medical data", "pharmacovigilance"]
+    source: "https://open.fda.gov"
+---
+
+# Medical Data API Guide (openFDA + WHO GHO)
+
+## Overview
+
+This skill covers two major open medical data APIs for academic research:
+
+**openFDA** is the U.S. Food and Drug Administration's public API providing access to drug labeling (SPL), adverse event reports (FAERS), recalls, and NDC directory. The FAERS dataset contains over 722,000 reports for common drugs like aspirin, making it a primary pharmacovigilance resource.
+
+**WHO Global Health Observatory (GHO)** is the WHO's OData v4 API serving over 2,000 health indicators across 194 member states -- life expectancy, mortality, disease burden, health system coverage, risk factors, and SDG targets. Returns structured JSON with numeric values, confidence intervals, and dimensional breakdowns by country, sex, and year.
+
+Both APIs are free, require no authentication, and return JSON.
+
+## Authentication
+
+**openFDA**: No authentication required. An optional API key (free, via https://open.fda.gov/apis/authentication/) increases rate limits from 240/min to 120,000/day. Register at https://open.fda.gov/apis/ to obtain a key, then append `&api_key=YOUR_KEY` to requests.
+
+**WHO GHO**: No authentication required. No API key needed. All endpoints are publicly accessible with no registration.
+
+## Core Endpoints
+
+### openFDA: Drug Labels
+
+Search FDA-approved drug labeling data (Structured Product Labeling). Returns boxed warnings, indications, dosage, contraindications, and adverse reactions text.
+
+- **URL**: `GET https://api.fda.gov/drug/label.json`
+- **Parameters**:
+
+| Parameter | Type   | Required | Description                                         |
+|-----------|--------|----------|-----------------------------------------------------|
+| search    | string | No       | Search query using openFDA query syntax              |
+| limit     | int    | No       | Number of results (default 1, max 1000)              |
+| skip      | int    | No       | Offset for pagination                                |
+| count     | string | No       | Count unique values of a field                       |
+
+- **Example**:
+
+```bash
+curl "https://api.fda.gov/drug/label.json?search=aspirin&limit=1"
+```
+
+- **Response**: Returns `meta.results.total` (26,564 for "aspirin") and `results` array. Each result contains `boxed_warning`, `indications_and_usage`, `dosage_and_administration`, `warnings`, `adverse_reactions`, `drug_interactions`, and `openfda` cross-references (brand/generic names, manufacturer, NDC, pharmacologic class).
+
+### openFDA: Adverse Events (FAERS)
+
+Search the FDA Adverse Event Reporting System. Each record describes a safety report including patient demographics, suspect drugs, reported reactions, and outcomes.
+
+- **URL**: `GET https://api.fda.gov/drug/event.json`
+- **Parameters**:
+
+| Parameter | Type   | Required | Description                                         |
+|-----------|--------|----------|-----------------------------------------------------|
+| search    | string | No       | Query (e.g., `patient.drug.openfda.brand_name:"aspirin"`) |
+| limit     | int    | No       | Number of results (default 1, max 1000)              |
+| skip      | int    | No       | Offset for pagination (max skip+limit = 26,000)      |
+| count     | string | No       | Count field values (e.g., `patient.reaction.reactionmeddrapt.exact`) |
+
+- **Example**:
+
+```bash
+curl 'https://api.fda.gov/drug/event.json?search=patient.drug.openfda.brand_name:"aspirin"&limit=1'
+```
+
+- **Response**: Returns `meta.results.total` (722,607 for aspirin). Each result: `safetyreportid`, `serious` (1=yes, 2=no), `primarysourcecountry`, `receivedate`, nested `patient` with `patientsex`, `reaction` array (MedDRA terms + `reactionoutcome`), and `drug` array with `drugcharacterization` (1=suspect, 2=concomitant, 3=interacting), `medicinalproduct`, `openfda` cross-references.
+
+### WHO GHO: Health Indicator Data
+
+Retrieve data points for a specific health indicator with country, year, and sex dimensions.
+
+- **URL**: `GET https://ghoapi.azureedge.net/api/{IndicatorCode}`
+- **Parameters** (OData v4 query options):
+
+| Parameter | Type   | Required | Description                                           |
+|-----------|--------|----------|-------------------------------------------------------|
+| $top      | int    | No       | Limit number of records returned                       |
+| $skip     | int    | No       | Skip records for pagination                            |
+| $filter   | string | No       | OData filter (e.g., `SpatialDim eq 'USA' and TimeDim eq 2020`) |
+| $select   | string | No       | Select specific fields                                 |
+| $orderby  | string | No       | Sort results                                           |
+
+- **Example**:
+
+```bash
+# Life expectancy at birth (WHOSIS_000001)
+curl "https://ghoapi.azureedge.net/api/WHOSIS_000001?\$top=2"
+```
+
+- **Response**: OData JSON with `value` array. Each record: `SpatialDim` (ISO country, e.g., "BTN"), `ParentLocation` (WHO region), `TimeDim` (year), `Dim1` (sex: "SEX_BTSX"/"SEX_MLE"/"SEX_FMLE"), `Value` ("67.8 [67.1-68.6]"), `NumericValue` (67.845665), `Low`/`High` confidence bounds.
+
+### WHO GHO: Indicator Directory
+
+List available health indicators with their codes and names.
+
+- **URL**: `GET https://ghoapi.azureedge.net/api/Indicator`
+- **Example**:
+
+```bash
+curl "https://ghoapi.azureedge.net/api/Indicator?\$top=5"
+```
+
+- **Response**: Array of entries with `IndicatorCode` (e.g., "Adult_curr_e-cig"), `IndicatorName` (e.g., "Prevalence of current e-cigarette use among adults (%)"), `Language` ("EN"). Over 2,000 indicators spanning mortality, morbidity, health systems, and risk factors.
+
+## Rate Limits
+
+**openFDA**:
+- Without API key: 240 requests per minute (burst), 1,000 requests per day
+- With free API key: 240 requests per minute, 120,000 requests per day
+- Pagination ceiling: `skip` + `limit` cannot exceed 26,000 (use `search` + `sort` for deeper access)
+
+**WHO GHO**:
+- No documented rate limits; the service runs on Azure CDN (azureedge.net)
+- Recommended: keep requests under 10/second for courtesy
+- For bulk downloads, use the GHO data portal CSV exports at https://www.who.int/data/gho
+
+## Academic Use Cases
+
+### Pharmacovigilance: Adverse Event Signal Detection
+
+Count reactions by MedDRA term to identify safety signals:
+
+```python
+import requests
+
+resp = requests.get("https://api.fda.gov/drug/event.json", params={
+    "search": 'patient.drug.openfda.brand_name:"aspirin"',
+    "count": "patient.reaction.reactionmeddrapt.exact",
+    "limit": 10
+})
+for r in resp.json()["results"]:
+    print(f"  {r['term']}: {r['count']} reports")
+```
+
+### Epidemiology: Cross-National Health Comparisons
+
+Compare health indicators across countries and time periods:
+
+```python
+import requests
+
+resp = requests.get("https://ghoapi.azureedge.net/api/WHOSIS_000001", params={
+    "$filter": "SpatialDim eq 'JPN' and Dim1 eq 'SEX_BTSX'",
+    "$orderby": "TimeDim desc",
+    "$top": 10
+})
+for row in resp.json()["value"]:
+    print(f"  Japan {row['TimeDim']}: {row['Value']}")
+```
+
+### Public Health: Drug Label Comparison
+
+Compare safety language across drug labels for regulatory research:
+
+```python
+import requests
+
+for drug in ["ibuprofen", "naproxen", "celecoxib"]:
+    resp = requests.get("https://api.fda.gov/drug/label.json",
+        params={"search": f'openfda.generic_name:"{drug}"', "limit": 1})
+    results = resp.json().get("results", [])
+    if results:
+        warning = results[0].get("boxed_warning", ["None"])[0][:200]
+        print(f"{drug.upper()}: {warning}...\n")
+```
+
+## Key Indicator Codes (WHO GHO)
+
+| Code | Indicator |
+|------|-----------|
+| WHOSIS_000001 | Life expectancy at birth |
+| NCDMORT3070 | NCD mortality (30-70 years) |
+| MDG_0000000001 | Under-five mortality rate |
+| WHS4_100 | Physicians per 10,000 population |
+| NCD_BMI_30A | Prevalence of obesity (BMI >= 30) |
+| SA_0000001688 | Alcohol per capita consumption |
+| TOBACCO_0000000262 | Tobacco smoking prevalence |
+
+## References
+
+- openFDA documentation: https://open.fda.gov/apis/
+- openFDA API key registration: https://open.fda.gov/apis/authentication/
+- openFDA query syntax: https://open.fda.gov/apis/query-syntax/
+- openFDA GitHub: https://github.com/FDA/openfda
+- WHO GHO API documentation: https://www.who.int/data/gho/info/gho-odata-api
+- WHO GHO OData endpoint: https://ghoapi.azureedge.net/api/
+- WHO GHO indicator list: https://ghoapi.azureedge.net/api/Indicator
+- WHO Global Health Observatory portal: https://www.who.int/data/gho