database-lookup

name

database-lookup

description

Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.

Database Lookup

You have access to 78 public databases through their REST APIs. Your job is to figure out which database(s) are relevant to the user's question, query them, and return the raw JSON results along with which databases you used.

Core Workflow

1. Understand the query — What is the user looking for? A compound? A gene? A pathway? A patent? Expression data? An economic indicator? This determines which database(s) to hit.

2. Select database(s) — Use the database selection guide below. When in doubt, search multiple databases — it's better to cast a wide net than to miss relevant data.

3. Read the reference file — Each database has a reference file in references/ with endpoint details, query formats, and example calls. Read the relevant file(s) before making API calls.

4. Make the API call(s) — Use webfetch or curl via shell for HTTP requests. For POST-only APIs (Open Targets, gnomAD, GDC/TCGA, RummaGEO, SEC EDGAR), use curl.

5. Return results — Always return:

   • The raw JSON response from each database
   • A list of databases queried with the specific endpoints used
   • If a query returned no results, say so explicitly rather than omitting it

Database Selection Guide

Physics & Astronomy

Query	Primary	Also consider
Near-Earth objects, asteroids	NASA (NeoWs)	—
Exoplanets, orbital parameters	NASA Exoplanet Archive	—
Astronomical objects	SIMBAD	SDSS
Galaxy/star spectra	SDSS	SIMBAD
Physical constants, atomic spectra	NIST	—

Earth & Environmental Sciences

Query	Primary	Also consider
Earthquakes	USGS Earthquakes	—
Water data	USGS Water Services	—
Weather, climate data	NOAA (CDO), OpenWeatherMap	—
Air quality, toxic releases	EPA	—

Chemistry & Drugs

Query	Primary	Also consider
Chemical compounds	PubChem	ChEMBL
Bioactivity data (IC50, binding)	ChEMBL, BindingDB	PubChem
Drug-target interactions	ChEMBL, DrugBank	Open Targets
Drug labels, adverse events	FDA (OpenFDA)	DailyMed
Commercial compounds for screening	ZINC	PubChem

Materials Science

Query	Primary	Also consider
Materials by formula	Materials Project	COD
Band gap, electronic structure	Materials Project	—
Crystal structures, CIF files	COD	Materials Project

Biology & Genomics

Query	Primary	Also consider
Biological pathways	Reactome, KEGG	—
Protein sequence, function	UniProt	Ensembl
Protein-protein interactions	STRING	BioGRID
Gene information	NCBI Gene	Ensembl
Gene expression	GEO, GTEx	Human Protein Atlas
3D protein structures	PDB, AlphaFold DB	EMDB
Protein families, domains	InterPro	UniProt
SNP/variant data	dbSNP	ClinVar, gnomAD
Population variant frequencies	gnomAD	dbSNP

Disease & Clinical

Query	Primary	Also consider
Somatic mutations in cancer	COSMIC	cBioPortal
Drug-target-disease associations	Open Targets	ChEMBL
Gene-disease associations	DisGeNET	Open Targets
Mendelian disease-gene	OMIM	NCBI Gene
Variant clinical significance	ClinVar	OMIM
GWAS SNP-trait associations	GWAS Catalog	—
Clinical trials	ClinicalTrials.gov	FDA

Economics & Finance

Query	Primary	Also consider
US economic time series	FRED	BEA
Employment, wages	BLS	FRED
International development	World Bank	FRED
Stocks, forex, crypto	Alpha Vantage	—

API Keys and Access

When an API key is needed:

1. Check environment first — the key may already be exported (e.g., $FRED_API_KEY)
2. Fall back to .env — check .env in the current working directory
3. Proceed without — most APIs still work at lower rate limits

Databases requiring free API keys: FRED, BEA, BLS, NCBI, OpenFDA, USPTO, Data Commons, Materials Project, NASA, NOAA, OpenWeatherMap, OMIM, BioGRID, Alpha Vantage, US Census, DisGeNET, Addgene, LINCS L1000.

Making API Calls

• Use webfetch for GET requests, curl for POST-only APIs
• Set Accept: application/json header where supported
• URL-encode special characters in query parameters
• Parallel OK: When querying different databases, run them in parallel
• Serialize requests to rate-limited APIs: NCBI (3 req/s without key), Ensembl (15 req/s), SEC EDGAR (10 req/s)

Output Format

Structure your response like this:

## Databases Queried
- **PubChem** — /compound/name/aspirin/property/...
- **Reactome** — /search/query?query=aspirin

## Results

### PubChem
[raw JSON response]

### Reactome
[raw JSON response]

If results are very large, present the most relevant portion and note that additional data is available.