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) — See the Making API Calls section below for which HTTP fetch tool to use on your platform.

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

Match the user's intent to the right database(s). Many queries benefit from hitting multiple databases.

Physics & Astronomy

Earth & Environmental Sciences

Chemistry & Drugs

Materials Science & Crystallography

Biology & Genomics

Organism/species matters. Most biology databases cover multiple organisms. If the user's query is about a specific organism, pass it explicitly — don't assume human. Common patterns: Ensembl uses {species} in the URL path (e.g. homo_sapiens), STRING/BioGRID/QuickGO use NCBI taxon IDs (species=9606 for human, 10090 for mouse), UniProt uses organism_id:9606 in search queries, KEGG uses organism codes (hsa, mmu). GTEx and Human Protein Atlas are human-only. Check the reference file for each database's specific parameter.

Disease & Clinical

Patents & Regulatory

Economics & Finance

Social Sciences & Demographics

Cross-domain queries

When the user's query spans multiple domains (e.g. "what do we know about aspirin" or "find everything about BRCA1"), query all relevant databases in parallel.

Common Identifier Formats

Different databases use different identifier systems. If a query fails, the identifier format may be wrong. Here's a quick reference:

Identifier Resolution

When a database doesn't recognize an identifier, convert it using these workflows:

Genes: Symbol (e.g. "TP53") → look up in NCBI Gene (esearch by symbol) → get NCBI Gene ID → convert to Ensembl ID via Ensembl /xrefs/symbol/homo_sapiens/{symbol}, or to UniProt accession via UniProt search (gene_exact:{symbol} AND organism_id:9606).

Compounds: Name → PubChem /compound/name/{name}/cids/JSON → get CID → convert to ChEMBL ID via UniChem or ChEMBL molecule search. If name lookup fails, try SMILES, InChIKey, or CAS number.

Variants: rsID (e.g. "rs334") works directly in dbSNP, ClinVar, GWAS Catalog, gnomAD. For genomic coordinates, use Ensembl VEP to get consequence annotations and linked rsIDs.

Diseases: Name → Open Targets or Monarch search → get EFO or MONDO ID → use in downstream queries.

POST-Only APIs

These databases require HTTP POST and will not work with WebFetch (GET-only). Use curl via your platform's shell tool instead:

API Keys and Access Restrictions

Some databases require API keys or have access restrictions. When an API key is needed:

1. Check the current environment first — the key may already be exported as a shell environment variable (e.g. $FRED_API_KEY). Read it directly from the environment.
2. Fall back to .env — if the variable isn't in the environment, check the .env file in the current working directory.
3. If neither has it — proceed without the key (most APIs still work at lower rate limits) and tell the user which key is missing and how to get one.

Databases requiring API keys (free registration)