database-lookup

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Database Selection Guide

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

Physics & Astronomy

User is asking about...

Primary database(s)

Also consider

Near-Earth objects, asteroids

NASA (NeoWs)

—

Mars rover images

NASA (Mars Rover Photos)

—

Exoplanets, orbital parameters

NASA Exoplanet Archive

—

Astronomical objects by name/coordinates

SIMBAD

SDSS

Galaxy/star spectra, photometry

SDSS

SIMBAD

Physical constants

NIST

—

Atomic spectra, spectral lines

NIST (ASD)

—

Earth & Environmental Sciences

User is asking about...

Primary database(s)

Also consider

Earthquakes, seismic events

USGS Earthquakes

—

Water data, streamflow, groundwater

USGS Water Services

—

Weather (current, forecast, historical)

OpenWeatherMap

NOAA

Climate data, historical weather stations

NOAA (CDO)

—

Air quality, toxic releases

EPA (Envirofacts)

—

Chemistry & Drugs

User is asking about...

Primary database(s)

Also consider

Chemical compounds, molecules

PubChem

ChEMBL

Molecular properties (weight, formula, SMILES)

PubChem

—

Drug synonyms, CAS numbers

PubChem (synonyms)

DrugBank

Bioactivity data, IC50, binding assays

ChEMBL

BindingDB, PubChem

Drug binding affinities (Ki, IC50, Kd)

ChEMBL, BindingDB

PubChem

Drug-target interactions

ChEMBL, DrugBank

BindingDB, Open Targets

Ligands for a protein target (by UniProt)

BindingDB

ChEMBL

Target identification from compound structure

BindingDB (SMILES similarity)

ChEMBL

Drug labels, adverse events, recalls

FDA (OpenFDA)

DailyMed

Drug labels (structured product labels)

DailyMed

FDA (OpenFDA)

Drug pharmacology, indications

DrugBank

FDA

Chemical cross-referencing

PubChem (xrefs)

ChEMBL

Commercially available compounds for screening

ZINC

PubChem

Similarity/substructure search (purchasable)

ZINC

PubChem, ChEMBL

Drug-like compound libraries, building blocks

ZINC

—

FDA-approved drug structures

ZINC (fda subset)

PubChem, FDA

Compound purchasability, vendor catalogs

ZINC

—

Materials Science & Crystallography

User is asking about...

Primary database(s)

Also consider

Materials by formula or elements

Materials Project

COD

Band gap, electronic structure

Materials Project

—

Crystal structures, CIF files

COD

Materials Project

Elastic/mechanical properties

Materials Project

—

Formation energy, thermodynamics

Materials Project

—

Cell parameters, space groups

COD

Materials Project

Biology & Genomics

User is asking about...

Primary database(s)

Also consider

Biological pathways

Reactome, KEGG

—

What pathways a gene/protein is in

Reactome (mapping), KEGG

—

Enzyme kinetics, catalytic activity

BRENDA

KEGG

Metabolomics studies, metabolite profiles

Metabolomics Workbench

PubChem

m/z or exact mass lookup

Metabolomics Workbench (moverz/exactmass)

PubChem

Protein sequence, function, annotation

UniProt

Ensembl

Protein-protein interactions

STRING

BioGRID

Gene information, genomic location

NCBI Gene

Ensembl

Genome sequences, variants, transcripts

Ensembl

NCBI Gene

Gene expression datasets

GEO (NCBI E-utilities)

—

Gene expression across tissues

GTEx

Human Protein Atlas

Gene expression signatures (CMap/L1000)

LINCS L1000

GEO

Gene set enrichment vs GEO

RummaGEO

GEO

Protein sequences (NCBI)

NCBI Protein

UniProt

Taxonomic classification

NCBI Taxonomy

—

SNP/variant data (dbSNP)

dbSNP

ClinVar, gnomAD

Population variant frequencies

gnomAD

dbSNP

Sequencing run metadata

SRA

ENA, GEO

Nucleotide sequences (European archive)

ENA

SRA, NCBI Gene

Genome assemblies, raw reads (European)

ENA

SRA, Ensembl

Cross-references from sequence accessions

ENA (xref)

NCBI Gene, UniProt

Genome annotations, tracks

UCSC Genome Browser

Ensembl

3D protein structures (experimental)

PDB (RCSB)

EMDB

3D protein structures (predicted)

AlphaFold DB

PDB

EM maps, cryo-EM structures

EMDB

PDB

Protein families, domains

InterPro

UniProt

Chemical entities (biological)

ChEBI

PubChem

Protein/genetic interactions

BioGRID

STRING

Gene function annotations (GO terms)

QuickGO

Gene Ontology

Regulatory elements, ChIP-seq, ATAC-seq

ENCODE

—

TF binding profiles/motifs

JASPAR

ENCODE

Protein expression across tissues

Human Protein Atlas

UniProt

Single-cell atlas projects

Human Cell Atlas

—

Proteomics datasets

PRIDE

—

Mouse gene data

MouseMine

NCBI Gene

Plasmid repository

Addgene

—

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

User is asking about...

Primary database(s)

Also consider

Somatic mutations in cancer

COSMIC

Open Targets, cBioPortal

Cancer genomics (TCGA)

GDC (TCGA)

COSMIC, cBioPortal

Cancer study mutations, CNA, expression

cBioPortal

GDC (TCGA), COSMIC

Tumor clinical data (survival, staging)

cBioPortal

GDC (TCGA)

Drug-target-disease associations

Open Targets

ChEMBL

Gene-disease associations

DisGeNET

Open Targets, Monarch

Mendelian disease-gene relationships

OMIM

NCBI Gene

Variant clinical significance

ClinVar (NCBI)

OMIM

GWAS SNP-trait associations

GWAS Catalog

—

Disease-phenotype-gene links

Monarch Initiative

HPO

Phenotype ontology, HPO terms

HPO

Monarch

Pharmacogenomics, drug-gene interactions

ClinPGx (PharmGKB)

DrugBank

Clinical trials for a drug/disease

ClinicalTrials.gov

FDA

Disease-related expression data

GEO

Open Targets

Patents & Regulatory

User is asking about...

Primary database(s)

Also consider

Patents by keyword or technology

USPTO (PatentsView)

—

Patents by inventor or assignee

USPTO (PatentsView)

—

Patent prosecution status

USPTO (PEDS)

—

Trademark lookup

USPTO (TSDR)

—

SEC company filings, 10-K, 10-Q

SEC EDGAR

—

Economics & Finance

User is asking about...

Primary database(s)

Also consider

US economic time series (GDP, CPI, rates)

FRED

BEA

Employment, wages, labor statistics

BLS

FRED

GDP, national accounts

BEA

FRED, World Bank

International development indicators

World Bank

FRED

Interest rates, money supply

Federal Reserve

FRED

Euro exchange rates, ECB monetary stats

ECB

—

US debt, yield curves, fiscal data

US Treasury

FRED

Stock prices, forex, crypto

Alpha Vantage

—

Statistical data across many topics

Data Commons

—

Social Sciences & Demographics

User is asking about...

Primary database(s)

Also consider

US population, housing, income data

US Census

Data Commons

EU statistics (economy, trade, health)

Eurostat

World Bank

Global health indicators (mortality, disease)

WHO GHO

World Bank

Cross-domain queries

User is asking about...

Primary database(s)

Also consider

Everything about a compound

PubChem + ChEMBL + DrugBank

BindingDB, ZINC, Reactome, FDA

Everything about a gene

NCBI Gene + UniProt + Ensembl

Reactome, STRING, COSMIC, cBioPortal, ENA

Everything about a variant

dbSNP + ClinVar + gnomAD

GWAS Catalog, COSMIC, cBioPortal

Drug target pathways

ChEMBL + Reactome

Open Targets, GEO

Prior art for a chemical invention

USPTO + PubChem

ChEMBL

Everything about a material

Materials Project + COD

—

US economic overview

FRED + BLS + BEA

Federal Reserve

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

Format

Example

Used by

UniProt accession

P##### or Q#####

P04637 (TP53)

UniProt, STRING, AlphaFold, Reactome mapping

Ensembl gene ID

ENSG###########

ENSG00000141510

Ensembl, Open Targets, GTEx

NCBI Gene ID

Integer

7157 (TP53)

NCBI Gene, GEO, DisGeNET, HPO

HGNC ID

HGNC:#####

HGNC:11998

Monarch

PubChem CID

Integer

2244 (aspirin)

PubChem

ZINC ID

ZINC + 15 digits

ZINC000000000053 (aspirin)

ZINC

ENA Project

PRJEB + digits

PRJEB40665

ENA

ENA Run

ERR + digits

ERR1234567

ENA

ENA Experiment

ERX + digits

ERX1234567

ENA

ENA Sample

ERS + digits

ERS1234567

ENA

ChEMBL ID

CHEMBL####

CHEMBL25 (aspirin)

ChEMBL

Reactome stable ID

R-HSA-######

R-HSA-109581

Reactome

HP term

HP:#######

HP:0001250 (seizure)

HPO (URL-encode colon as %3A)

MONDO disease

MONDO:#######

MONDO:0007947

Monarch

GO term

GO:#######

GO:0008150

QuickGO, Gene Ontology

dbSNP rsID

rs########

rs334

dbSNP, GWAS Catalog, gnomAD

GENCODE ID

ENSG###.## (versioned)

ENSG00000139618.17

GTEx (requires version suffix)

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:

Database

Why POST needed

Example

Open Targets

GraphQL endpoint

curl -X POST -H "Content-Type: application/json" -d '{"query":"..."}' https://api.platform.opentargets.org/api/v4/graphql

gnomAD

GraphQL endpoint

curl -X POST -H "Content-Type: application/json" -d '{"query":"..."}' https://gnomad.broadinstitute.org/api

RummaGEO

POST-only enrichment

curl -X POST -H "Content-Type: application/json" -d '{"genes":["..."]}' https://rummageo.com/api/enrich

GDC/TCGA

Complex filter queries

curl -X POST -H "Content-Type: application/json" -d '{"filters":...}' https://api.gdc.cancer.gov/ssms

SEC EDGAR

Requires User-Agent header

curl -H "User-Agent: YourApp you@email.com" https://efts.sec.gov/LATEST/search-index?q=...

API Keys and Access Restrictions

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

• 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.

• **Fall back to .env** — if the variable isn't in the environment, check the .env file in the current working directory.

• 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)

Database

Env Variable

Registration URL

FRED

FRED_API_KEY

https://fred.stlouisfed.org/docs/api/api_key.html

BEA

BEA_API_KEY

https://apps.bea.gov/API/signup/

BLS

BLS_API_KEY

https://data.bls.gov/registrationEngine/

NCBI (GEO, Gene)

NCBI_API_KEY

https://www.ncbi.nlm.nih.gov/account/settings/

OpenFDA

OPENFDA_API_KEY

https://open.fda.gov/apis/authentication/

USPTO (PatentsView)

PATENTSVIEW_API_KEY

https://patentsview.org/apis/keyrequest

Data Commons

DATACOMMONS_API_KEY

Google Cloud Console

Materials Project

MP_API_KEY

https://materialsproject.org (free account)

NASA

NASA_API_KEY

https://api.nasa.gov (free, DEMO_KEY available)

NOAA (CDO)

NOAA_API_KEY

https://www.ncdc.noaa.gov/cdo-web/token

OpenWeatherMap

OPENWEATHERMAP_API_KEY

https://openweathermap.org/appid

OMIM

OMIM_API_KEY

https://omim.org/api (free academic)

BioGRID

BIOGRID_API_KEY

https://webservice.thebiogrid.org (free)

Alpha Vantage

ALPHAVANTAGE_API_KEY

https://www.alphavantage.co/support/#api-key

US Census

CENSUS_API_KEY

https://api.census.gov/data/key_signup.html

DisGeNET

DISGENET_API_KEY

https://www.disgenet.org (free academic)

Addgene

ADDGENE_API_KEY

https://www.addgene.org (free account)

LINCS L1000 (CLUE)

CLUE_API_KEY

https://clue.io (free academic)

These are all free to obtain. The APIs work without keys but have lower rate limits. Always try with a key first — if the env variable isn't set, proceed without the key and note in your response that rate limits may be lower.

Databases with paid or restricted access

Database

Restriction

Free alternative

DrugBank

Paid API license required

Use ChEMBL + PubChem + OpenFDA instead

COSMIC

Free academic registration required (JWT auth)

Use Open Targets for cancer mutation data

BRENDA

Free registration required (SOAP, not REST)

Use KEGG for enzyme/pathway data

When a database requires paid access or registration the user hasn't set up:

• Fall back to a free alternative that can answer the same question

• Tell the user which database you couldn't access, why, and what you used instead

• If the user specifically requests a restricted database, explain the access requirements so they can set it up

Loading API keys

Step 1 — Check the current environment. The key may already be exported as a shell variable. For example, in Claude Code you can check with Bash: echo $FRED_API_KEY. If the variable is set and non-empty, use it.

**Step 2 — Check .env file.** If the environment variable isn't set, read .env from the current working directory. Format:

FRED_API_KEY=your_key_here

BEA_API_KEY=your_key_here

Step 3 — Proceed without. If neither source has the key, proceed without it (most APIs still work at lower rate limits) and mention this to the user.

Making API Calls

Use your environment's HTTP fetch tool to call REST endpoints. The tool name varies by platform:

Platform

HTTP Fetch Tool

Fallback

Claude Code

WebFetch

curl via Bash

Gemini CLI

web_fetch

curl via shell

Windsurf

read_url_content

curl via terminal

Cursor

No dedicated fetch tool

curl via run_terminal_cmd

Codex CLI

No dedicated fetch tool

curl via shell

Cline

No dedicated fetch tool

curl via execute_command

If you don't recognize your platform or the fetch tool fails, fall back to curl via whatever shell/terminal tool is available. Example:

curl -s -H "Accept: application/json" "https://api.example.com/endpoint"

Request guidelines

• Set Accept: application/json header where supported

• URL-encode special characters in query parameters — SMILES strings (/, #, =, @), compound names with parentheses, and ontology terms with colons (HP:0001250 → HP%3A0001250) are common sources of failures. With curl, use --data-urlencode for safety.

• Parallel OK: When querying different databases (e.g., PubChem + ChEMBL + Reactome), run them in parallel — most APIs have generous rate limits.

• Serialize requests to rate-limited APIs: NCBI APIs (Gene, GEO, Protein, Taxonomy, dbSNP, SRA) at 3 req/sec without key, 10 with key. Also watch: Ensembl (15 req/sec), BLS v1 (25 req/day without key), SEC EDGAR (10 req/sec), NOAA (5 req/sec with token).

• If you get a rate-limit error (HTTP 429 or 503), wait briefly and retry once

Error recovery

If an API returns an error or empty results:

• Check the identifier format — use the Common Identifier Formats table above. A gene symbol may need to be converted to NCBI Gene ID or Ensembl ID first.

• Try alternative identifiers — if a compound name fails in PubChem, try SMILES, InChIKey, or CID. If a gene symbol fails, try the NCBI Gene ID.

• Try a different database — if one database is down or returns nothing, check the "Also consider" column in the selection guide for alternatives.

• Report the failure — tell the user which database failed, the error, and what you tried instead.

Pagination

Many APIs return paginated results — if you only read the first page, you may miss data. Common patterns:

• Offset/Limit: offset=0&limit=100 → increment offset by limit for the next page (ChEMBL, FRED, NOAA, USGS, NCBI E-utilities, ENA, GDC, FDA)

• Cursor-based: Response includes a nextPageToken or cursor value — pass it in the next request (ClinicalTrials.gov, UniProt)

• Page number: page=1&per_page=50 → increment page (World Bank, cBioPortal, ZINC)

Check the reference file for each database's specific pagination parameters. If a response includes total, totalCount, or next and the number of returned results is less than the total, there are more pages.

For targeted lookups (single gene, single compound), the first page is usually sufficient. Paginate when the user needs comprehensive results (e.g., "all clinical trials for X" or "all known variants in gene Y").

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. But default to showing the full raw JSON — the user asked for it.

Adding New Databases

This skill is designed to grow. Each database is a self-contained reference file in references/. To add a new database:

• Create references/<database-name>.md following the same format as existing files

• Add an entry to the database selection guide above

• The reference file should include: base URL, key endpoints, query parameter formats, example calls, rate limits, and response structure

Available Databases

Read the relevant reference file before making any API call.

Physics & Astronomy

Database

Reference File

What it covers

NASA

references/nasa.md

NEO asteroids, Mars rover, APOD

NASA Exoplanet Archive

references/nasa-exoplanet-archive.md

Exoplanets, orbital parameters

NIST

references/nist.md

Physical constants, atomic spectra

SDSS

references/sdss.md

Galaxy/star spectra, photometry

SIMBAD

references/simbad.md

Astronomical object catalog

Earth & Environmental Sciences

Database

Reference File

What it covers

USGS

references/usgs.md

Earthquakes, water data

NOAA

references/noaa.md

Climate, weather station data

EPA

references/epa.md

Air quality, toxic releases

OpenWeatherMap

references/openweathermap.md

Weather current/forecast

Chemistry & Drugs

Database

Reference File

What it covers

PubChem

references/pubchem.md

Compounds, properties, synonyms

ChEMBL

references/chembl.md

Bioactivity, drug discovery

DrugBank

references/drugbank.md

Drug data, interactions (paid)

FDA (OpenFDA)

references/fda.md

Drug labels, adverse events, recalls

DailyMed

references/dailymed.md

Drug labels (NIH/NLM)

KEGG

references/kegg.md

Pathways, genes, compounds

ChEBI

references/chebi.md

Chemical entities of biological interest

ZINC

references/zinc.md

Commercially available compounds, virtual screening

BindingDB

references/bindingdb.md

Experimentally measured binding affinities

Materials Science

Database

Reference File

What it covers

Materials Project

references/materials-project.md

Band gaps, elastic properties, crystal structures

COD

references/cod.md

Crystal structures, CIF files

Biology & Genomics

Database

Reference File

What it covers

Reactome

references/reactome.md

Biological pathways, reactions

BRENDA

references/brenda.md

Enzyme kinetics, catalysis (SOAP)

UniProt

references/uniprot.md

Protein sequences, function

STRING

references/string.md

Protein-protein interactions

Ensembl

references/ensembl.md

Genomes, variants, sequences

NCBI Gene

references/ncbi-gene.md

Gene information, links

NCBI Protein

references/ncbi-protein.md

Protein sequences, records

NCBI Taxonomy

references/ncbi-taxonomy.md

Taxonomic classification

GEO (NCBI)

references/geo.md

Gene expression datasets

GTEx

references/gtex.md

Gene expression across tissues

PDB

references/pdb.md

Protein 3D structures

AlphaFold DB

references/alphafold.md

Predicted protein structures

EMDB

references/emdb.md

Electron microscopy maps

InterPro

references/interpro.md

Protein families, domains

BioGRID

references/biogrid.md

Protein/genetic interactions

Gene Ontology

references/gene-ontology.md

GO terms, gene annotations

QuickGO

references/quickgo.md

GO annotations (EBI, recommended)

dbSNP

references/dbsnp.md

SNP/variant data

SRA

references/sra.md

Sequencing run metadata

gnomAD

references/gnomad.md

Population variant frequencies (POST)

UCSC Genome Browser

references/ucsc-genome.md

Genome annotations, tracks

ENCODE

references/encode.md

DNA elements, ChIP-seq, ATAC-seq

JASPAR

references/jaspar.md

TF binding profiles/motifs

Human Protein Atlas

references/human-protein-atlas.md

Protein expression across tissues

Human Cell Atlas

references/hca.md

Single-cell atlas data

LINCS L1000

references/lincs-l1000.md

Gene expression signatures (CMap)

RummaGEO

references/rummageo.md

GEO gene set enrichment (POST)

PRIDE

references/pride.md

Proteomics data repository

Metabolomics Workbench

references/metabolomics-workbench.md

Metabolomics studies, metabolites

MouseMine

references/mousemine.md

Mouse genome informatics

ENA

references/ena.md

Nucleotide sequences, reads, assemblies, taxonomy (EMBL-EBI)

Addgene

references/addgene.md

Plasmid repository

Disease & Clinical

Database

Reference File

What it covers

Open Targets

references/opentargets.md

Target-disease associations (POST)

COSMIC

references/cosmic.md

Somatic mutations in cancer

ClinPGx (PharmGKB)

references/clinpgx.md

Pharmacogenomics

ClinicalTrials.gov

references/clinicaltrials.md

Clinical trial registry

OMIM

references/omim.md

Mendelian disease-gene data

ClinVar

references/clinvar.md

Variant clinical significance

GDC (TCGA)

references/tcga-gdc.md

Cancer genomics, mutations (POST)

cBioPortal

references/cbioportal.md

Cancer study mutations, CNA, expression, clinical data

DisGeNET

references/disgenet.md

Gene-disease associations

GWAS Catalog

references/gwas-catalog.md

GWAS SNP-trait associations

Monarch Initiative

references/monarch.md

Disease-phenotype-gene links

HPO

references/hpo.md

Human Phenotype Ontology

Patents & Regulatory

Database

Reference File

What it covers

USPTO

references/uspto.md

Patents, trademarks

SEC EDGAR

references/sec-edgar.md

Company filings (needs User-Agent header)

Economics & Finance

Database

Reference File

What it covers

FRED

references/fred.md

US economic time series

Federal Reserve

references/federal-reserve.md

Monetary/financial data

BEA

references/bea.md

GDP, national accounts

BLS

references/bls.md

Employment, wages, CPI

World Bank

references/worldbank.md

Development indicators

ECB

references/ecb.md

Euro exchange rates, monetary stats

US Treasury

references/treasury.md

Debt, yield curves, fiscal data

Alpha Vantage

references/alphavantage.md

Stocks, forex, crypto

Data Commons

references/datacommons.md

Statistical knowledge graph

Social Sciences & Demographics

Database

Reference File

What it covers

US Census

references/census.md

Population, housing, economic surveys

Eurostat

references/eurostat.md

EU statistics

WHO GHO

references/who.md

Global health indicators