database-lookup

What this skill does

# 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
| 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 ED