Required: OPENBIO_API_KEY environment variable.

export OPENBIO_API_KEY=your_key_here

Base URL: https://openbio-api.fly.dev/

Quick Start

# List available tools
curl -X GET "https://openbio-api.fly.dev/api/v1/tools" \
  -H "X-API-Key: $OPENBIO_API_KEY"

# Get tool schema (always do this first!)
curl -X GET "https://openbio-api.fly.dev/api/v1/tools/{tool_name}" \
  -H "X-API-Key: $OPENBIO_API_KEY"

# Invoke tool
curl -X POST "https://openbio-api.fly.dev/api/v1/tools" \
  -H "X-API-Key: $OPENBIO_API_KEY" \
  -F "tool_name=search_pubmed" \
  -F 'params={"query": "CRISPR", "max_results": 5}'

Decision Tree: Which Tools to Use

What do you need?
│
├─ Protein/structure data?
│   └─ Read rules/protein-structure.md
│       → PDB, AlphaFold, UniProt tools
│
├─ Literature search?
│   └─ Read rules/literature.md
│       → PubMed, arXiv, bioRxiv, OpenAlex
│
├─ Genomics/variants?
│   └─ Read rules/genomics.md
│       → Ensembl, GWAS, VEP, GEO
│
├─ Small molecule analysis?
│   └─ Read rules/cheminformatics.md
│       → RDKit, PubChem, ChEMBL
│
├─ Cloning/PCR/assembly?
│   └─ Read rules/molecular-biology.md
│       → Primers, restriction, Gibson, Golden Gate
│
├─ Structure prediction/design?
│   └─ Read rules/structure-prediction.md
│       → Boltz, Chai, ProteinMPNN, LigandMPNN
│
├─ Pathway analysis?
│   └─ Read rules/pathway-analysis.md
│       → KEGG, Reactome, STRING
│
└─ Clinical/drug data?
    └─ Read rules/clinical-data.md
        → ClinicalTrials, ClinVar, FDA, Open Targets

Critical Rules

1. Always Check Tool Schema First

# Before invoking ANY tool:
curl -X GET "https://openbio-api.fly.dev/api/v1/tools/{tool_name}" \
  -H "X-API-Key: $OPENBIO_API_KEY"

Parameter names vary (e.g., pdb_ids not pdb_id). Check schema to avoid errors.

2. Long-Running Jobs (submit_* tools)

Prediction tools return a job_id. Poll for completion:

# Check status
curl -X GET "https://openbio-api.fly.dev/api/v1/jobs/{job_id}/status" \
  -H "X-API-Key: $OPENBIO_API_KEY"

# Get results with download URLs
curl -X GET "https://openbio-api.fly.dev/api/v1/jobs/{job_id}" \
  -H "X-API-Key: $OPENBIO_API_KEY"

3. Quality Thresholds

Don't just retrieve data—interpret it:

AlphaFold pLDDT: > 70 = confident, < 50 = disordered Experimental resolution: < 2.5 Å for binding sites GWAS p-value: < 5×10⁻⁸ = genome-wide significant Tanimoto similarity: > 0.7 = similar compounds

See individual rule files for detailed thresholds.

Rule Files

Read these for domain-specific knowledge:

| rules/api.md | Core endpoints, job management

| rules/protein-structure.md | PDB, PDBe, AlphaFold, UniProt

| rules/literature.md | PubMed, arXiv, bioRxiv, OpenAlex

| rules/genomics.md | Ensembl, ENA, Gene, GWAS, GEO

| rules/cheminformatics.md | RDKit, PubChem, ChEMBL

| rules/molecular-biology.md | Primers, PCR, restriction, assembly

| rules/structure-prediction.md | Boltz, Chai, ProteinMPNN, etc.

| rules/pathway-analysis.md | KEGG, Reactome, STRING

| rules/clinical-data.md | ClinicalTrials, ClinVar, FDA

Tool Categories Summary

| Protein structure | 23 | fetch_pdb_metadata, get_alphafold_prediction

| Literature | 14 | search_pubmed, arxiv_search, biorxiv_search_keywords

| Genomics | 27 | lookup_gene, vep_predict, search_gwas_associations_by_trait

| Cheminformatics | 20+ | calculate_molecular_properties, chembl_similarity_search

| Molecular biology | 15 | design_primers, restriction_digest, assemble_gibson

| Structure prediction | 15+ | submit_boltz_prediction, submit_proteinmpnn_prediction

| Pathway analysis | 24 | analyze_gene_list, get_string_network

| Clinical data | 22 | search_clinical_trials, search_clinvar

Common Mistakes

Not checking schemas → Parameter errors
Ignoring quality metrics → Using unreliable data
Wrong tool for task → Check decision trees in rule files
Not polling jobs → Missing prediction results

Tip: When in doubt, search for tools: GET /api/v1/tools/search?q=your_query

安装