openbio

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name: openbio description: > OpenBio API for biological data access and computational biology tools. Use when: (1) Querying biological databases (PDB, UniProt, ChEMBL, etc.), (2) Searching scientific literature (PubMed, bioRxiv, arXiv), (3) Running structure prediction (Boltz, Chai, ProteinMPNN), (4) Performing pathway/enrichment analysis, (5) Designing molecular biology experiments (primers, cloning), (6) Analyzing variants and clinical data. metadata: tags: [biology, protein, genomics, chemistry, bioinformatics, drug-discovery]

Installation

bunx skills add https://github.com/openbio-ai/skills --skill openbio

Authentication

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:

File	Tools Covered
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

Category	Count	Examples
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

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

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