openbio

Installation

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

Authentication

Required: OPENBIO_API_KEY environment variable.

Tell the user to create their API key at: http://openbio.tech/profile#apikeys and securely store it in their environment variables.

If the user has not signed in to OpenBio, tell them to sign in to OpenBio (https://openbio.tech/auth) and create their account first and then create their API key.

export OPENBIO_API_KEY=your_key_here

Base URL: https://api.openbio.tech/api/v1

Version Check (Do This First)

Before using the API, verify your skill is up to date:

curl -s "https://api.openbio.tech/api/v1/tools/skill-version"

This returns {"skill": "openbio", "version": "X.Y.Z", ...}. Compare against the version field at the top of this file (currently 1.0.4). If the API returns a newer version:

bunx skills update

If that fails, remove and re-install:

bunx skills remove openbio --global -y
bunx skills add openbio-ai/skills --skill openbio --global --agent '*' -y

Quick Start

# Health check (no auth required)
curl -X GET "https://api.openbio.tech/api/v1/tools/health"

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

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

# Validate parameters before invoking (optional)
curl -X POST "https://api.openbio.tech/api/v1/tools/validate" \
  -H "X-API-Key: $OPENBIO_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{"tool_name": "search_pubmed", "params": {"query": "CRISPR", "max_results": 5}}'

# Invoke tool
curl -X POST "https://api.openbio.tech/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
│
├─ Sequence similarity search (BLAST)?
│   └─ Read rules/blast.md
│       → submit_blast, check_blast_status, get_blast_results
│
├─ Small molecule analysis?
│   └─ Read rules/cheminformatics.md
│       → RDKit, PubChem, ChEMBL
│
├─ Cloning/PCR/assembly?
│   └─ Read rules/molecular-biology.md
│       → Primers, restriction, Gibson, Golden Gate
│
├─ Plasmid analysis/editing?
│   └─ Read rules/plasmid.md
│       → parse_plasmid_file, edit_plasmid
│
├─ Structure prediction/design?
│   └─ Read rules/structure-prediction.md
│       → Boltz, Chai, ProteinMPNN, LigandMPNN
│
├─ Pathway analysis?
│   └─ Read rules/pathway-analysis.md
│       → KEGG, Reactome, STRING, g:Profiler (GO enrichment)
│
└─ 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://api.openbio.tech/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://api.openbio.tech/api/v1/jobs/{job_id}/status" \
  -H "X-API-Key: $OPENBIO_API_KEY"

# Get results with download URLs
curl -X GET "https://api.openbio.tech/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:

Core API

File	Description
rules/api.md	Core endpoints, authentication, job management

Data Access Tools

File	Tools Covered
rules/protein-structure.md	PDB, PDBe, AlphaFold, UniProt
rules/literature.md	PubMed, arXiv, bioRxiv, OpenAlex
rules/genomics.md	Ensembl, ENA, Gene, GWAS, GEO
rules/blast.md	NCBI BLAST sequence similarity search
rules/cheminformatics.md	RDKit, PubChem, ChEMBL
rules/molecular-biology.md	Primers, PCR, restriction, assembly
rules/plasmid.md	parse_plasmid_file, edit_plasmid
rules/pathway-analysis.md	KEGG, Reactome, STRING, g:Profiler
rules/clinical-data.md	ClinicalTrials, ClinVar, FDA

ML Prediction Tools (Detailed)

File	Tool	Use Case
rules/structure-prediction.md	Index	Decision tree for all prediction tools
rules/boltz.md	Boltz-2	Structure + binding affinity
rules/chai.md	Chai-1	Multi-modal (protein+ligand+RNA+glycan)
rules/simplefold.md	SimpleFold	Quick single-protein folding
rules/proteinmpnn.md	ProteinMPNN	Fixed-backbone sequence design
rules/ligandmpnn.md	LigandMPNN	Ligand-aware sequence design
rules/thermompnn.md	ThermoMPNN	Stability (ΔΔG) prediction
rules/geodock.md	GeoDock	Protein-protein docking
rules/pinal.md	Pinal	De novo design from text
rules/boltzgen.md	BoltzGen	End-to-end binder design

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, gwas_search_associations_by_trait
Sequence similarity	3	submit_blast, check_blast_status, get_blast_results
Cheminformatics	20+	calculate_molecular_properties, chembl_similarity_search
Molecular biology	15	design_primers, restriction_digest, assemble_gibson
Plasmid	2	parse_plasmid_file, edit_plasmid
Structure prediction	15+	submit_boltz_prediction, submit_proteinmpnn_prediction
Pathway analysis	26	analyze_gene_list, get_string_network, go_enrichment, convert_gene_ids
Clinical data	22	search_clinical_trials, clinvar_search

Troubleshooting: Updating the Skill

If the API returns a newer version than the one in this file (see Version Check above), update your skill. See the Version Check section at the top for commands.

Common Mistakes

1. Not checking schemas → Parameter errors. Use POST /api/v1/tools/validate to pre-check params.
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
5. Wrong tool name → 404 responses include "Did you mean?" suggestions with similar tool names

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