Health check (no auth required) Skill

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

Not checking schemas → Parameter errors. Use POST /api/v1/tools/validate to pre-check params.
Ignoring quality metrics → Using unreliable data
Wrong tool for task → Check decision trees in rule files
Not polling jobs → Missing prediction results
Wrong tool name → 404 responses include "Did you mean?" suggestions with similar tool names

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

Agent Skills: Health check (no auth required)

Install this agent skill to your local

Skill Files