OpenBio

Installation#

bash

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.

bash

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:

bash

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:

bash

bunx skills update

If that fails, remove and re-install:

bash

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

Quick Start#

bash

# 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#

text

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#

bash

# 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:

bash

# 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#

FileDescriptionrules/api.mdCore endpoints, authentication, job management

Data Access Tools#

FileTools Coveredrules/protein-structure.mdPDB, PDBe, AlphaFold, UniProtrules/literature.mdPubMed, arXiv, bioRxiv, OpenAlexrules/genomics.mdEnsembl, ENA, Gene, GWAS, GEOrules/blast.mdNCBI BLAST sequence similarity searchrules/cheminformatics.mdRDKit, PubChem, ChEMBLrules/molecular-biology.mdPrimers, PCR, restriction, assemblyrules/plasmid.mdparse_plasmid_file, edit_plasmidrules/pathway-analysis.mdKEGG, Reactome, STRING, g:Profilerrules/clinical-data.mdClinicalTrials, ClinVar, FDA

ML Prediction Tools (Detailed)#

FileToolUse Caserules/structure-prediction.mdIndexDecision tree for all prediction toolsrules/boltz.mdBoltz-2Structure + binding affinityrules/chai.mdChai-1Multi-modal (protein+ligand+RNA+glycan)rules/simplefold.mdSimpleFoldQuick single-protein foldingrules/proteinmpnn.mdProteinMPNNFixed-backbone sequence designrules/ligandmpnn.mdLigandMPNNLigand-aware sequence designrules/thermompnn.mdThermoMPNNStability (ΔΔG) predictionrules/geodock.mdGeoDockProtein-protein dockingrules/pinal.mdPinalDe novo design from textrules/boltzgen.mdBoltzGenEnd-to-end binder design

Tool Categories Summary#

CategoryCountExamplesProtein structure23fetch_pdb_metadata, get_alphafold_predictionLiterature14search_pubmed, arxiv_search, biorxiv_search_keywordsGenomics27lookup_gene, vep_predict, gwas_search_associations_by_traitSequence similarity3submit_blast, check_blast_status, get_blast_resultsCheminformatics20+calculate_molecular_properties, chembl_similarity_searchMolecular biology15design_primers, restriction_digest, assemble_gibsonPlasmid2parse_plasmid_file, edit_plasmidStructure prediction15+submit_boltz_prediction, submit_proteinmpnn_predictionPathway analysis26analyze_gene_list, get_string_network, go_enrichment, convert_gene_idsClinical data22search_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

---

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