Skill: ravishar313/openbio (version 1.0.6)

--- name: openbio version: 1.0.4 updated_at: 2026-02-15 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, (7) Analyzing and editing plasmid files (GenBank, SnapGene). metadata: tags: [biology, protein, genomics, chemistry, bioinformatics, drug-discovery] --- ## 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-[REDACTED_SECRET]" # Get tool schema (always do this first!) curl -X GET "https://api.openbio.tech/api/v1/tools/{tool_name}" \ -H "X-[REDACTED_SECRET]" # Validate parameters before invoking (optional) curl -X POST "https://api.openbio.tech/api/v1/tools/validate" \ -H "X-[REDACTED_SECRET]" \ -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-[REDACTED_SECRET]" \ -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 ```bash # Before invoking ANY tool: curl -X GET "https://api.openbio.tech/api/v1/tools/{tool_name}" \ -H "X-[REDACTED_SECRET]" ``` 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-[REDACTED_SECRET]" # Get results with download URLs curl -X GET "https://api.openbio.tech/api/v1/jobs/{job_id}" \ -H "X-[REDACTED_SECRET]" ``` ### 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](rules/api.md) | Core endpoints, authentication, job management | ### Data Access Tools | File | Tools Covered | |------|---------------| | [rules/protein-structure.md](rules/protein-structure.md) | PDB, PDBe, AlphaFold, UniProt | | [rules/literature.md](rules/literature.md) | PubMed, arXiv, bioRxiv, OpenAlex | | [rules/genomics.md](rules/genomics.md) | Ensembl, ENA, Gene, GWAS, GEO | | [rules/blast.md](rules/blast.md) | NCBI BLAST sequence similarity search | | [rules/cheminformatics.md](rules/cheminformatics.md) | RDKit, PubChem, ChEMBL | | [rules/molecular-biology.md](rules/molecular-biology.md) | Primers, PCR, restriction, assembly | | [rules/plasmid.md](rules/plasmid.md) | parse_plasmid_file, edit_plasmid | | [rules/pathway-analysis.md](rules/pathway-analysis.md) | KEGG, Reactome, STRING, g:Profiler | | [rules/clinical-data.md](rules/clinical-data.md) | ClinicalTrials, ClinVar, FDA | ### ML Prediction Tools (Detailed) | File | Tool | Use Case | |------|------|----------| | [rules/structure-prediction.md](rules/structure-prediction.md) | **Index** | Decision tree for all prediction tools | | [rules/boltz.md](rules/boltz.md) | Boltz-2 | Structure + binding affinity | | [rules/chai.md](rules/chai.md) | Chai-1 | Multi-modal (protein+ligand+RNA+glycan) | | [rules/simplefold.md](rules/simplefold.md) | SimpleFold | Quick single-protein folding | | [rules/proteinmpnn.md](rules/proteinmpnn.md) | ProteinMPNN | Fixed-backbone sequence design | | [rules/ligandmpnn.md](rules/ligandmpnn.md) | LigandMPNN | Ligand-aware sequence design | | [rules/thermompnn.md](rules/thermompnn.md) | ThermoMPNN | Stability (ΔΔG) prediction | | [rules/geodock.md](rules/geodock.md) | GeoDock | Protein-protein docking | | [rules/pinal.md](rules/pinal.md) | Pinal | De novo design from text | | [rules/boltzgen.md](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 --- **Tip**: When in doubt, search for tools: `GET /api/v1/tools/search?q=your_query`


Security scan verdicts — ClawScan: suspicious | static analysis:  | VirusTotal: suspicious | SkillSpector: suspicious (CRITICAL)