openscience-mcp

# aipoch-openscience-mcp One-install access to **23 life-sciences MCP servers** — PubChem, ChEMBL, Ensembl, UniProt, PDB, AlphaFold, GEO, ArrayExpress, gnomAD, ClinVar, GWAS Catalog, GTEx, OpenAlex, PubMed, ClinicalTrials.gov, and more. The servers are vendored from Claude Science and **fully self-contained**: the plugin bootstraps its own Python virtualenv on first run, so **no Claude Science installation is required**. ## What you get A single plugin, `openscience`, that registers 23 MCP servers (233 tools total). Each server maps to a public life-sciences database group: | Server | Sources | Server | Sources | |--------|---------|--------|---------| | `chemistry` | PubChem, ChEBI, Rhea, BindingDB | `genomes` | Ensembl (incl. VEP), UCSC | | `chembl` | ChEMBL | `genes-ontologies` | MyGene, UniProt, GO, Reactome, OLS | | `zinc` | ZINC | `variants` | gnomAD, ClinVar, dbSNP | | `pubmed` | PubMed / NCBI E-utilities | `human-genetics` | GWAS Catalog, eQTL, FinnGen | | `literature` | OpenAlex, arXiv | `clinical-genomics` | ClinGen, CIViC, Open Targets | | `biorxiv` | bioRxiv | `expression` | GTEx | | `clinical-trials` | ClinicalTrials.gov | `regulation` | ENCODE, JASPAR, UniBind | | `drug-regulatory` | openFDA | `protein-annotation` | InterPro, Pfam, HPA, STRING | | `structures-interactions` | PDB, AlphaFold, EMDB, Complex Portal, IntAct | `rna` | Rfam | | `omics-archives` | GEO, ArrayExpress, PRIDE, MGnify, MetaboLights | `cancer-models` | cBioPortal | | `cellguide` | CELLxGENE cell types | `biomart` | BioMart | | `research-resources` | Grants.gov, Antibody Registry | | | All tools are read-only retrieval against public databases. ## Requirements - **Claude Code** (recent version with plugin support). - **Python ≥ 3.11** on your `PATH` (used once to build the plugin's private virtualenv). - Network access on first run (to `pip install` the pinned dependencies). ## Install Installation depends on your agent host. Currently supported: ### Claude Code ```shell /plugin marketplace add aipoch/openscience-mcp /plugin install openscience@aipoch-openscience ``` Restart Claude Code when prompted. On the first tool call, the plugin builds its virtualenv and installs dependencies (about a minute, one time). Subsequent starts are instant. _More agent frameworks and MCP hosts are on the [roadmap](ROADMAP.md)._ ## Configuration (optional) When you enable the plugin, Claude Code prompts for two optional values: - **Contact email (NCBI etiquette)** — NCBI E-utilities (PubMed, dbSNP, ClinVar, GEO) ask callers to identify themselves. A few tools (e.g. `pubmed` metadata) require it; set this to use them. - **NCBI API key** — optional, raises the NCBI rate limit from 3 to 10 requests/second. Both can be left blank; servers that don't need them work regardless. ## Usage Just describe what you need, or name a source. Examples: - "Look up the PubChem properties of aspirin." → `chemistry` - "Find GWAS associations for height." → `human-genetics` - "Get the AlphaFold structure for UniProt P04637." → `structures-interactions` - "Search OpenAlex for CRISPR review authors." → `literature` ## Verification Every server is covered by an integration test harness. The launcher's own unit + integration tests run standalone: ```shell bash tests/launch_smoke.sh # unit + integration tests for the plugin launcher ``` Per-server results — every server booted, all 233 tools enumerated, and a representative live call per server — come from the integration harness (needs network; upstream databases may rate-limit): ```shell python tests/test_all_servers.py # boots each server, enumerates tools, runs representative calls ``` ## How it works - `plugins/openscience/runtime/lib/` — the vendored MCP server packages (Python). - `plugins/openscience/bin/launch.sh` — bootstraps a private virtualenv in the plugin's data directory and launches a server over stdio. No Claude Science dependency. - `plugins/openscience/.mcp.json` — registers the 23 servers with Claude Code. ## Roadmap Phase 1 (this release) ships the 23 servers over stdio. Phase 2 introduces a gateway with dynamic tool discovery to cut process count and context cost. See [ROADMAP.md](ROADMAP.md). ## License The vendored server code originates from the Claude Science bundled `bio-tools` MCP servers; see [`plugins/openscience/runtime/VENDOR_SOURCE.txt`](plugins/openscience/runtime/VENDOR_SOURCE.txt) for provenance. Each upstream database has its own terms of use — review the individual source licenses for your use case.