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MCP Surface Reference

Generated page — do not edit by hand

Rendered by scripts/build_reference_pages.py from the committed

537 contract trinity. Run python scripts/build_reference_pages.py build

after changing a source; CI runs check and fails on stale output.

Per-server tool reference from config/mcp-server-registry.json (18 registered servers) and the generated tool manifest. The science-runtime server pattern is being promoted to the org standard via #537.

Registered MCP servers

Server Version pin Launch command
biocontext7 npm:@biocontext7/mcp@1.0.0 npx -y @biocontext7/mcp@1.0.0
biorender http:https://mcp.services.biorender.com/mcp ``
biorxiv http:https://mcp.deepsense.ai/biorxiv/mcp ``
chembl http:https://mcp.deepsense.ai/chembl/mcp ``
clinical-trials http:https://mcp.deepsense.ai/clinical_trials/mcp ``
code-review-graph pypi:code-review-graph==2.3.6 uvx --from code-review-graph==2.3.6 code-review-graph mcp --auto-watch
context7 npm:@upstash/context7-mcp@3.2.2 npx -y @upstash/context7-mcp@3.2.2
eval-os repo:hordago@local-package python3 -m hordago_eval.mcp
hordago-kg repo:hordago-knowledge-graph@operator-pinned python3 scripts/mcp_server.py
huggingface-mcp repo:hordago@local-package python3 -m hordago.huggingface_mcp
open-targets http:https://mcp.platform.opentargets.org/mcp ``
paper-intelligence repo:paper-intelligence@operator-pinned python3 -m src.paper_intelligence.server
phase-runtime repo:hordago@local-package python3 -m hordago.operational_mcp_servers --server phase-runtime
pubmed http:https://pubmed.mcp.claude.com/mcp ``
sci-lock repo:hordago@local-package python3 -m hordago.operational_mcp_servers --server sci-lock
science-runtime repo:hordago@local-package python3 -m hordago.operational_mcp_servers --server science-runtime
semble pypi:semble==0.4.1 uvx --from semble[mcp]==0.4.1 semble --content code
synapse http:https://mcp.synapse.org/mcp ``

Generated tool surface

Tools generated into templates/surface-template/generated/mcp/tools.json from specs/example.openapi.yaml via the x-hordago-mcp-tool OpenAPI extension:

Tool operationId Method Path Description
list_items listItems GET /items List item records for downstream tools.
create_item createItem POST /items Create an item record.
get_item getItem GET /items/{item_id} Fetch one item by identifier.

SURFACE_MANIFEST mcp bindings

surfaces.mcp[] bindings from src/hordago/SURFACE_MANIFEST.yaml (surface science-runtime, contract hordago-contracts):

operationId MCP tool Module Request Response
runScienceLoop run_science_loop hordago.science_runtime_surfaces.mcp ScienceRuntimeRunRequest ScienceRuntimeRunResponse

hordago-kg tool-count drift

hordago-kg is operator-pinned (repo:hordago-knowledge-graph@operator-pinned) and advertises a tool count that drifts from its runtime registration. Reconciliation is tracked with #537; this page renders the registry pin, not a hand-copied tool count.