uniprot-mcp-server

Plugin uniprot-mcp-server in cyanheads/uniprot-mcp-server. Commands read from the repo's manifest — 6 days ago.

Skills (35)

• add-app-tool

  Scaffold an MCP App tool + UI resource pair. Use when the user asks to add a tool with interactive UI, create an MCP App, or build a visual/interactive tool. author: cyanheads version: "1.8" audience: external type: reference

• add-prompt

  Scaffold a new MCP prompt template. Use when the user asks to add a prompt, create a reusable message template, or define a prompt for LLM interactions. author: cyanheads version: "1.5" audience: external type: reference

• add-resource

  Scaffold a new MCP resource definition. Use when the user asks to add a resource, expose data via URI, or create a readable endpoint. author: cyanheads version: "1.8" audience: external type: reference

• add-service

  Scaffold a new service integration. Use when the user asks to add a service, integrate an external API, or create a reusable domain module with its own initialization and state. author: cyanheads version: "1.12" audience: external type: reference

• add-skill

  Author a skill the server publishes to the agents that use it — a root `skills/<name>/SKILL.md` per the Agent Skills specification, validated by `lint:packaging`, discovered by plugin hosts, shipped in the MCPB bundle, and optionally served over MCP. Use when the user asks to add, write, or publish

• add-test

  Scaffold a test file for an existing tool, resource, or service. Use when the user asks to add tests, improve coverage, or when a definition exists without a matching test file. author: cyanheads version: "1.10" audience: external type: reference

• add-tool

  Scaffold a new MCP tool definition. Use when the user asks to add a tool, create a new tool, or implement a new capability for the server. author: cyanheads version: "2.37" audience: external type: reference

• api-auth

  Authentication, authorization, and multi-tenancy patterns for `@cyanheads/mcp-ts-core`. Use when implementing auth scopes on tools/resources, configuring auth modes (none/jwt/oauth), working with JWT/OAuth env vars, or understanding how tenantId flows through ctx.state. author: cyanheads version: "1

• api-canvas

  DataCanvas primitive reference — a Tier 3 SQL/analytical workspace for tabular MCP servers, backed by DuckDB. Use when registering tables from upstream APIs, running ad-hoc SQL across them, and exporting results. Covers the acquire → register → query → export flow, per-table TTL, the token-sharing p

• api-config

  Reference for core and server configuration in `@cyanheads/mcp-ts-core`. Covers env var tables with defaults, priority order, server-specific Zod schema pattern, and Workers lazy-parsing requirement. author: cyanheads version: "1.28" audience: external type: reference

• api-context

  Canonical reference for the unified `Context` object passed to every tool and resource handler in `@cyanheads/mcp-ts-core`. Covers the full interface, its `RequestContext` base, all sub-APIs (`ctx.log`, `ctx.state`, `ctx.requestInput`, `ctx.inputs`, `ctx.clientCapabilities`, `ctx.enrich`, `ctx.conte

• api-errors

  McpError constructor, JsonRpcErrorCode reference, and error handling patterns for `@cyanheads/mcp-ts-core`. Use when looking up error codes, understanding where errors should be thrown vs. caught, or using ErrorHandler.tryCatch in services. author: cyanheads version: "1.24" audience: external type:

• api-linter

  MCP definition linter rules reference. Use when `bun run lint:mcp` or `bun run devcheck` reports a lint error or warning (`format-parity`, `schema-is-object`, `name-format`, `server-json-*`, etc.) and you need to understand the rule, its severity, and how to fix it. Every rule ID the linter emits ha

• api-mirror

  Stand up a persistent, self-refreshing local mirror of a bulk upstream dataset with the MirrorService (@cyanheads/mcp-ts-core/mirror). Use when a server wraps a large or slow API and should query a synced local index (embedded SQLite + FTS5) instead of paginating the live API per request. author: cy

• api-services

  API reference for built-in service providers (LLM, Speech, Graph). Use when looking up service interfaces, provider capabilities, or integration patterns. author: cyanheads version: "1.5" audience: external type: reference

• api-telemetry

  Catalog of OpenTelemetry instrumentation built into framework `@cyanheads/mcp-ts-core` — spans, metrics, completion logs, env config, runtime caveats, custom instrumentation patterns, and cardinality rules. Use when enabling OTel export, adding custom spans or metrics in services, debugging missing

• api-testing

  Testing patterns for MCP tool/resource handlers using `createMockContext` and Vitest. Covers mock context options, handler testing, McpError assertions, format testing, Vitest config setup, and test isolation conventions. author: cyanheads version: "1.16" audience: external type: reference

• api-utils

  API reference for all utilities exported from `@cyanheads/mcp-ts-core/utils`. Use when looking up utility method signatures, options, peer dependencies, or usage patterns. author: cyanheads version: "2.20" audience: external type: reference

• api-workers

  Cloudflare Workers deployment using `createWorkerHandler` from `@cyanheads/mcp-ts-core/worker`. Covers the full handler signature, binding types, CloudflareBindings extensibility, runtime compatibility guards, and wrangler.toml requirements. author: cyanheads version: "1.11" audience: external type:

• code-simplifier

  Cleanup pass that edits the working tree — over a session's uncommitted changes, or a named path or whole codebase. Reads `git diff` (or the named target) and simplifies, consolidates, and aligns code with the existing codebase — modernize syntax, cut unnecessary complexity and slop, consolidate dup

• design-mcp-server

  Design the tool surface, resources, and service layer for a new MCP server. Use when starting a new server, planning a major feature expansion, or when the user describes a domain/API they want to expose via MCP. Produces a design doc at docs/design.md that drives implementation. author: cyanheads v

• field-test

  Exercise tools, resources, and prompts against a live HTTP server via MCP JSON-RPC over curl. Starts the server, surfaces the catalog, runs real and adversarial inputs, measures every call (bytes, token estimate, wall-clock) and weighs the catalog, renders app tools' views in a headless MCP Apps hos

• git-wrapup

  Land working-tree changes as logical commits — the work grouped by concern, topped by a release commit (version bump, changelog, regenerated artifacts). The work commits land first, then the version bump, verification, and the release commit on top. Stops at "committed locally on main" — or, when th

• maintenance

  Investigate, adopt, and verify dependency updates — with special handling for `@cyanheads/mcp-ts-core`. Captures what changed, understands why, cross-references against the codebase, adopts framework improvements, syncs project skills, and runs final checks. Supports two entry modes: run the full fl

• orchestrations

  Pick and run a multi-phase workflow that chains foundational task skills (`git-wrapup`, `release-and-publish`, `maintenance`, `field-test`, `setup`, etc.) end-to-end. Routes user intent to a workflow file under `workflows/` — greenfield builds, maintenance + release, field-test + fix, or known-work

• polish-docs-meta

  Finalize documentation and project metadata for a ship-ready MCP server. Use after implementation is complete, tests pass, and devcheck is clean. Safe to run at any stage — each step checks current state and only acts on what still needs work. author: cyanheads version: "2.26" audience: external typ

• release-and-publish

  Ship a release end-to-end across every registry the project targets (npm, MCP Registry, GitHub Releases for `.mcpb` bundles, GHCR). Runs the final verification gate, fast-forwards `main` when the release rode a release PR, creates the annotated tag on the commit `main` now points at, pushes commits

• release-pr-review

  Review pass on an open release PR (`release/<version>` → `main`) — the step between `git-wrapup` and `release-and-publish` when a project releases in gated release PR mode. Reads the PR's commit range through the `code-simplifier` lens plus a correctness review, verifies whatever an automated review

• report-issue-framework

  File a bug or feature request against @cyanheads/mcp-ts-core when you hit a framework issue. Use when a builder, utility, context method, or config behaves contrary to the documented API — not for server-specific application bugs. author: cyanheads version: "1.15" audience: external type: workflow

• report-issue-local

  File a bug or feature request against this MCP server's own repo. Use for server-specific issues — tool logic, service integrations, config problems, or domain bugs that aren't caused by the framework. author: cyanheads version: "1.13" audience: external type: workflow

• security-pass

  Review an MCP server for common security gaps: LLM-facing surfaces as injection vector (tools, resources, prompts, descriptions), scope blast radius, destructive ops without consent, upstream auth shape, input sinks (URL / path / roots / shell / schema strictness / ReDoS), tenant isolation, leakage

• setup

  Post-init orientation for an MCP server built on @cyanheads/mcp-ts-core. Use after running `@cyanheads/mcp-ts-core init` to understand the project structure, conventions, and skill sync model. Also use when onboarding to an existing project for the first time. author: cyanheads version: "1.13" audie

• techniques

  Catalog of reusable response- and data-shaping techniques for MCP servers built on `@cyanheads/mcp-ts-core` — overflow handling, payload shaping, retrieval patterns. Use when a tool's payload is too large, awkwardly shaped, or expensive to retrieve and you want a proven pattern instead of inventing

• tool-defs-analysis

  Read-only audit of MCP definition language across an existing surface — tools, resources, prompts, server instructions. Walks every definition file and checks 16 categories the LLM reads to decide whether and how to call: voice & tense, internal leaks, audience leaks, defaults, recovery hints, field

• uniprot-guide

  Resolve protein identity and organism scope with uniprot_* tools before interpreting annotations, mapping identifier sets, or comparing proteomes. Use for ambiguous gene names, species versus strain searches, evidence-backed protein dossiers, and claims that a protein or annotation is absent.

MCP servers (1)

• uniprot-mcp-server

  runs: npx -y @cyanheads/uniprot-mcp-server

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