Connect-MCP

org.brainkb/brainkb

org.brainkb/brainkb · v0.1.0

MCP server for querying BrainKB, a knowledge base for neuroscience knowledge graphs.

MCPremoteno credentialsScience & open dataEmail

Reported outcomes

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Last check

Reachable, 55 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 75/100

What it does: 55 tools · 0 read, 3 write (incl. delete/pay) · Email

No tool could be tested safely. Only read-only tools that need no input are called.

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +2
  • Read/write annotations: 0
  • Safe test call: +8
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://mcp.brainkb.org/mcp

Tools

55 tools listed at last check
  • brainkb_login Authenticate to BrainKB with the user's credentials and cache the JWT for THIS session only (isolated per caller). The password/token are never echoed. Uses single sign-on: one login mints a refresh token, cached for THIS session, which is exchanged on demand for per-service access toke
  • brainkb_globus_login Start an OAuth login (Globus / ORCID / GitHub) for THIS session — use this instead of brainkb_login when the user signs in with Globus rather than a password. Returns a URL to open in a browser; after signing in, the page shows a short one-time code — pass it to brainkb_finish_login(code
  • brainkb_finish_login Complete an OAuth login started with brainkb_globus_login by exchanging the one-time code shown in the browser for a session token. The code is single-use and never echoed back.
  • brainkb_logout Forget the cached token for this session.
  • brainkb_whoami Report the current caller's auth state (email, authenticated, and when the cached session expires). When signed in it also returns base_url — the backend THIS SERVER talks to, which on a hosted deployment is an internal address and says nothing about the caller's own machine.
  • brainkb_create_token Generate a Personal Access Token (PAT) for browser-free auth. Requires you to be logged in already (brainkb_login or brainkb_globus_login). The token is shown ONCE and never again — copy it and set it as BRAINKB_TOKEN in your MCP/skill config; then no login or browser is needed until it
  • brainkb_list_tokens List your Personal Access Tokens (metadata only — the secret is never shown): id, name, prefix, created/last-used/expiry, and whether each is active/revoked/expired. Use the id with brainkb_revoke_token.
  • brainkb_revoke_token Revoke one of your Personal Access Tokens by id (see brainkb_list_tokens). Takes effect immediately — the next call using that token fails.
  • brainkb_use_token Use a Personal Access Token (brainkb_pat_...) for THIS session — an alternative to setting BRAINKB_TOKEN in the config. Validates the token, then caches it so subsequent calls authenticate with it. The token is never echoed.
  • brainkb_list_spaces List spaces the user can see (their own/member spaces + public ones), each annotated with THIS caller's permission so you know what they may do: - your_role: 'owner' | 'editor' | 'viewer' | null (their space membership) - is_owner: they own the space - access: 'owner' | 'me
  • brainkb_create_space Create a workspace/space. The caller becomes owner. slug: lowercase/hyphen id, **globally unique** — if it's already taken the call returns 409 (pick another slug; slugs are never reused/deleted). visibility: 'private' or 'public'; description: short human description (recommended —
  • brainkb_set_space_visibility Set a space 'public' (anyone, even anonymous, can read) or 'private' (members only). Owner only.
  • brainkb_add_space_member Add/update a space member. role: 'owner' | 'editor' | 'viewer'. Owner only.
  • brainkb_add_space_graph Register a named graph and bind it to a space, so ingest/read on that graph are governed by the space's membership and visibility. Owner/editor only. The named_graph_iri is **globally unique** — one graph belongs to exactly one space. If it's already registered (to any space) the call re
  • brainkb_ingest_text Ingest raw RDF text (Turtle / N-Triples / JSON-LD, auto-detected) into a named graph. Returns a job_id; ingestion runs in the background — poll with brainkb_job_status. The graph must be registered (see brainkb_add_space_graph) and the caller must have write access to its space. `sh
  • brainkb_list_uploads List RDF files YOU have staged with POST /upload but not yet ingested. Shows each upload_id, its size, sha256 and when it expires. Only your own uploads are visible.
  • brainkb_upload_status State of one of your staged/submitted uploads. `state` is `staged` (waiting for brainkb_ingest_upload), `submitting` (the server is streaming it to the ingest API), `submitted` (accepted — `job_id` is set, poll brainkb_job_status) or `failed` (the staged bytes were KEPT, so retry with
  • brainkb_discard_upload Delete one of your staged uploads without ingesting it.
  • brainkb_ingest_upload Ingest a file you staged with `POST /upload` into a named graph. This is the route for a large local file: your HTTP client streams the bytes straight to this server over HTTPS, then you name the resulting upload_id here. The server reads its own staged copy and posts it to the ingest A
  • brainkb_ingest_files Ingest local RDF files (ttl/nt/nq/rdf/owl/jsonld/json) into a named graph. Returns a job_id; runs in the background — poll with brainkb_job_status.
  • brainkb_list_jobs List the user's ingest jobs (newest first) with status and progress.
  • brainkb_job_status Detailed status of one ingest job: status, progress %, current file/stage, per-file failures, and (when complete) a summary.
  • brainkb_recover_job Attempt to recover a stuck/errored ingest job (marks it recoverable/errored).
  • brainkb_search Full-text search over the knowledge graphs, access-filtered by space visibility. Pass `space` to scope to one workspace, omit for a full search. No login needed: an unauthenticated caller searches public spaces only. Anonymous/other users never see private-space data.
  • brainkb_read_space Read all RDF (JSON-LD) in a space's graphs. Public spaces are readable by anyone without logging in (read-only); private spaces require login and membership. Don't ask the user to log in just to read a public space.
  • brainkb_list_registered_graphs List registered named graphs visible to the caller (private-space graphs the caller can't access are hidden).
  • brainkb_sparql Run an arbitrary SPARQL query. Requires an Admin/SuperAdmin role (the sparql_admin capability) — for ordinary questions prefer brainkb_search, brainkb_read_space, or the provenance/delta tools, which need no admin role.
  • brainkb_qa_list Find a canned question BrainKB can answer, then run it with brainkb_qa_run. Prefer these over writing SPARQL: they are vetted against BrainKB's actual vocabulary. Discovery is two steps, so you never read every query at once: 1. brainkb_qa_list() -> the menu: each category's name, a de
  • brainkb_qa_run Run a canned question from brainkb_qa_list by id. `params` maps parameter names to values; they are validated and escaped, never spliced in raw. Runs through the same SPARQL endpoint as brainkb_sparql, so it needs the same role.
  • brainkb_provenance_job PROV-O provenance bundle (JSON-LD) for one ingest job.
  • brainkb_provenance_graph PROV-O ingestion/activity history (JSON-LD) for a named graph.
  • brainkb_delta The exact triples a job added (its delta), as JSON-LD.
  • brainkb_delta_history A named graph's change history: one entry per ingest delta (job, triple count, timestamp), newest first.
  • brainkb_delta_compare Compare two jobs' deltas: A-only / B-only / shared triple counts + triples.
  • brainkb_capabilities (Admin only) Show a user's roles, effective capabilities, and delegated grants. Useful to check why someone can/can't create team spaces, ingest, etc.
  • brainkb_grant_capability (Admin only) Delegate a capability to a user — e.g. 'create_team_space' or 'manage_team_space' so a Curator/Lab Member can create/manage team spaces. Grantable: create_private_space, create_team_space, manage_team_space, ingest, recover, read_private (NOT the admin-only 'grant'/'sparql_a
  • brainkb_revoke_capability (Admin only) Revoke a previously granted capability from a user.
  • brainkb_list_capabilities (Admin only) Catalog of all KG capabilities, which are delegatable ('grantable'), which are admin-only, and a description of each. Use this to see the available permission options before granting to a user or group/role.
  • brainkb_role_capabilities (Admin only) List the capabilities granted to a role/group (e.g. 'uk_collaborator', 'Lab Member').
  • brainkb_grant_role_capability (Admin only) Grant a capability to a whole role/group so EVERY member gets it — e.g. give a custom group 'uk_collaborator' the 'ingest' or 'create_private_space' capability. Grantable: create_private_space, create_team_space, manage_team_space, ingest, recover, read_private (NOT the
  • brainkb_revoke_role_capability (Admin only) Revoke a capability from a role/group.
  • brainkb_list_access_rules List a space's fine-grained access rules (member/manager of the space).
  • brainkb_add_access_rule (Space manager) Restrict a space action to a subject. action: 'read' | 'write' | 'manage'. subject_type: 'global_role' (e.g. 'Admin','Lab Member') | 'member' (an email) | 'space_role' ('viewer'|'editor'|'owner', matched as >=). When rules exist for an action, only matching callers ma
  • brainkb_remove_access_rule (Space manager) Delete a fine-grained access rule by its id (see brainkb_list_access_rules).
  • brainkb_list_users (Admin) List users (profiles) — filter by `q` (name/email/orcid) or `role`. Shows profile_id, email, roles, providers, ban status.
  • brainkb_available_roles (Admin) List the available roles/groups (Admin, Lab Member, Curator, …).
  • brainkb_create_role (Admin) Create a new role/group — e.g. an 'External' collaborator group — which can then be assigned with brainkb_assign_role.
  • brainkb_assign_role (Admin) Assign a role/group to a user by email (e.g. 'Lab Member', 'External', or a custom group). The user must already have a profile (created on first login/registration). NOTE: assigning the 'Admin'/'SuperAdmin' role is SuperAdmin-only (hierarchy: SuperAdmin > Admin).
  • brainkb_remove_role (Admin) Remove a role/group from a user by email.
  • brainkb_activate_user (Admin) Activate a user's account (sets the JWT user active) by email.
  • brainkb_deactivate_user (Admin) Deactivate a user's account by email.
  • brainkb_ban_user (Admin) Ban a user by email (reversible; preserves history). This is how accounts are removed — there is NO hard delete. Banning an Admin is SuperAdmin-only; SuperAdmin accounts cannot be banned.
  • brainkb_unban_user (Admin) Lift a ban on a user by email.
  • brainkb_list_permissions (Admin) List all usermanagement permissions (resource/action pairs used for page-access and role-permission mapping). These are the addable 'permission' options; KG action-capabilities are listed by brainkb_list_capabilities.
  • brainkb_create_permission (Admin) Create a new usermanagement permission, e.g. name='dataset.export', resource='dataset', action='export'. Attach it to roles via the usermanagement role-permissions API.

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