MCP server

Brainkb Official

org.brainkb/brainkb

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Source

At a glance

Type

MCP server

Publisher

brainkb.org (verified by the MCP Registry)

Status

Working at last check

Tools

72

Token cost

About 12,384 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http brainkb https://mcp.brainkb.org/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.brainkb]
url = "https://mcp.brainkb.org/mcp"

Gemini CLI

{"mcpServers":{"brainkb":{"httpUrl":"https://mcp.brainkb.org/mcp"}}}

Cursor

{"mcpServers":{"brainkb":{"url":"https://mcp.brainkb.org/mcp"}}}

VS Code

{"servers":{"brainkb":{"type":"http","url":"https://mcp.brainkb.org/mcp"}}}

Antigravity

agy mcp add brainkb https://mcp.brainkb.org/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"brainkb","server_url":"https://mcp.brainkb.org/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"brainkb","server_url":"https://mcp.brainkb.org/mcp"}

Tools

• brainkb_activate_user ~78 tokens
  (Admin) Activate a user's account (sets the JWT user active) by email.
• brainkb_add_access_rule ~257 tokens
  (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_add_space_graph ~206 tokens
  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_add_space_member ~117 tokens
  Add/update a space member. role: 'owner' | 'editor' | 'viewer'. Owner only.
• brainkb_assign_role ~152 tokens
  (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_available_roles ~62 tokens
  (Admin) List the available roles/groups (Admin, Lab Member, Curator, …).
• brainkb_ban_user ~129 tokens
  (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_capabilities ~102 tokens
  (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_create_permission ~164 tokens
  (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.
• brainkb_create_role ~132 tokens
  (Admin) Create a new role/group — e.g. an 'External' collaborator group — which can then be assigned with brainkb_assign_role.
• brainkb_create_space ~394 tokens
  Create a workspace/space, or a subspace inside one. The caller becomes owner. slug: lowercase/hyphen id, **globally unique** — if it's already taken the call returns 409 (pick another slug). visibility: 'private' or 'public' (set per space: a private space may hold a public subspace)
• brainkb_create_token ~204 tokens
  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_deactivate_user Changes accounts · ~72 tokens
  (Admin) Deactivate a user's account by email.
• brainkb_delete_space Deletes data · ~369 tokens
  PERMANENTLY delete a space and everything in it. SuperAdmin only; irreversible. Drops the space's named graphs and the ingestion-history (delta) graphs that hold copies of their data, removes the graphs' registry entries and the space's RDF manifest, and deletes the space with its membe
• brainkb_delta ~70 tokens
  The exact triples a job added (its delta), as JSON-LD.
• brainkb_delta_compare ~99 tokens
  Compare two jobs' deltas: A-only / B-only / shared triple counts + triples.
• brainkb_delta_history ~98 tokens
  A named graph's change history: one entry per ingest delta (job, triple count, timestamp), newest first.
• brainkb_discard_upload ~78 tokens
  Delete one of your staged uploads without ingesting it.
• brainkb_finish_login ~127 tokens
  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_get_space ~160 tokens
  A space's details: graphs, members (direct, plus `inherited_members` with the parent space each comes from), visibility, `parent_slug`, `ancestors` (root first) and direct `subspaces` — only the ones the caller may see — and the caller's `your_role` / `role_inherited`. Public spaces need
• brainkb_globus_login ~190 tokens
  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_grant_capability Changes accounts · ~168 tokens
  (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_grant_role_capability Changes accounts · ~207 tokens
  (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_ingest_files ~156 tokens
  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_ingest_text ~386 tokens
  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_ingest_upload ~528 tokens
  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_job_status ~94 tokens
  Detailed status of one ingest job: status, progress %, current file/stage, per-file failures, and (when complete) a summary.
• brainkb_list_access_rules ~80 tokens
  List a space's fine-grained access rules (member/manager of the space).
• brainkb_list_capabilities ~108 tokens
  (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_list_jobs ~73 tokens
  List the user's ingest jobs (newest first) with status and progress.
• brainkb_list_permissions ~109 tokens
  (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_list_registered_graphs ~78 tokens
  List registered named graphs visible to the caller (private-space graphs the caller can't access are hidden).
• brainkb_list_reserved_graphs ~138 tokens
  (Admin/SuperAdmin) List reserved named graphs: graph IRIs, or every IRI under a prefix, that only an Admin/SuperAdmin — or, when reserved for a space, that space's managers/editors — may register or bind. Includes the built-in system reservations (BrainKB's metadata and provenance graphs
• brainkb_list_spaces ~376 tokens
  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, including a role inherited from a parent space)
• brainkb_list_tokens ~100 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_list_uploads ~90 tokens
  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_list_users ~121 tokens
  (Admin) List users (profiles) — filter by `q` (name/email/orcid) or `role`. Shows profile_id, email, roles, providers, ban status.
• brainkb_list_writable_spaces ~186 tokens
  Spaces the caller can ingest into, each with its graphs (and descriptions) and `parent_slug` for subspaces — decided by the same checks ingestion uses: owner/ editor membership (including a role inherited from a parent space), a space write access rule, or Admin/SuperAdmin. `can_ingest`
• brainkb_login ~258 tokens
  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_logout ~48 tokens
  Forget the cached token for this session.
• brainkb_provenance_graph ~86 tokens
  PROV-O ingestion/activity history (JSON-LD) for a named graph.
• brainkb_provenance_job ~75 tokens
  PROV-O provenance bundle (JSON-LD) for one ingest job.
• brainkb_qa_list ~337 tokens
  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 ~232 tokens
  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. Results page the same way: a query without its own LIMIT re
• brainkb_read_space ~120 tokens
  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_recover_job ~80 tokens
  Attempt to recover a stuck/errored ingest job (marks it recoverable/errored).
• brainkb_remove_access_rule ~104 tokens
  (Space manager) Delete a fine-grained access rule by its id (see brainkb_list_access_rules).
• brainkb_remove_role ~84 tokens
  (Admin) Remove a role/group from a user by email.
• brainkb_reserve_graph ~275 tokens
  (Admin/SuperAdmin) Reserve a named graph so other users can't create it. match_type 'exact' reserves one graph IRI; 'prefix' reserves every IRI starting with it (e.g. 'https://brainkb.org/graph/allen/'). Give a `reason` — it is shown to anyone who is refused. Optional `space_slug` reser
• brainkb_revoke_capability Changes accounts · ~98 tokens
  (Admin only) Revoke a previously granted capability from a user.
• brainkb_revoke_role_capability Changes accounts · ~95 tokens
  (Admin only) Revoke a capability from a role/group.
• brainkb_revoke_token Changes accounts · ~101 tokens
  Revoke one of your Personal Access Tokens by id (see brainkb_list_tokens). Takes effect immediately — the next call using that token fails.
• brainkb_role_capabilities ~89 tokens
  (Admin only) List the capabilities granted to a role/group (e.g. 'uk_collaborator', 'Lab Member').
• brainkb_search ~179 tokens
  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_set_space_visibility ~180 tokens
  Set a space 'public' (anyone, even anonymous, can read) or 'private' (members only). Owner only. Everything in a public space is public: making a space public also makes all its subspaces public, and a subspace of a public space cannot be made private (409). Under a private space each su
• brainkb_space_tree ~122 tokens
  A space and every subspace below it (any depth), nested: each node has slug, name, visibility, the caller's role and whether it's inherited from a parent, and its graph count. Only subspaces the caller may see are included.
• brainkb_sparql ~314 tokens
  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. Large results come back a page at a time. A SELECT without its own
• brainkb_synthscholar_evidence ~252 tokens
  Evidence spans of an ingested review: the quoted text its claims rest on, with the study, section, relevance, and whether the quote was matched verbatim in the source (`grounded`). Filter by text, claim type, PMID or grounding.
• brainkb_synthscholar_find_study ~166 tokens
  Which ingested reviews (that you can read) include or screened a study — by DOI, PMID or part of its title (6+ characters) — and what happened to it in each: included (read in full or from the abstract) or each screening decision with its reason.
• brainkb_synthscholar_get_review ~169 tokens
  One ingested review: summary, its graph and space, the files kept (path, kind, media type, size, sha256), the run's search log and verification, the screening basis and full-text retrieval. Long texts and the per-study list are left out here — read them from the graph or the review page.
• brainkb_synthscholar_ingest ~359 tokens
  Ingest a SynthScholar review — the output directory of a run (the folder holding review.json and review.ttl, as the synthscholar skill writes it) — into a space you may write to (see brainkb_list_writable_spaces; you need to be its owner or an editor). A review is unique per space:
• brainkb_synthscholar_list_reviews ~138 tokens
  Ingested SynthScholar reviews you can read (public spaces: anyone): id, title, research question, space, graph, included count, when ingested, ingest job. `q` filters on text in the title or research question.
• brainkb_synthscholar_records ~306 tokens
  Per-study records an ingested review produced. `kind`: `charting` (the data-charting form's answers per study), `appraisal` (critical appraisal by domain) or `narrative` (narrative synthesis rows: design, methods, outcomes, limitations). `q`: text in the answers (e.g. "neo4j" finds the s
• brainkb_synthscholar_screening ~352 tokens
  The screening audit trail of an ingested review: every decision with its stage (title_abstract | full_text), decision (include | exclude), what it was judged on (title_abstract | full_text | abstract_only), the full-text route and the reason. Filter by any of those, by text or criterion
• brainkb_synthscholar_studies ~374 tokens
  The included studies of an ingested review, filtered. `q`: text in title, authors, journal, DOI, PMID or keywords. `full_text`: true = read in full, false = abstract only. `source`: full-text route (europe_pmc, unpaywall, ezproxy, arxiv, …). `rob`: risk-of-bias rating (low, high, some co
• brainkb_synthscholar_text ~164 tokens
  An ingested review's own text: `abstract`, `introduction`, `synthesis`, `bias`, `limitations`, `conclusions`, `research_question`, `search_queries` or `per_group` (the per-group analysis) — or all of them when `section` is empty.
• brainkb_unban_user ~67 tokens
  (Admin) Lift a ban on a user by email.
• brainkb_unreserve_graph ~104 tokens
  (Admin/SuperAdmin) Remove a reservation by its id (see brainkb_list_reserved_graphs). System reservations cannot be removed.
• brainkb_update_space ~376 tokens
  Rename a space, change its description, and/or give it a new slug. Owner/manager only. Pass only what changes; description="" clears it. `new_slug` (lowercase letters, digits and hyphens, 3-64 chars) moves the space's IRI and every graph whose IRI is built from the old slug (https://bra
• brainkb_upload_status ~163 tokens
  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_use_token ~140 tokens
  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_whoami ~119 tokens
  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.

Browse

• Email
• Notes and wikis

Related MCP servers

• Tresslers Intelligence MCP Server
  Sovereign intelligence dossiers, daily briefings, RAG search, knowledge graph, codon optimizer.
• Apex Edge — x402-paid machine services
  x402-paid MCP tools: utils, audit screens, corpus search, inference. USDC Base+Solana.
• Awareness — Memory, Knowledge & Agent Markets
  Memory + public knowledge graph for AI agents: 1,000+ sourced papers, deal board, agent market.
• Artsdata
  Search Artsdata for authoritative data on Canadian events, artists, organizations, and places.
• Monarch Initiative
  Monarch Initiative MCP — biomedical knowledge graph.
• VineVerse — Bible Knowledge Graph
  Bible knowledge graph: 31,102 verses, 341,289 cross references, people, places, themes.
• INITE Brain
  Long-term memory for AI agents: a bitemporal knowledge graph with cited answers.
• RationalBloks
  Deploy production REST and Neo4j Graph APIs from JSON schemas in seconds.

Badge for your README

[![AptLynx](https://aptlynx.net/badge/org.brainkb/brainkb.svg)](https://aptlynx.net/servers/org.brainkb/brainkb)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents