org.brainkb/brainkb

up checked 2026-11-11T12:37:58.570Z

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Publisher-provided description

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

Summary by lookupd

Manages neuroscience knowledge graphs: ingest RDF into named graphs, query spaces and records, and handle spaces, members and tokens.

Install

Claude Code, remote (streamable-http)

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

Codex, remote (streamable-http)

codex mcp add brainkb --url https://mcp.brainkb.org/mcp

Cursor, remote (streamable-http) → .cursor/mcp.json

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

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (showing 30 of 72)

Publisher-provided text

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.
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 pas
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
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
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
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/rev
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
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: - you
brainkb_create_space 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 cal
brainkb_get_space A space's details: graphs, members (direct, plus `inherited_members` with the parent space each comes from), visibility, `parent_slug`, `ancestors` (root
brainkb_space_tree 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,
brainkb_set_space_visibility 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
brainkb_update_space 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` (lo
brainkb_delete_space PERMANENTLY delete a space and everything in it. SuperAdmin only; irreversible. Drops the space's named graphs and the ingestion-history (delta) graphs tha
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. Th
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 bra
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 upload
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
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
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_synthscholar_ingest 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
brainkb_synthscholar_list_reviews Ingested SynthScholar reviews you can read (public spaces: anyone): id, title, research question, space, graph, included count, when ingested, ingest job.
brainkb_synthscholar_studies The included studies of an ingested review, filtered. `q`: text in title, authors, journal, DOI, PMID or keywords. `full_text`: true = read in full, fal
brainkb_synthscholar_screening The screening audit trail of an ingested review: every decision with its stage (title_abstract | full_text), decision (include | exclude), what it was j
brainkb_synthscholar_evidence 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
brainkb_synthscholar_records Per-study records an ingested review produced. `kind`: `charting` (the data-charting form's answers per study), `appraisal` (critical appraisal by domai

Details

Version: 0.1.0
Transports: streamable-http
Uptime (7 days): 100%
Median latency: 297 ms
First indexed: 2026-11-01T10:08:01.949Z
Last seen in registry: 2026-11-01T10:08:01.949Z
Repository: https://github.com/sensein/BrainKB

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