Brainkb

Compare two jobs' deltas: A-only / B-only / shared triple counts + triples.

A named graph's change history: one entry per ingest delta (job, triple count, timestamp), newest first.

Delete one of your staged uploads without ingesting it.

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.

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 no login; member emails are shown to members and admins only.

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) to complete. (The browser step is unavoidable: only the user can consent at the provider.)

(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_admin').

(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 admin-only 'grant'/'sparql_admin'). Create the group first with brainkb_create_role, then assign it to users with brainkb_assign_role.

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.

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. `sha256` / `expected_bytes` are an integrity contract, and you should use them whenever the RDF came from a file. Ingest is append-only — no delete for triples, no unregister for a graph — so RDF that arrives here mangled is permanent. Because `data` is a string, it passes through the calle…

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 API internally, so the RDF never passes through a model's context — nothing to transcribe, no context-window ceiling, and no reason to split the document (splitting breaks blank-node identity and silently detaches triples, permanently). Stage a file with any HTTP client — the point i…

Detailed status of one ingest job: status, progress %, current file/stage, per-file failures, and (when complete) a summary.

List a space's fine-grained access rules (member/manager of the space).

(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.

List the user's ingest jobs (newest first) with status and progress.

(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.

List registered named graphs visible to the caller (private-space graphs the caller can't access are hidden).

(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), which nobody can bind.

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) - role_inherited: the role comes from a parent space, not this one - parent_slug: the parent space, when this is a subspace the caller can see the parent of (build the tree from it) - is_owner: they own the space - access: 'owner' | 'member' | 'public' (…

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.

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.

(Admin) List users (profiles) — filter by `q` (name/email/orcid) or `role`. Shows profile_id, email, roles, providers, ban status.

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` false means the caller has no write-capable role at all. `unmapped_graphs` are registered graphs in no space. Use this, not brainkb_list_registered_graphs, to choose where to ingest.

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 tokens (query_service, usermanagement, …). Falls back to a legacy per-service token if the backend has no SSO. On the hosted multi-user remote you can skip this and instead have your client send an 'Authorization: Bearer <token>' header (a refresh token unlocks all services).

Forget the cached token for this session.

PROV-O ingestion/activity history (JSON-LD) for a named graph.

PROV-O provenance bundle (JSON-LD) for one ingest job.

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 description of the questions it covers, and how many queries it has. Pick the category whose description matches the user's question. 2. brainkb_qa_list(category="<name>") -> that category's queries. Each has `question` (what it answers), `notes` (when to use it, where paramet…

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 returns `limit` rows from `offset`, and `page.next_offset` says where to continue.

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.

Attempt to recover a stuck/errored ingest job (marks it recoverable/errored).

(Space manager) Delete a fine-grained access rule by its id (see brainkb_list_access_rules).

(Admin) Remove a role/group from a user by email.

(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` reserves it for that space, whose managers/editors may then bind it. Graphs already bound stay where they are; the response lists them under `already_bound`. 409 if it is already reserved, overlaps a system graph, or is bound to another space than `space_slug`.

(Admin only) Revoke a previously granted capability from a user.

(Admin only) Revoke a capability from a role/group.

Revoke one of your Personal Access Tokens by id (see brainkb_list_tokens). Takes effect immediately — the next call using that token fails.

(Admin only) List the capabilities granted to a role/group (e.g. 'uk_collaborator', 'Lab Member').

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.

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 subspace can be public or private on its own.

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.

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 LIMIT/OFFSET returns at most `limit` rows (0 = the server's page size, 500 by default) starting at `offset`; the response's `page` says whether there is more (`has_more`) and where to continue (`next_offset`). Add ORDER BY for stable pages. A query that sets its own LIMIT runs as wri…

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.

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.

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.

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: the same run can go into several spaces, once each. Its graph, https://brainkb.org/synthscholar/<space>/reviews/<protocol.review_id>/, is registered in the space; review.ttl plus an import record (PROV-O: who, when, every kept file with media type, size and sha256, what was left out) are…

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.

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 studies that report it); `study`: source id (S-001), title, DOI or PMID; `fields`: comma-separated fields to return (the response lists the available ones).

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 code in the reason (e.g. "EC2"), or by PMID. Also returns counts for the filtered set: by stage and decision, what decisions were judged on, and exclusion reasons by criterion.

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 concerns). Years inclusive. Each study: ids, title, authors, year, journal, how it was read and by which route, RoB. Paged (`total`, at most 200 per call).

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.

(Admin) Lift a ban on a user by email.

(Admin/SuperAdmin) Remove a reservation by its id (see brainkb_list_reserved_graphs). System reservations cannot be removed.

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://brainkb.org/graph/<slug>/…, …/synthscholar/<slug>/…) to the new slug, with their registry, search and history records and SynthScholar reviews; graphs with other IRIs keep theirs. The old slug and IRIs stay as aliases: they keep resolving and nobody else can take them, but ingest into a…

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_ingest_upload rather than re-uploading).

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.

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.