Article Galaxy

Check article availability, access options, and pricing for scientific articles. Returns the available access options for each DOI: - Open Access: freely available, with URL. No purchase needed. - PDF Library: already in the user's archive; includes pdfDownloadUrl when present. - Subscription: available through an institutional subscription. - Token Access: available using prepaid tokens. - GenAI Rights: licensing for AI/LLM use, with price; this is the access option relevant to AI use cases. - Document Delivery: a purchase or rental option for the full document, with price. The response also includes a nextSteps field describing the access summary and the confirmation flow. Pairs with place_order, which is rejected unless the order is confirmed.

check_availability

Check the status of article orders placed with place_order, and get PDF download links when complete. Returns the order status, article metadata, and download links when ready. Order statuses: - Sourcing: the order is still being processed (see subStatus for details). Orders typically remain in this state for a period after placement before completing. - Completed / Delivered / Order Complete: the article is ready; downloadUrls contains the PDF link. - Failed: the order could not be fulfilled. downloadUrls fields, in priority order: 1. pdfUrl: direct PDF download (time-limited pre-signed S3 URL). 2. supplementalUrl: supplemental materials accompanying the PDF (archive containing PDFs, video, or audio). 3. rentalViewerUrl: rental viewer link (not a PDF), available when pdfUrl is not; supports an upgrade to a full PDF purchase. 4. accessUrl: external link to the publisher or unpaywall, from the initial check_availability result, available when none of the above are.

check_order

Check what reuse rights exist for a scientific article. Returns, for each intended use type (personal research, presentation, course pack, etc.): - a reuse right value: one of Unknown, ExplicitlyGranted, ExplicitlyDenied, RequestAQuote - whether the article can be ordered for that intended use Complements check_availability: check_availability reports access and pricing options, while check_reuse_rights reports the permitted uses of the content.

check_reuse_rights

Traverse the scite citation graph from seed DOIs to discover connected papers by citation topology rather than keyword. Each edge is a citation: `s` (citing paper) -> `t` (cited paper). Use it to find prior art / foundations (`direction="out"`), impact and follow-on work (`direction="in"`), or both. Get seed DOIs from `search_literature` first, then traverse; feed interesting nodes back into `search_literature` or `read_fulltext` for content. This tool returns structure (edges + titles), not abstracts or full text. Seeds are automatically expanded to their linked preprint/published versions (e.g. an arXiv DOI and its journal DOI), so a paper split across two DOIs is traversed as one work with a merged citation pool; the extra DOIs appear in `seeds` and `seed_coverage`. Response: `edges` is a deduped list of `{"s","t","d"}` (d = hop distance from a seed); `papers` maps every DOI in the graph to its `{title, year}`. `truncated` is true when the `max_edges` cap was hit. **Coverage — check before trusting the topology.** `seed_coverage` maps each seed to how many of its edges resolved directly (hop 1); `low_coverage_seeds` lists seeds with too few to be reliable. Coverage is per-paper: it only follows references/citers scite resolved to DOIs, and arXiv-heavy (e.g. ML) papers often under-resolve, so a thin graph means missing edges, not a poorly-connected paper. For any seed in `low_coverage_seeds`, treat its topology as incomplete and fall back to `search_literature` for that paper. **Citation intent (scite's differentiator).** Set `include_intent=true` to annotate each edge with the smart-citation `type` (supporting / contrasting / mentioning) and the `section` it appears in — this turns the structure into an *intent graph*: you can see agreement vs. dissent, and method vs. background citations. Set `include_snippets=true` to additionally attach up to 3 `snippets` of the actual citing text (implies intent). Snippet text is returned only for open-access / unrestricted sources; closed-publisher citations still carry type and section. **Custom "why was it cited?" classifications from `snippets`.** scite's `type` is a fixed 3-way label (supporting / contrasting / mentioning). When you need a finer or domain-specific taxonomy — e.g. *uses as baseline*, *extends the method*, *reuses the dataset*, *critiques an assumption*, *motivates the problem* — read the `snippets` (the verbatim sentence the citing paper used) and classify each edge yourself into whatever scheme the task calls for. The snippet is the ground truth; treat scite's `type`/`section` as a prior, not the final answer. Group edges by your derived label to answer "why does this literature cite X?". When a snippet is too short to judge the intent, chain `read_fulltext` on the citing paper (edge `s`) to read the surrounding paragraph / section and recover the full rationale — snippets are ~1 sentence each, `read_fulltext` gives you the argument around them. Typical flow: `citation_graph` (structure + snippets) -> pick the edges that matter -> `read_fulltext(dois=[citing paper])` with a targeted `term` to confirm *why* it was cited before you label it. **Recording a screen.** When you use this tool to screen literature — keeping some papers and dropping others with a reason — record those keep/drop decisions with `report_citations` (cited / excluded + reason_code), and `citation_report` will summarize the include/exclude funnel as a PRISMA-style audit. **Deriving analyses from `edges` (no extra calls).** The edge list is all you need for the classic citation-analysis questions — compute them directly: - *Common references* (shared foundations): traverse `direction="out"` from multiple seeds; take the DOIs that appear as `t` for every seed. - *Common citers* (who cites all of them, e.g. surveys/syntheses): `direction="in"`; DOIs appearing as `s` for every seed. - *Bibliographic coupling* (papers similar to a seed): `direction="out"` at depth 2; rank other papers by how many `t` references they share with the seed. - *Co-citation* (papers cited alongside a seed): `direction="in"` then `out`; rank papers frequently cited by the same citers. - *Citation classics* (most influential in the network): rank DOIs by in-degree (how often they appear as `t`). Filter any of these to supporting/contrasting edges by adding `include_intent=true` first.

citation_graph

Create a new personal Article Galaxy References folder for the user and return its folder_id, for save_to_references.

create_reference_folder

List the customer reference fields this Article Galaxy account records on orders (cost center, project, "My Reference" and similar), with each field's type, options, whether it is required, and the default that place_order would use. Use it to show the fields, pre-filled with their defaults, before ordering, so the user can keep or change them; then call place_order with customer_references keyed by field id. Value rules by fieldType: Textbox/TextArea = free text; Dropdown = the chosen option's "value"; Checkbox = "true" or "false"; ComboBox (multiValue) = a list of option "value"s. Returns customerReferencesEnabled=false when the account records none.

get_customer_references

Report the user's current Article Galaxy MCP quota. Returns: - status: AG plan tier (active, trial, freemium, disabled, or not_connected) - limit: monthly cap on AG tool calls (0 when not enabled) - used: AG tool calls consumed this month - remaining: calls still available this month - upgrade_url: link to upgrade the AG plan Usage counters reset monthly on the UTC calendar month boundary. This tool is read-only and does not consume quota.

get_mcp_usage

List the user's Article Galaxy order history, newest first by default. Use this when the user asks what they have ordered. Examples: - "Get my latest 10 orders" -> limit=10 (the default) - "Get my latest 50 orders" -> limit=50 - "Get my oldest orders" / "sort ascending" -> sort_order="asc" - "Get my August orders" -> month="YYYY-MM" for August; with no year given, use the most recent August that has already started - "Get my orders for DOI 10.1038/nature12373" -> doi="10.1038/nature12373" Filters combine, e.g. month plus status="completed". Results: - table: a ready-made markdown table with columns Order Date, Order ID, DOI, Article, Status (Date), PDF. Show it to the user as-is. The Order Date header carries ↓ (newest first) or ↑ (oldest first). The PDF column holds a link icon to the delivered PDF on Article Galaxy, only for orders with a PDF available. - orders: the same rows as data (orderDate, orderId, doi, article, status, statusTime, pdfUrl). - totalRecords: how many orders match in total, when AG reports it. When the user refers to an order from the list, call check_order with its orderId for live status, reuse rights, or a direct (presigned) download link.

get_order_history

List the citations saved in one of the user's Article Galaxy References folders (folder_id from list_reference_folders), up to 100 per page. Each citation comes back with only its title, DOI and PubMed ID: show the user just those. To show a citation's full record (authors, journal, date, volume/issue/pages, abstract, notes, tags, attachments), call again with its doi or pmid. `query` searches the folder by free text (title, journal, abstract, authors, DOI, PMID, notes) or by field expression, e.g. title:"cancer" AND author:"smith"; fields: title, journal, notes, year, author, tag, abstract, publisher. When the response has nextPage, more citations exist: pass it as page to continue.

list_folder_citations

List the user's own Article Galaxy References folders (folder id, name and existing tags), for save_to_references and list_folder_citations.

list_reference_folders