PyEuropePMC

Analyze citation context for a paper using an LLM (requires an LLM provider).

Aggregate statistics about a search without returning its records. Every metric says where it comes from in `basis`: `exact` is counted by Europe PMC over all `hit_count` records (`by_year`: one count per year; `open_access`; the `thresholds` of `citations`), `sample` is computed from the first `limit` records of the search and describes only those (`journals`, `authors`, `types`, `countries`, `funders` and the `citations` statistics). When `limit` covers the whole result, those are `exact` too. The sample metrics need `pip install pyeuropepmc[analytics]`.

Merge multiple BibTeX libraries, deduplicating by DOI.

Parse a BibTeX string into structured entries.

Convert BibTeX entries to CSL-JSON format.

Convert BibTeX entries to RIS format.

Validate BibTeX entries for completeness and correctness.

Build a Europe PMC query from structured input instead of writing syntax by hand, and check the result. Returns the query, a plain-language explanation of what it asks for, and any warnings. At least one of all_of, any_of or a filter is needed (none_of alone would match almost everything). The same filters are available on `search_papers`.

How full are the server's caches and how often do they help? For the search, article and annotation clients and for the full-text XML cache: entries, capacity, size, hits, misses and hit rate. Counts only: no cache keys (they can contain query text), no cached content and no file paths.

Walk the citation graph forward (cited-by), backward (references), or both, with configurable depth and a minimum-citation-count filter.

Empty one of the server's in-memory caches, so that the next call asks Europe PMC again. Only worth doing when you suspect a cached answer is stale (the caches hold results for a day); every cleared entry has to be fetched again, which is load on Europe PMC. It changes server state, so a client may ask for approval. It never touches files on disk.

Search ClinicalTrials.gov for studies by condition, intervention, or free-text query.

Compare citations between two papers using an LLM (requires an LLM provider).

Number of Europe PMC records matching a query, without fetching them. Use it to size a search before choosing ``limit`` for `search_papers`.

One compact record for a paper from Europe PMC, Crossref, OpenAlex, Semantic Scholar, iCite and Unpaywall, merged: citation impact, funders and grants, authors with their institutions, open-access status and licence, and corrections and retractions. The sources are asked at the same time; `sources` in the answer says for each whether it answered (ok), had nothing (empty), failed (error, with the reason), or was still running when `time_budget` ended (timeout). A failed source gives a partial record, not an error. Institutions come with name, country and ROR ID; `ror_details` adds their place and website. Nothing is written to disk.

Is Europe PMC up right now? Probes the endpoints this server depends on (search, full text, citations, annotations) and returns ok, degraded (some fail), down (none answers) or unknown (only 4xx answers: a blocked probe or a moved endpoint), with the HTTP status and the time in milliseconds of each. Use it before retrying a tool that failed with a network error, a timeout or a 5xx. The answer is kept for 30 seconds, so asking again does not probe again (`cached` says so), and it contains no URLs or response bodies.

Score a Europe PMC query against papers you already know, for systematic-review work: recall (how many of the included PMIDs it finds) and how many excluded ones it still finds, with the PMIDs it misses. This runs the query on Europe PMC itself, so it measures what the search really returns, not a local reading of the syntax. PMIDs that Europe PMC does not know are reported apart and left out of the scores. A query with errors is refused; see `validate_query`.

Export papers as a file's worth of text to hand to a reference manager or a spreadsheet: BibTeX, RIS or CSL-JSON (Zotero, Mendeley, EndNote, Pandoc) or CSV, JSON or Markdown. Give a search `query` or a list of `ids`. BibTeX keys look like `vasiliou2005analysis`, are unique within the export and do not change when it is cut to size; text that LaTeX reads as syntax (& % # _ $) is escaped. A paper with more than 100 authors lists the first 100 (BibTeX adds `and others`). The export is never cut in the middle of a record: `truncated` says that records were left out; `next_skip` (query) or `remaining` (ids) say where to continue. Nothing is written to disk.

Where can this paper be read for free? Looks the DOI up in Unpaywall and returns the open-access status (gold, green, hybrid, bronze, closed), the best copy with its PDF link and licence, and a few alternatives. ``europepmc_fulltext`` says whether `get_paper_fulltext` will work for it. Needs UNPAYWALL_EMAIL in the server's environment.

Articles in which Europe PMC found a given entity, with how often and where it is mentioned. One page per call: pass ``next_cursor`` back as ``cursor`` for the next. Europe PMC's entity search ignores type, section and provider, so the three filters here apply to the mentions it returns: an article without a matching mention is left out and counted in ``articles_filtered_out``.

Search the local SQLite FTS5 full-text index for papers whose full text matches a query. A fresh index handle is opened per call rather than cached: SQLite connections are only safe to use from the thread that created them, and each call may run on a different worker thread.

Genes, proteins, chemicals, diseases, organisms and other entities that Europe PMC text-mined from a paper, grouped by entity with mention counts, sections and example mentions. A review with hundreds of mentions comes back as a short entity list.

Get papers that cite a given paper (Europe PMC).

Where is the data of this paper? Accession numbers Europe PMC text-mined from the full text (dbSNP, RefSeq, OMIM, ClinicalTrials.gov, cited DOIs) and records that providers link to the paper (BioStudies supplementary data, model-organism databases, Altmetric), as one flat list. `kind` separates supporting_data and related_data from altmetrics and recommended_reviews; `origin` says whether a link was text_mined or supplied by a provider. A paper without links gives an empty list, which is a valid answer.

Get detailed paper information by PMID, PMCID, or DOI (Europe PMC).

Fetch the structured full text of an open-access paper from Europe PMC. Returns metadata, the list of available section titles, and the content in the requested format. When the content is longer than ``max_chars`` it is cut at a block boundary and ``truncated`` is true: ask again with ``sections`` for the part you need. Only open-access articles have full text; anything else fails with the reason.

Links that third parties publish for a paper, grouped by provider with the provider's description: BioStudies supplementary material, model-organism databases, GO annotations, Faculty Opinions recommendations, Altmetric. Use get_paper_data_links for the data accessions mentioned in the text.

Get the reference list of a paper (backward citations, Europe PMC).

Look up many papers at once: one combined Europe PMC query per 50 identifiers instead of one call per paper. Every input gets a result in the order given, with a status: ok, not_found, invalid (malformed identifier) or error (that request failed). One bad identifier never fails the batch; a repeated identifier repeats its result.

Markdown full text of several open-access papers in one call, within a size budget. The identifiers are resolved with one query, papers that are not open access are reported without being downloaded, and the rest are fetched four at a time. The total budget is handed out in the order given: once it is used up, the remaining papers are reported as skipped_budget and not downloaded. Each result has a status: ok, not_found, invalid, not_in_pmc, not_open_access, no_matching_section, duplicate, error or skipped_budget. Use `get_paper_fulltext` for one paper at a larger size.

Build a knowledge graph from research literature using an LLM (requires an LLM provider).

Generate a comprehensive literature review using an LLM (requires an LLM provider).

MeSH headings for search terms: the descriptor (ID, heading, tree numbers), its entry terms and a ready Europe PMC fragment `(MESH:"Heading" OR "entry term" OR ...)` for each term, and the fragments joined into one query that is checked like `validate_query`. By default it works offline from a bundled snapshot of 244 common clinical headings taken from NLM's published MeSH (heading, entry terms and tree numbers as published): a term that is not in it comes back with `matched: false` and is searched as written, never guessed. `use_api` asks NLM instead, which covers all of MeSH and needs the network (the terms are sent to id.nlm.nih.gov); a failed or skipped request is reported for that term and does not fail the call, and `time_budget` bounds the whole call.

Extract figures, tables and supplementary files from a PMC Open Access article. Each item carries its label, caption and the Europe PMC URL its file can be downloaded from. A figure supplement also names the figure it belongs to.

Automated paper screening with PRISMA-compliant criteria, using an LLM (requires an LLM provider).

Split a research question into PICO, PICOS, PICOT or SPIDER elements and build a Europe PMC query from them. Rule-based and offline: no model, no key, no request. Every element is a verbatim piece of the question, given with its position; an element the question does not state is listed in `missing`, never filled in. The rules cover the usual clinical phrasings ("In P, does I reduce O compared with C?", "What is the effect of I on O in P?", "Is I more effective than C for O?", "Is I associated with O?", "Effectiveness of I for O in P", "P treated with I"). A question phrased differently is only partly understood: check `elements` and `missing` before using the query, and ask for clarification when the question is incomplete. The query is checked with the same linter as `validate_query`.

Preprint-specific quality assessment using an LLM (requires an LLM provider).

Resolve a DOI to bibliographic metadata.

Resolve a PubMed ID to bibliographic metadata.

Expand and analyze a research question using an LLM (requires an LLM provider).

Search for authors in Europe PMC.

Search Europe PMC for papers (single source — prefer `unified_search` for multi-source coverage). At most ``limit`` records are fetched; optional filters narrow the query by date, open access, full text availability and source.

Summarize citation activity for a paper using an LLM (requires an LLM provider).

The sentences of an open-access paper's body, grouped by what they do: background, motivation, method, result, claim (the authors' interpretation), limitation, conclusion. Front matter, the reference list and administrative sections (acknowledgments, funding, conflicts) are left out. Rule-based and offline apart from the download: the section a sentence is in sets its default role and cues in the sentence correct it. Where no rule is sure the sentence is `unknown` instead of a guess; in a paper without recognisable headings only background, method and conclusion sentences are recognised. Measured precision per role is in the guide; discussion sections are the hardest part. Sentences come in reading order and are never cut: `truncated` says whether some were left out. Use it to pull the methods or the results of a paper without knowing what its sections are called.

Rewrite a Europe PMC query for another database. For PubMed the field codes map where they have an equivalent (TITLE[ti], AUTH[au], JOURNAL[ta], dates[dp], ...); a construct that does not map (CITES, HAS_*, CITED, ...) is left out and named in `warnings` and `dropped`, and `exact` is false whenever the translation is narrower, broader or only approximate. The other targets search free text, so field codes and operators are stripped and `exact` is always false. A query with errors is refused; see `validate_query`.

Search across multiple literature sources (PubMed, arXiv, Semantic Scholar, OpenAlex, ClinicalTrials.gov) in parallel, with automatic cross-source deduplication. A source that fails does not fail the call; set `diagnostics` to see which one did and why, and to tell an empty source from an unavailable one.

Check a Europe PMC query before running it. Europe PMC does not reject a malformed query, it answers a different one: an unclosed parenthesis or a dangling operator is dropped silently, an unknown field, a flag that is not y/n and a date range with a missing or reversed bound match nothing, and AND mixed with OR without parentheses is not read as either grouping. Each problem comes with its position. `valid` is false when there are errors; warnings are things worth a second look. `normalized` is the cleaned-up query (capital operators, explicit AND) and is only given for a query without errors.