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PubMed Scraper: Articles, Abstracts & Evidence Table to Excel

pubmed_evidence_table
Read-only

Run PubMed queries to build a screening-ready evidence table with PMID, journal, study design, sample size, retraction status, and PRISMA counts for systematic-review screening.

Instructions

Run one or more PubMed queries and return a screening-ready evidence table: one row per article with PMID, journal, study design, sample size, retraction status and citation, plus PRISMA-style counts for the whole search. Unlike literature_search (all disciplines, OpenAlex ranking, citation-network walks), this uses native PubMed syntax and MeSH and is built for systematic-review screening. Use when the question is biomedical/clinical and you need reproducible PubMed queries or design filters (RCT, meta-analysis, cohort). Do not use for non-biomedical topics (use literature_search), for trial registrations (use clinical_trial_leads) or to verify a reference list (use reference_checker). Parameters: queries accept PubMed field tags ([tiab], [mh], [pt]) and Boolean operators; several queries are de-duplicated into one table. Filters (studyDesigns, excludeAnimalOnly, hasAbstract, freeFullTextOnly, excludePreprints) run before billing, and PRISMA counts still report what they removed. retractedArticles=flag bills retracted rows marked FIX; exclude drops them unbilled. sampleSize is parsed from the abstract and comes with sampleSizeConfidence; treat low confidence as unverified. Returns per item: summary, status, pmid, title, year, journal, studyDesign, sampleSize, sampleSizeConfidence, retractionStatus, retracted, citation. Excel, PRISMA and RIS/Rayyan import files stay in the run's Apify key-value store.

Behavior: read-only; runs the Apify Actor pandadad0214/pubmed-evidence-table (https://apify.com/pandadad0214/pubmed-evidence-table) on your own Apify account. Price: $0.004 per article found. Runs that find nothing are not charged per result, and spending is capped per call by run_max_charge_usd (default $0.50). run_max_items (default 50) limits items returned and fills maxResults when you leave it unset, so it also limits what is billed; setting maxResults higher can bill more than is returned. Most calls finish in 5-15 s for a few inputs; large inputs or crawls can take minutes, so raise run_timeout_secs (max 300) or shrink the input after a timeout error. Returns JSON {actor, count, items}; long text output is trimmed to whole items, with all items in structuredContent.

Input Schema

NameRequiredDescriptionDefault
dateToNoPublished to. Optional. 2025, 2025-12 or 2025-12-31.
sortByNoOrder. Order of the table. PubMed best match or most recent first. Choices: relevance = Best match (PubMed relevance); newest = Most recent.relevance
queriesYesPubMed search strings. One or more PubMed queries, written exactly as you would in PubMed (field tags like [tiab], [mh], [pt] and AND / OR / NOT work). Records found by more than one query are counted once and reported as duplicates.
dateFromNoPublished from. Optional. 2020, 2020-06 or 2020-06-30 (publication date).
languagesNoLanguages. Optional, e.g. english, spanish. Leave empty for all.
maxResultsNoMaximum articles. You pay per returned article ($0.004 each), so this also caps the cost. Counts for everything not included are still reported. Whole number, 1 to 10,000 results; default 200.
hasAbstractNoOnly records with an abstract. Removes records without an abstract (often letters, editorials and older records). Default: off.
contactEmailNoContact email for NCBI / Crossref (optional). Sent to NCBI and Crossref as the contact for this tool. Leave empty to use ours.
studyDesignsNoStudy designs. Keep only these designs (PubMed publication types / MeSH). Leave empty for all.
citationStyleNoCitation style. Style for the citation column and the CITATIONS file. Formatted by citeproc-js with the official CSL style. Choices: vancouver = Vancouver (NLM); apa = APA 7th edition; ieee = IEEE; harvard = Harvard (Cite Them Right); chicago = Chicago author-date; mla = MLA 9th edition.vancouver
run_max_itemsNoOptional. Most results to return from this call (default from PANDA_MAX_ITEMS, 50). Also limits how many results the Actor produces and charges for, unless you set its own max field.
excludePreprintsNoExclude preprints. Removes records with the Preprint publication type. Default: off.
freeFullTextOnlyNoFree full text only. Keep only records PubMed links to a free full text. Default: off.
includeAbstractsNoInclude abstracts. Include the abstract in the table and import files (recommended for screening). Default: on.
run_timeout_secsNoOptional. Seconds to wait for results (default from PANDA_TIMEOUT_SECS, 120; max 300).
excludeAnimalOnlyNoExclude animal-only studies. Removes records indexed with Animals but not Humans. Records not yet indexed are kept. Default: off.
retractedArticlesNoRetracted articles. Flag keeps them in the table, marked FIX (charged as returned articles). Exclude removes them before they are returned (not charged) and counts them in PRISMA. Choices: flag = Flag them (FIX); exclude = Exclude them.flag
run_max_charge_usdNoOptional. Hard spending cap for this call in USD (default from PANDA_MAX_CHARGE_USD, 0.50).

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.6/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only, non-destructive, open-world, non-idempotent, so the description focuses on what annotations cannot carry: per-article pricing, which filters are applied before billing, that PRISMA counts still report removed records, the run_max_items vs maxResults billing interaction, the 300s timeout ceiling, and that long text output is trimmed to whole items. The only gap is no statement about how failures or partial results surface beyond the timeout hint.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with purpose, then alternatives, then parameter behavior, then runtime/cost — a sensible order for an 18-parameter tool, and nearly every sentence carries information. It is long and repeats billing language already present in the maxResults and retractedArticles schema descriptions, which costs it a point.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For an 18-parameter tool with no output schema, the description supplies the return field list, the envelope shape {actor, count, items}, the structuredContent trimming rule, latency expectations, and where Excel/PRISMA/RIS artifacts are stored. Combined with full schema coverage and annotations, an agent has everything needed to call it and interpret the result.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3, but the description adds genuinely non-obvious semantics: queries accept field tags and are de-duplicated across queries, retractedArticles=flag bills flagged rows while exclude does not, and sampleSizeConfidence should be treated as unverified at low values. The subtle warning that raising maxResults can bill more than run_max_items returns is the kind of interaction the schema alone cannot convey.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Specific verb and resource: 'Run one or more PubMed queries and return a screening-ready evidence table', with the row schema (PMID, journal, study design, sample size, retraction status) enumerated. It explicitly distinguishes itself from literature_search, clinical_trial_leads and reference_checker by scope and data source, so an agent can route between them without opening a schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

States the positive condition ('biomedical/clinical and you need reproducible PubMed queries or design filters') and four explicit when-not cases with the sibling to use instead. Nothing about selection is left to inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.