Biomedical search: Consensus, PubMed and Europe PMC

PubMed and Europe PMC are the reference sources for biomedical literature. PubMed, run by the US National Library of Medicine, holds more than 40 million citations and abstracts¹. Europe PMC, run by EMBL-EBI, holds 49.2 million abstracts and 12.5 million full-text articles, including preprints². Both are free, and both are excellent for exhaustive Boolean searching. Consensus covers all of PubMed and the rest of science, and is built for a different job: finding the strongest evidence for a question asked in plain language. It searches full text from top medical publishers such as BMJ, JAMA Network and Wolters Kluwer, and its research agent has tools that find better papers than a single query can: it crawls citations from key studies, traces an author’s work and plans multi-step searches.

Pyramid showing three layers: abstracts and metadata across all publishers from Semantic Scholar, OpenAlex, and PubMed; all open-access full text; and full text of paywalled papers from partner publishers — All of PubMed is one source in the Consensus index, alongside Semantic Scholar, OpenAlex, all open-access full text, and paywalled full text from publisher partners.

What each API does best

	Best for	Watch out for
Consensus	Natural-language questions Ranking the most relevant evidence first Filtering by study design, sample size and journal quartile	Up to 1,000 results per query, ranked by relevance Paid past 30 calls a month
PubMed	Reproducible Boolean strategies with MeSH³ Systematic review searches	Biomedicine and life sciences only No full text in PubMed itself¹
Europe PMC	Searching full text as well as abstracts Preprints alongside published papers²	Life sciences only Full text through the API for open-access articles⁴

Semantic search over PubMed’s records

PubMed matches the terms in your query, mapping them to MeSH headings where it can, and can sort the matches with its Best Match algorithm^{3, 5}. That works well when you know the vocabulary. A question worded differently from the abstracts that answer it can still miss them. Consensus searches the same records by meaning and by keyword together, then ranks the results for scientific relevance. You send the question as written, for example “does creatine improve working memory in older adults”, and get the most relevant papers first. Boolean operators and exact phrases still work when you want them. Europe PMC also matches keywords, but against full text as well as abstracts, so it can find papers whose abstracts never use your terms².

Filtering by study design and evidence quality

All three APIs let you narrow results by study type. Consensus adds the other signals a reviewer looks at.

	Study design	Other evidence filters
Consensus	`study_types`, such as `rct`, `meta-analysis`, `systematic review`, `cohort study` and `case-control study`	`sample_size_min` `human`, `controlled` `sjr_min` and `sjr_max` for journal quartile `duration_min` and `duration_max`, `country`, `citation_min`, `exclude_preprints`
PubMed	Publication types assigned by NLM indexers, such as `randomized controlled trial[pt]`⁶	MeSH terms and date filters³
Europe PMC	Publication type, such as clinical trials or preprints²	Search within sections, such as Methods²

Each Consensus result also returns its study_type, sample_size, population_type and sjr_best_quartile, so your code can sort or grade the evidence after the search.

Top medical journals and clinical guidelines

Two Consensus filters are built for clinical work:

medical_mode=true limits results to about 8 million documents from the top 1,000 medical journals, plus about 50,000 clinical guidelines. Use it when general literature is too noisy.
clinical_guideline=true returns only papers classified as clinical guidelines.

When a Boolean strategy is the right tool

For the search you report in a systematic review, use a Boolean query in PubMed or Europe PMC. Reviewers can rerun it term for term, and it returns every match rather than a ranked top 1,000. Consensus fits around that search: scope the topic before you write the strategy, then check afterwards that the strongest studies on the question all made it into your set.

Full text

Consensus searches the full text of open-access papers and of paywalled papers from its publisher partners. On paid plans, include_full_text_chunks=true returns up to 3 query-relevant passages per paper from open-access papers. See Full text in the API.
PubMed has no full text. Its sister archive, PubMed Central, holds more than 10 million full-text records⁷.
Europe PMC returns open-access articles as XML through fullTextXML⁴.

The same question on each API

Consensus takes the question as written. PubMed and Europe PMC need it rewritten as terms and filters.

Consensus
PubMed
Europe PMC

curl -G "https://api.consensus.app/v1/search" -H "x-api-key: $CONSENSUS_API_KEY" \
  --data-urlencode "query=does creatine improve working memory" \
  --data-urlencode "study_types=rct,meta-analysis" \
  --data-urlencode "human=true"

import os
import requests

resp = requests.get(
    "https://api.consensus.app/v1/search",
    headers={"x-api-key": os.environ["CONSENSUS_API_KEY"]},
    params={
        "query": "does creatine improve working memory",
        "study_types": "rct,meta-analysis",
        "human": True,
    },
    timeout=30,
)
resp.raise_for_status()

for paper in resp.json()["results"]:
    print(paper["study_type"], paper["sample_size"], paper["title"])

cURL

curl -G "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" \
  --data-urlencode "db=pubmed" \
  --data-urlencode "term=creatine AND memory AND randomized controlled trial[pt]" \
  --data-urlencode "sort=relevance" \
  --data-urlencode "retmode=json"

Returns PubMed IDs. Fetch titles and abstracts with a second call to esummary or efetch.

cURL

curl -G "https://www.ebi.ac.uk/europepmc/webservices/rest/search" \
  --data-urlencode 'query=creatine AND memory AND PUB_TYPE:"randomized controlled trial"' \
  --data-urlencode "format=json"

Compare scholarly APIs

Why teams choose Consensus, and every API at a glance.

Swap a hand-maintained paper corpus

How Owkin replaced a curated set of PubMed abstracts with Consensus.

Sources

Facts about other providers were checked against their official documentation on 5 November 2026. Limits and prices change, so check the source before you build on a number.

About PubMed: “more than 40 million citations and abstracts of biomedical literature”; “does not include full text journal articles”; a free resource.
About Europe PMC: 49.2 million abstracts and 12.5 million full-text articles; searches abstracts and full text; searches can be limited to clinical trials, preprints or article sections such as Methods; free to anyone.
PubMed User Guide: Boolean operators, field tags, MeSH and Best Match sorting.
Europe PMC developer resources: REST, SOAP, OAI-PMH and FTP access to open-access content and metadata; automated bulk download of other content isn’t allowed. The Articles RESTful API includes /{id}/fullTextXML.
E-utilities in depth, ESearch: sort=relevance is the default Best Match order on web PubMed.
NLM publication types.
About PMC: “more than 10 million full-text article records”.

Introduction

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Threads

Biomedical search: Consensus, PubMed and Europe PMC

What each API does best

Semantic search over PubMed’s records

Filtering by study design and evidence quality

Top medical journals and clinical guidelines

When a Boolean strategy is the right tool

Full text

The same question on each API

Compare scholarly APIs

Swap a hand-maintained paper corpus

Sources

​What each API does best

​Semantic search over PubMed’s records

​Filtering by study design and evidence quality

​Top medical journals and clinical guidelines

​When a Boolean strategy is the right tool

​Full text

​The same question on each API

​Related

Compare scholarly APIs

Swap a hand-maintained paper corpus

​Sources

What each API does best

Semantic search over PubMed’s records

Filtering by study design and evidence quality

Top medical journals and clinical guidelines

When a Boolean strategy is the right tool

Full text

The same question on each API

Related

Sources