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PubMed (NCBI E-utilities)

eutils.ncbi.nlm.nih.gov

Search and fetch bibliographic records across PubMed and the other NCBI databases through E-utilities.

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1Request

One PMID or up to 100 comma-separated. PMIDs only - passing a PMCID 400s with {"detail":"Could not retrieve publications"}; convert it with the idconvert capability first.

Set to true to annotate the whole article body instead of just title and abstract. Only works where the paper is in the PMC open-access subset, and inflates the response roughly 20x.

1 credit⌘ ↵
Code follows the fields above
curl "https://api.fastcrw.com/v1/data/pubmed/annotations?pmids=33301246" \
  -H "Authorization: Bearer $FASTCRW_API_KEY"

2Response example

A sample shape. Press Run to see live data from PubMed (NCBI E-utilities).

_ididinfonspassagesrelationspmidpmcidmeta
33301246|None33301246{}[{"infons":{"journal":"N Engl J Med. 2020 Dec 31;383(27):2603-2615. doi: 10.1056/NEJMoa2034577. Epub ","year":"2020","article-id_pmc":"PMC7745181","type":"title","authors":"Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A, Lockhart S, Perez JL, Perez Marc G, Moreira ED, Zerbini C, Bailey R, Swanson KA, Roychoudhury S, Koury K, Li P, Kalina WV, Cooper D, Frenck RW Jr, Hammitt LL, Tureci O, Nell H, Schaefer A, Unal S, Tresnan DB, Mather S, Dormitzer PR, Sahin U, Jansen KU, Gruber WC"},"offset":0,"text":"Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine.","sentences":[],"annotations":[{"id":"1","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]}],"relations":[]},{"infons":{"type":"abstract"},"offset":59,"text":"BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the resulting coronavirus disease 2019 (Covid-19) have afflicted tens of millions of people in a worldwide pandemic. Safe and effective vaccines are needed urgently. METHODS: In an ongoing multinational, placebo-controlled, observer-blinded, pivotal efficacy trial, we randomly assigned persons 16 years of age or older in a 1:1 ratio to receive two doses, 21 days apart, of either placebo or the BNT162b2 vaccine candidate (30 mug per dose). BNT162b2 is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine that encodes a prefusion stabilized, membrane-anchored SARS-CoV-2 full-length spike protein. The primary end points were efficacy of the vaccine against laboratory-confirmed Covid-19 and safety. RESULTS: A total of 43,548 participants underwent randomization, of whom 43,448 received injections: 21,720 with BNT162b2 and 21,728 with placebo. There were 8 cases of Covid-19 with onset at least 7 days after the second dose among participants assigned to receive BNT162b2 and 162 cases among those assigned to placebo; BNT162b2 was 95% effective in preventing Covid-19 (95% credible interval, 90.3 to 97.6). Similar vaccine efficacy (generally 90 to 100%) was observed across subgroups defined by age, sex, race, ethnicity, baseline body-mass index, and the presence of coexisting conditions. Among 10 cases of severe Covid-19 with onset after the first dose, 9 occurred in placebo recipients and 1 in a BNT162b2 recipient. The safety profile of BNT162b2 was characterized by short-term, mild-to-moderate pain at the injection site, fatigue, and headache. The incidence of serious adverse events was low and was similar in the vaccine and placebo groups. CONCLUSIONS: A two-dose regimen of BNT162b2 conferred 95% protection against Covid-19 in persons 16 years of age or older. Safety over a median of 2 months was similar to that of other viral vaccines. (Funded by BioNTech and Pfizer; Clinica…","sentences":[],"annotations":[{"id":"16","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection","locations":["{ 2 keys }"]},{"id":"17","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"coronavirus disease 2019","locations":["{ 2 keys }"]},{"id":"18","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]},{"id":"19","infons":{"identifier":"MESH:D008055","type":"Chemical","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D008055","biotype":"chemical","name":"Lipids","accession":"@CHEMICAL_Lipids"},"text":"lipid","locations":["{ 2 keys }"]},{"id":"20","infons":{"identifier":"MESH:D009705","type":"Chemical","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D009705","biotype":"chemical","name":"Nucleosides","accession":"@CHEMICAL_Nucleosides"},"text":"nucleoside","locations":["{ 2 keys }"]},{"id":"21","infons":{"identifier":"43740568","type":"Gene","valid":true,"normalized":"[ 1 item ]","database":"ncbi_gene","normalized_id":43740568,"biotype":"gene","name":"S","accession":"@GENE_S"},"text":"spike","locations":["{ 2 keys }"]},{"id":"22","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]},{"id":"23","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]},{"id":"24","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]},{"id":"25","infons":{"identifier":"MESH:D000086382","type":"Disease","valid":true,"normalized":"[ 1 item ]","database":"ncbi_mesh","normalized_id":"D000086382","biotype":"disease","name":"COVID-19","accession":"@DISEASE_COVID_19"},"text":"Covid-19","locations":["{ 2 keys }"]},"… 4 more items"],"relations":[]}][]33301246{}

4 more columns in JSON.

Attribution: Source: NCBI / PubMed

Licence: Public domain information on the National Library of Medicine (NLM) Web pages may be freely distributed and copied.

Ask with this source

A prompt for your agent that names this source and how to call it through the crw MCP.

  • Article text with entity annotations (PubTator3)

    Use PubMed (NCBI E-utilities) (pubmed) from fastCRW Pergamon, capability "Article text with entity annotations (PubTator3)" (annotations). You need the actual abstract text of a PMID as JSON, or the normalised biomedical entities inside a paper - E-utilities cannot give you either. Example options: pmids=33301246, full=true. Use the crw MCP tools: crw_find_data to confirm the source and its options, then crw_get_data with provider "pubmed" and capability "annotations". Tell me the credits used and cite the licence from the response. If the crw MCP tools are missing, install them with: npx -y crw-mcp install --api-key <your fastCRW API key>

  • Database directory and field list (einfo)

    Use PubMed (NCBI E-utilities) (pubmed) from fastCRW Pergamon, capability "Database directory and field list (einfo)" (einfo). You are composing an Entrez query and need to know which databases exist or which field tags and links a database accepts. Example options: db=pubmed. Use the crw MCP tools: crw_find_data to confirm the source and its options, then crw_get_data with provider "pubmed" and capability "einfo". Tell me the credits used and cite the licence from the response. If the crw MCP tools are missing, install them with: npx -y crw-mcp install --api-key <your fastCRW API key>

  • Biomedical entity lookup (PubTator3)

    Use PubMed (NCBI E-utilities) (pubmed) from fastCRW Pergamon, capability "Biomedical entity lookup (PubTator3)" (entity-lookup). You have a gene, drug, disease or species name as text and need its canonical identifier before running entity-search or relations. Example options: query=asthma, concept=disease, limit=5. Use the crw MCP tools: crw_find_data to confirm the source and its options, then crw_get_data with provider "pubmed" and capability "entity-lookup". Tell me the credits used and cite the licence from the response. If the crw MCP tools are missing, install them with: npx -y crw-mcp install --api-key <your fastCRW API key>

  • Entity-aware literature search (PubTator3)

    Use PubMed (NCBI E-utilities) (pubmed) from fastCRW Pergamon, capability "Entity-aware literature search (PubTator3)" (entity-search). You want papers about a concept rather than a string - every synonym of a gene or disease at once - or want the gene/disease breakdown of a result set. Example options: text=@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms, page=2, sort=score desc. Use the crw MCP tools: crw_find_data to confirm the source and its options, then crw_get_data with provider "pubmed" and capability "entity-search". Tell me the credits used and cite the licence from the response. If the crw MCP tools are missing, install them with: npx -y crw-mcp install --api-key <your fastCRW API key>