PubMed API - adilnumancelik/sonar GitHub Wiki

Query base

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Documentation

Link

Useful queries

Search

Format

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>

Database can be pubmed, protein, nuccore etc. but pubmed seems to be that we can use.
Can be used to search for any term or DOIs.

Example

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=10.1126/science.1165395

This query returns this xml:

<eSearchResult>
  <Count>1</Count>
  <RetMax>1</RetMax>
  <RetStart>0</RetStart>
  <IdList>
    <Id>19008416</Id>
  </IdList>
  <TranslationSet/>
  <TranslationStack>
    <TermSet>
      <Term>10.1126/science.1165395[All Fields]</Term>
      <Field>All Fields</Field>
      <Count>1</Count>
      <Explode>N</Explode>
    </TermSet>
    <OP>GROUP</OP>
  </TranslationStack>
  <QueryTranslation>10.1126/science.1165395[All Fields]</QueryTranslation>
</eSearchResult>

Document Summaries:

Format

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=<database>&id=<uid_list>

Using the id returned from doi search we can get document summaries.
Document summaries include most of the needed data such as authors, journal, published year etc.

Example

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=6678417,9507199,28558982,28558984,28558988,28558990,19008416

Downloading Full Records :

Format

https://eutils.ncbi.nlm.nih.gov/entrez/eutils\efetch.fcgi?db=<database>&id=<uid_list>&rettype=<retrieval_type> &retmode=<retrieval_mode> Using rettype = txt we can get detailed information such as author orcids, abstract, cited articles and their ids etc.

Example

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=31953402&rettype=txt

Getting Pdf

Not a part of api but we can get pdf from this link:

https://pubmed.ncbi.nlm.nih.gov/<id>/
like
https://pubmed.ncbi.nlm.nih.gov/19008416/

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