Destination Database

  -related    Neighbors in same database
  -target     Links in different database

Direct Record Selection

  -db         Database name
  -id         Unique identifier(s)
  -input      Read identifier(s) from file instead of stdin

PubMed Citation Lookup*

  -cited      References to this paper
  -cites      Publication reference list

Command Mode

  -cmd        Command type

-cmd Options

  edirect     Instantiate results in ENTREZ_DIRECT message
  uid         Return results as sorted and uniqued UID list
  history     Save results in Entrez history server
  neighbor    Neighbors or links
  score       Neighbors with computed similarity scores
  acheck      All links available
  ncheck      Existence of neighbors
  lcheck      Existence of external links (LinkOuts)
  llinks      Non-library LinkOut providers
  llibs       All LinkOut providers
  prlinks     Primary LinkOut provider

Restrict Neighbor Links

  -name       Link name (e.g., pubmed_protein_refseq, pubmed_pubmed_citedin)

Note

  * -cited and -cites use the NIH Open Citation Collection
    dataset (see PMID 31600197) to follow reference lists

Examples

  esearch -db pubmed -query "lycopene cyclase" |
  elink -related |
  elink -target protein |
  efilter -organism rodents -source refseq |
  efetch -format docsum |
  xtract -pattern DocumentSummary -element AccessionVersion Title |
  grep -i carotene

  esearch -db pubmed -query "Beadle GW [AUTH] AND Tatum EL [AUTH]" |
  elink -cited |
  efilter -days 365 |
  efetch -format abstract

  esearch -db pubmed -query "conotoxin AND dopamine [MAJR]" |
  elink -target protein -cmd neighbor |
  xtract -pattern LinkSet -if Link/Id -element IdList/Id Link/Id

  elink -db pubmed -id 20210808 -cmd score |
  xtract -pattern LinkSet -max Link/Score

  elink -db assembly -id GCF_000001405.25,GCF_000001215.3 -cmd acheck |
  xtract -pattern LinkSet -sep "\n" -element Id,LinkName

  elink -db pubmed -id 19880848 -cmd prlinks |
  xtract -pattern LinkSet -first Id -element ObjUrl/Url

  esearch -timer -db biosample -query "package mims metagenome/environmental, water version 5 0 [PROP]" |
  efilter -query "ncbi [FILT] AND biosample sra [FILT]" |
  elink -target bioproject -log |
  efetch -format native
