Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.
Entrez Direct uses environment modules. Type
module load edirect
at the prompt.
To see the help menu, type
efetch -help
at the prompt.
NOTE: The Entrez Direct utilities will work on Helix or the Biowulf compute nodes.
esearch -db pubmed -query "opsin gene conversion" | elink -related
Find all protein sequences for 'lycopene cyclase' and then fetch those sequences in Fasta format.
esearch -db protein -query "lycopene cyclase" | efetch -format fastaFind SRA IDs that are part of a bioproject, or SRA ID(s) associated with a biosample
esearch -db sra -query 'PRJID[bioproject]' | efetch -format runinfo (replace PRJID with the project ID)
And a more complicated example:
esearch -db pubmed -query "Beadle AND Tatum AND Neurospora" | \
elink -related | \
efilter -query "NOT historical article [FILT]" | \
efetch -format docsum | \
xtract -pattern DocumentSummary -present Author -and Title \
-element Id -first "Author/Name" -element Title | \
grep -i -e enzyme -e synthesis | \
sort -t $'\t' -k 2,3f | \
column -s $'\t' -t | \
head -n 10 | \
cut -c 1-80