fetch-pubmed
NCBI Entrez utilities on the command line
Install
- All systems
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curl cmd.cat/fetch-pubmed.sh
- Debian
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apt-get install ncbi-entrez-direct - Ubuntu
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apt-get install ncbi-entrez-direct - Kali Linux
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apt-get install ncbi-entrez-direct - Windows (WSL2)
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sudo apt-get updatesudo apt-get install ncbi-entrez-direct - Raspbian
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apt-get install ncbi-entrez-direct - Dockerfile
- dockerfile.run/fetch-pubmed
ncbi-entrez-direct
NCBI Entrez utilities on the command line
Entrez Direct (EDirect) is an advanced method for accessing NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal window or script. 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.