Original source http://www.incodom.kr/Entrez_Direct ================================================================================ Entrez Direct (EDirect) - CLI version of NCBI E-utilities - Functions for search data ((publication, sequence, structure, gene, variation, expression) from Entrez databases ================================================================================ Install EDirect cd ~ perl -MNet::FTP -e '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.zip");' gunzip -u -q edirect.zip rm edirect.zip export PATH=$PATH:$HOME/edirect ./edirect/setup.sh ================================================================================ Example - Keyword: "somatic copy number" - Who wrote most number of papers related to keyword esearch -db pubmed -query "somatic copy number" | \ efetch -format xml | xtract -pattern PubmedArticle -block Author -sep " " -tab "\n" -element LastName,Initials |\ sort-uniq-count-rank | head 30 Meyerson M 25 Zhang J 24 Getz G 16 Beroukhim R 16 Li J 16 Wang J 16 Zhang Y 15 Wilson RK 15 Zhang Z 14 Wang Y ================================================================================ Functions esearch - input keywords into specific database to search data elink - search links of data inside of database or between databases efilter - Detail search on result efetch - download specific data in the format you want xtract - parse XML format file into table format data einfo - search "indexed field" from Entrez epost - upload identifier number, sequence accession number nquire - send direct URL request to the server