Last commit

Dump XML results from pubmed/Eutils


Usage: pubmeddump [options] Files
    -e, --email
      optional user email
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
      NCBI API Key see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ 
      .If undefined, it will try to get in that order:  1) environment 
      variable ${NCBI_API_KEY} ;  2) the jvm property "ncbi.api.key" ;	3) A 
      java property file ${HOME}/.ncbi.properties and key api_key
    -o, --output
      Output file. Optional . Default: stdout
    -r, --retmax
      value for 'retmax' parameter for Eutils.
      Default: 10000
    -skip, --skip
      [20180302]  Optional set of elements names to be ignored in the output. 
      Spaces or comma separated. .eg: 'AuthorList PubmedData '
      Default: <empty string>
      print version and exit


See also in Biostars


Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew pubmeddump

The java jar file will be installed in the dist directory.

Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite pubmeddump ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030


$  java -jar dist/pubmeddump.jar "Lindenbaum P" | grep ArticleTitle
	<ArticleTitle>NGS library preparation may generate artifactual integration sites of AAV vectors.</ArticleTitle>
    <ArticleTitle>Mutations in FAM111B cause hereditary fibrosing poikiloderma with tendon contracture, myopathy, and pulmonary fibrosis.</ArticleTitle>
    <ArticleTitle>[The Spanish Association of Surgeon's audited teaching programme for rectal cancer. Results after six years].</ArticleTitle>
    <ArticleTitle>Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death.</ArticleTitle>
    <ArticleTitle>The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.</ArticleTitle>
    <ArticleTitle>Mass spectrometry-based identification of native cardiac Nav1.5 channel alpha subunit phosphorylation sites.</ArticleTitle>
    <ArticleTitle>BioStar: an online question &amp; answer resource for the bioinformatics community.</ArticleTitle>
    <ArticleTitle>Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.</ArticleTitle>
    <ArticleTitle>Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis.</ArticleTitle>
    <ArticleTitle>The Gene Wiki: community intelligence applied to human gene annotation.</ArticleTitle>
    <ArticleTitle>Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta.</ArticleTitle>
    <ArticleTitle>Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.</ArticleTitle>
    <ArticleTitle>Haplotypes in the gene encoding protein kinase c-beta (PRKCB1) on chromosome 16 are associated with autism.</ArticleTitle>
    <ArticleTitle>RoXaN, a novel cellular protein containing TPR, LD, and zinc finger motifs, forms a ternary complex with eukaryotic initiation factor 4G and rotavirus NSP3.</ArticleTitle>
    <ArticleTitle>CloneIt: finding cloning strategies, in-frame deletions and frameshifts.</ArticleTitle>
    <ArticleTitle>In vivo and in vitro phosphorylation of rotavirus NSP5 correlates with its localization in viroplasms.</ArticleTitle>

See also