jvarkit

PubmedDump

Last commit

Dump XML results from pubmed/Eutils

Usage

Usage: pubmeddump [options] Files
  Options:
    -e, --email
      optional user email
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ncbi-api-key
      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
    -skip, --skip
      [20180302]  Optional set of elements names to be ignored in the output. 
      Spaces or comma separated. .eg: 'AuthorList PubmedData '
      Default: <empty string>
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

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.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedDump.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedDumpTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

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

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

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

Example

$  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