Pubmed404

Last commit

Test if URL in the pubmed abstracts are reacheable.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar pubmed404  [options] Files

Usage: pubmed404 [options] Files
  Options:
    -c, --collapse
      Only one URL per article. Print the '200/OK' first.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -t, --timeout
      timeout in seconds
      Default: 5
    --version
      print version and exit

Keywords

pubmed
url

Creation Date

20181210

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/Pubmed404.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite pubmed404 ? 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 'bioinformatics 2001' 2> /dev/null |\
    java -jar dist/pubmed404.jar  2> /dev/null 

#PMID   TITLE   YEAR    URL Status
29520589    Expression of Colocasia esculenta tuber agglutinin in Indian mustard provides resistance against Lipaphis erysimi and the expressed protein is non-allergenic.2018  http://www.fao.org/docrep/007/y0820e/y0820e00.HTM   200
29520589    Expression of Colocasia esculenta tuber agglutinin in Indian mustard provides resistance against Lipaphis erysimi and the expressed protein is non-allergenic.2018  http://www.icmr.nic.in/guide/Guidelines%20for%20Genetically%20Engineered%20Plants.pdf   -1
28482857    Horizontal gene transfer is not a hallmark of the human genome. 2017    https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3  200
27899642    The UCSC Genome Browser database: 2017 update.  2017    http://genome.ucsc.edu/ 200
27797935    High hospital research participation and improved colorectal cancer survival outcomes: a population-based study.    2017    http://www.bmj.com/company/products-services/rights-and-licensing/  403
25505092    NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. 2015    http://pine.nmrfam.wisc.edu/download_packages.html  200
25505092    NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. 2015    http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm   200
25428374    The UCSC Genome Browser database: 2015 update.  2015    http://genome.ucsc.edu  200
26356339    A Simple but Powerful Heuristic Method for Accelerating k-Means Clustering of Large-Scale Data in Life Science. null    http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/boostKCP/  200
24794704    Usefulness of the Shock Index as a secondary triage tool.   2015    http://group.bmj.com/group/rights-licensing/permissions 403
24225322    Progenetix: 12 years of oncogenomic data curation.  2014    http://www.progenetix.org   200
24137000    Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.   2014    http://globin.bx.psu.edu/hbvar  200
24137000    Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.   2014    http://www.findbase.org 200
24137000    Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.   2014    http://www.lovd.nl  200
23564938    DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.  2013    http://dambe.bio.uottawa.ca 200
22689647    SIFT web server: predicting effects of amino acid substitutions on proteins.    2012    http://sift-dna.org 200
22600740    Cyber-T web server: differential analysis of high-throughput data.  2012    http://cybert.ics.uci.edu/  200
21742331    An open source lower limb model: Hip joint validation.  2011    https://simtk.org/home/low_limb_london  200
21593132    Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA.  2011    http://www.compbio.dundee.ac.uk/jabaws  200
20228129    DensiTree: making sense of sets of phylogenetic trees.  2010    http://compevol.auckland.ac.nz/software/DensiTree/  404
19380317    CELLULAR OPEN RESOURCE (COR): current status and future directions. 2009    http://www.cellml.org/specifications/   200
18948284    OperonDB: a comprehensive database of predicted operons in microbial genomes.   2009    http://operondb.cbcb.umd.edu    200
18368364    Simulator for neural networks and action potentials.    2007    http://snnap.uth.tmc.edu    -1
18367465    An improved general amino acid replacement matrix.  2008    http://atgc.lirmm.fr/LG 404
18238804    Interoperability with Moby 1.0--it's better than sharing your toothbrush!   2008    http://www.biomoby.org/ 200
18174178    PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.    2008    http://www.ibi.vu.nl/programs/pralinewww    200
17221864    HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. 2007    http://globin.bx.psu.edu/hbvar  200
17221864    HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. 2007    http://www.goldenhelix.org/xprbase  403
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