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README.md

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gladstonePublications

usage:

php makePubTable.php

prerequisites:

  • curl
  • on ubuntu: 
    sudo apt-get install curl libcurl3 libcurl3-dev php5-curl
    then 
    sudo apache2ct restart

key files:

  • makePubTable.php - main script; takes results from other scripts and composes final CSV
  • bioXML2pubmedXML.php - takes bio.xml, queries pubmed by name and Profiles by id, returns XML of pubmed ids
  • wosQuery.php - takes XML of pubmed ids, queries isinet (thomson routers) for structured data, returns CSV table
  • bio.xml - query set of investigator names and profile ids
  • out - dir where CSV output is written