NXML Uploader

About NXML file uploading Show

This page allows a user to submit an open-source PubMed document file for processing by the Reach information extraction system. The document file, in NXML format, is uploaded from the user's local computer. Reach processing results are returned directly to the browser, or downloaded to the user's computer, in the JSON output format selected at upload time.

To upload a PubMed NXML file for Reach processing, select the file from your local filesystem by clicking the Choose File button.

Note: only valid NXML files with extensions .nxml or .xml are permitted.

Next, select the desired output format for the results:

  • fries, for FRIES Consortium JSON,
  • indexcard, for MITRE IndexCard JSON,
  • tsv, for the Arizona tab-separated output format,
  • serial-json, for a JSON serialization of the entire Reach internal document

    The serial-json format can return VERY large result files (10s of megabytes). Use this format with caution.

  • To initiate processing, click the Upload File button.

    After a minute or two of processing, results will be returned to the browser and either displayed or downloaded to a file, depending on the selection of the Download Output checkbox and the browser content settings.

Choose an NXML file for processing:

Click the 'Browse' or 'Choose File' button to select an NXML file (with extension .nxml or .xml) for uploading and processing:

fries indexcard tsv serial-json