Notes on wp7datascripts

Background

This repository contains some of the many scripts developed during the ViBRANT project by work package 7, Biodiversity literature access and data mining.

The scripts are released for general use under GPLv2 in accordance with the project's formal description of work, Section B 3.2 Plan for the use and dissemination of foreground, sub-section Software and training resources:

ViBRANT will adopt the IPR framework set in place under the EDIT FP6 project. All source code generated through ViBRANT will be freely available under GNU General Public Licence version 2.

Contents

Files

brat_sorter.py : Python 3 script to reorder entities in a brat stand-off file

call_ggws.php : PHP script to invoke GoldenGATE web services. This sample uses the geolocation service to extract longitude and latitude from the embedded text. The script shows how to submit a request to GgWS and then repeatedly poll the service until the request is completed.

visualise.py : Python 3 script to apply brat stand-off mark-up to its matching text file and produce a standalone HTML page to visualise the mark-up; accepts optional parameters to add navigation buttons to two other HTML pages, prev and next

Folders

call_gnrd : How to call Global Names Recognition and Discovery, GNRD, running at the Oxford eResearch Centre, OeRC. Individual files are:

• call_gnrd.py - samples Python script to invoke the service
• call_gnrd_sample.txt and call_gnrd_sample_big.txt are two sample texts to use with the script
• call_gnrd_sample_results.json and call_gnrd_sample_big_results.json are the output from running the script to compare your results against; the script writes its output to call_gnrd_sample.json and call_gnrd_sample_big.json

Licence

This software is released under GNU General Public Licence version 2. A copy of the licence is included in this folder.