bids_term_to_table

bids_terms_to_pdf_table: Utilty for creating Markdown table of BIDS terms and adding new BIDS terms


License
Apache-2.0
Install
pip install bids_term_to_table==1.0.0

Documentation

BIDS_Terms

Project Description

In this project we aim to create a user friendly python tool for creating and exporting BIDS specification terms in PDF form tables for incorporation into the BIDS specification documents. This project is a part of the effort of the NIDM-Terms project allowing the the BIDS working group to select amongst our curated BIDS terms , search our information resource “Interlex” for existing BIDS terms, or add a new BIDS term, which will constantly result in term dictionary in JSON-LD form added to our family of BIDS Specification terms. The user will be able to select which properties he/she would like to include in the table (e.g. description, label, comment, etc..). The user will then have a PDF table of the chosen/added terms and their properties as an output. Such an effort will provide the BIDS working group with a user-friendly tool to build tables for the BIDS documentation while ensuring they have not re-purposed an existing BIDS specification term giving it conflicting definitions.

Purpose and Goals of The Project:

  • Provide the BIDS community with a tool to create PDF tables for their BIDS specification documents.
  • Create well structured and clear instructions on how to use our tool.
  • Facilitate community engagement through adding missing BIDS specification terms for further use to enhance our ability to search across brain Initiative datasets.
  • Create JSON-LD file for new terms.
  • Create an automated way to push newly created JSON-LD files to the Interlex information resource (see: https://scicrunch.org/nidm-terms).

Story board:

Interlex API Key:

To be able to search and query BIDS terms in Interlex, an Interlex account and an API key are required. Here’s how you can obtain one:

  • Create a Scicrunch account if don’t have one already
  • Once your account is all set, go to MY ACCOUNT in the top right corner and click on API Keys
  • Enter your password
  • Click on “Generate an API key” and under key you will have your new API key!

Related readings and links:

Install

  • conda create -n pynidm_py3 python=3
  • source activate pynidm_py3
  • cd bids_term_to_pdf_table
  • python setup.py install

Running the script

  • bids_term_to_table -in [PATH TO bids_term_to_pdf_table cloned repo] -out [OUTPUT DIRECTORY]