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:
- Our NIDM-Terms website (https://scicrunch.org/nidm-terms)
- Our NIDM-terms github repository (https://github.com/NIDM-Terms/terms)
- For additional information on the background for this project see BIDS specification issue 423 (https://github.com/bids-standard/bids-specification/issues/423)
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]