BEP028

This repository contains BIDS Extension Proposal 028 : BIDS-prov, a provenance framework for BIDS.

Our goal

Interpreting and comparing scientific results and enabling reusable data and analysis output require understanding provenance, i.e. how the data were generated and processed. To be useful, the provenance must be understandable, easily communicated, and captured automatically in machine accessible form. Provenance records are thus used to encode transformations between digital objects.

Contributors

Camille Maumet (@cmaumet) and Satrajit Ghosh (@satra) are the BEP co-moderators. Here is the list of all contributors (emoji key):

• Camille Maumet (@cmaumet)💻👀📖 🐛🖋 🤔🚧

• Satrajit Ghosh (@satra)💻👀📖 🐛🤔

• Stefan Appelhoff (@sappelhoff)🤔

• Chris Markiewicz (@effigies)🤔

• Yaroslav Halchenko (@yarikoptic)🤔

• Jean-Baptiste Poline (@jbpoline)🤔

• Rémi Adon (@remiadon)💻👀📖 🐛

• Hermann Courteille (@hermann74)💻👀📖 🐛

• Thomas Betton (@thomasbtnfr)💻👀📖 🐛

• Cyril Regan (@cyril-data)💻👀📖 🐛

• Boris Clénet (@bclenet)💻📖🐛

This project follows the all-contributors specification. Contributions of any kind welcome!

BIDS-prov in the NIDM project

The Neuroimaging Data Model (NIDM) is a collection of specification documents that define extensions the W3C PROV standard for the domain of human brain mapping.

BIDS-prov is a BIDS extension that is compatible with NIDM.

How to help

Our goal is to extends BIDS to be able to track provenance at every stage of an experiment.

For this purpose we have to propose changes to the BIDS specification.

The BIDS specification is rendered as a webpage at https://bids-specification.readthedocs.io.

The website is built from a GitHub repository that consists of mostly markdown files at https://github.com/bids-standard/bids-specification. If you don't know much about markdown, here's a good intro guide.

Finding information and getting in touch

BIDS-Prov in the BIDS specification

The BEP028 is now merged in the BIDS specification (see § Provenance).

The community review of the BEP took place here on Github.

We published a summary document about the community review as well as the consequent answers and changes.

Google doc

The BEP028 was in a google doc.

Contact BIDS-Prov

The group is always open to new contributors interested in neuroimaging data sharing. To participate in discussions or to ask any question, please email us at incf-nidash-nidm@googlegroups.com.

Additional resources

Mature building blocks of NIDM:

• NIDM-terms
• NIDM-results

New features (to be included)

Using the code

Warning

Except for parsers (AFNI, SPM, FSL, fieldtrip), the code in bids_prov is outdated. The new repository pybidsprov exposes the code as a python package.

Note

pybidsprov comes with the bids_prov command lines, providing the following features:

• merge: Aggregates all provenance metadata available in a BIDS dataset to generate a provenance graph inside a single JSON-LD file.
• extract: Isolates the provenance graph of a given prov:Entity (e.g. a file, dataset or another prov:Entity) and generates a provenance graph inside a JSON-LD file.
• check: Perform a sanity check on a provenance graph contained in a JSON-LD file.
• visualize: Generates an image (graphviz graph) representing a provenance graph contained in a JSON-LD file.

(Outdated) Visualize your BIDSprov data

To visualize your BIDSprov data, perform the following steps :

1. clone the code inside a BEP028_BIDSprov directory, and cd into this directory :

git clone git@github.com:bids-standard/BEP028_BIDSprov.git
cd BEP028_BIDSprov

3. install the bids_prov python package :

pip install .

4. you should be able to launch the visualizer on your .jsonld files with the command bids_prov_visualizer

bids_prov_visualizer --input_file graph.jsonld --output_file graph.png

bids_prov -h
  usage: bids_prov_visualizer [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]

  options:
    -h, --help            show this help message and exit
    --input_file INPUT_FILE
                          input BIDSprov data as a .jsonld file
    --output_file OUTPUT_FILE
                          output .png file showing BIDSprov graph

Run parsers on the SPM, FSL and AFNI data

To obtain data in bids-prov format, you can use the developed parsers.

• Tutorial

Code of conduct

We are committed to building a welcoming and harrasement free experience for all our contributors. As a contributor to the BIDS-Prov specification, we ask you to follow our code of conduct

Credits: This README was build based on the BEP001 README.