Skip to content

README.md

Latest commit

 

History

History
executable file
·
74 lines (47 loc) · 4.56 KB

README.md

File metadata and controls

executable file
·
74 lines (47 loc) · 4.56 KB
Raw

Join the chat at https://gitter.im/INCF/neuroshapes Build Status GitHub release

Welcome to Neuroshapes

The goal of Neuroshapes is the development of open, use-case-driven and shared, validatable data models (schemas and vocabularies) to enable the FAIR principles (Findable, Accessible, Interoperable, and Reusable) for basic, computational, and clinical neuroscience (meta)data.

The data models developed so far cover entities for electrophysiology, neuron morphology, brain atlases, in vitro electrophysiology, and computational modeling. Future developments could include brain imaging, transcriptomic, and clinical form data, as determined by community interests.

Table of contents

Goal

The main goal is to promote:

  • The use of standard semantic markups and linked data principles as ways to structure metadata and related data. The W3C RDF format is leveraged, specifically its developer-friendly JSON-LD serialization. Adoption of linked data principles and JSON-LD eases federated access and discoverability of distributed neuroscience (meta)data over the web.

  • The use of the W3C SHACL (Shape Constraint Language) recommendation as a rich metadata schema language that is formal, expressive, interoperable, machine-interpretable, and domain-agnostic. With SHACL, (meta)data quality can be enforced based on schemas and vocabularies rather than being fully encoded in procedural code. SHACL also provides key interoperability capabilities to ensure the evolution of standard data models and data longevity.

  • The reuse of existing schemas and semantic markups (like schema.org) and existing ontologies and controlled vocabularies (including NIFSTD – NIF Standard Ontologies).

  • The use of the W3C PROV-O recommendation as a format to record (meta)data provenance. A SHACL version of W3C PROV-O is provided.

Neuroshapes also aims to create a community for open, use-case-driven development of data models (schemas and vocabularies), tools around them, and guidelines for FAIR neuroscience (meta)data.

Tutorials

A set of tutorials from the Blue Brain Nexus Forge project are available and use the schemas defined in Neuroshapes as data models to create and validate datasets as well as register them in Blue Brain Nexus.

Try them in Binder:
https://mybinder.org/v2/gh/BlueBrain/nexus-forge/v0.4.0?filepath=examples%2Fnotebooks%2Fgetting-started

Adoption

The following projects have adopted Neuroshapes:

Formats and standards

All schemas in this repository conform to the W3C SHACL recommendation and are serialized using JSON-LD.

Testing the schemas

Two different tests are executed in the unit tests. The first test validates that schemas conform to the SHACL specifications. The second test uses valid and invalid data samples that are tested against the modeled shapes. These examples are placed in the examples directory and follow the directory structure of the shape they should be tested against.

Tests require Python > 3.6 and pytest. To run them: python3 -m venv env source env/bin/activate pip install pytest pyshacl pytest

To test a specific set of shapes: pytest --testdir=shapes/neurosciencegraph/datashapes/atlas

Roadmap

  • Creation of an INCF/neuroshapes Special Interest Group
  • INCF endorsement as a standard and best practice supporting FAIR neuroscience data
  • Extension of the current data model specifications

License

The license for all schemas and data is CC-BY-4.0.