albangaignard / fair-checker

Web tool to assess FAIR principles and promote their implementation

fair-checker

Web tool to assess FAIR principles and promote their implementation.

Monitoring progress in FAIRification through self-assessment of resources maturity indicators

FAIRMetrics based part

This demo is based on the FAIRMetrics framework [Wilkinson, Dumontier et al., Scientific Data 6:174] that is composed of Maturity Indicators (MI), compliance tests and the evaluator application itself.

Few efforts have been done so far to take advantage from their concrete implementation, in the process of improving FAIRness of users/community resources. Furthermore, this does not provide concrete help or guidelines to developers for better sharing their published works.

In this repository we propose a web demonstrator, leveraging existing web APIs, aimed at i) evaluating FAIR maturity indicators and ii) providing hints to progress in the FAIRification process.

Custom part

These FAIR checks aim at leveraging semantic web technologies to check that metadata use standards and recognized ontologies or controlled vocabularies.

First, embedded semantic annotations are extracted from web pages, forming a minimal knowledge graph. Then, these knowledge graphs are completed based on already deployed knowledge graphs (Datacite, OpenAire, WikiData). Finally, the resulting knowledge graph is tested to check that classes and properties are recognized through Linked Open Vocabularies (LOV), or Ontology Lookup Service (OLS). In addition we implemented SHACL validation to check the conformance with BioSchemas profiles.

Installation

Using Docker

Clone the repo:

git clone https://github.com/IFB-ElixirFr/fair-checker.git

Move to the folder:

cd fair-checker

Build with the correct env: 'production' or 'development':

sudo docker build -t fair-checker-webapp --build-arg FLASK_ENV=production .

Run attached:

sudo docker run --network="host" -p 5000:5000 --name fair-checker-webapp fair-checker-webapp

Run dettached:

sudo docker run --network="host" -p 5000:5000 --name fair-checker-webapp -d fair-checker-webapp

In case of code update:

sudo docker rm -f fair-checker-webapp

Then build and run again

Using Conda

Clone the repo:

git clone https://github.com/IFB-ElixirFr/fair-checker.git

Move to the folder:

cd fair-checker

Create a new conda ENV:

conda create --name fair-check-env

Activate the new ENV:

conda activate fair-check-env

Run:

while read requirement; do conda install -c conda-forge --yes $requirement || pip install $requirement; done < requirements.txt

Start local server:

export FLASK_ENV=development
python3 app.py