EDAMannot

EDAMannot is a command-line toolbox leveraging the ShareFAIR-KG knowledge graph from the ShareFAIR Knowledge Base. It provides processing, metrics, and visualization features based on the EDAM ontology.
The toolbox is particularly useful for EDAM annotations of tools registered in the bio.tools registry. This knowledge base and toolbox are supported by the ShareFAIR project WP2.

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Table of Contents

• Installation
• Usage
• Features
• Examples
• License
• Authors and Contact

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Installation

1. Clone the EDAMannot repository

git clone https://github.com/ulysseLeclanche/EDAMannot.git

cd EDAMannot

2. Create a conda environment from the environment.yml file

conda env create -f environment.yml

conda activate EDAMannot

3. Connect to the ShareFAIR-KG knowledge graph

Clone the repository and its submodules:

git clone --recurse-submodules https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG

To locally deploy the knowledge base, run start_knowlegde_base_server.sh file:

./start_knowlegde_base_server.sh

You can follow the detailed deployment instructions here: ShareFAIR-KG deployment guide

Note: Full functionality of EDAMannot requires a deployed ShareFAIR-KG instance.

Usage

Once the knowledge graph is deployed, you can use the toolbox from the EDAMannot folder. You must be in the EDAMannot folder to use it:

cd EDAMannot

python3 CLI.py --help

It is recommended to initialize the toolbox (especially after updating the knowledge graph):

python3 CLI.py init

Features

EDAMannot provides the following main commands:

describe – Retrieve direct and inherited EDAM annotations for one or more bio.tools tools.

describe-viz – Generate a graph representing tool annotations, with colors indicating information content and highlighting intersections.

QC – Compute annotation quality metrics, including annotation counts, frequency, informative content (IC), and Shannon entropy.

Examples

All commands support --help for detailed options and examples of use:

python3 CLI.py command_name --help

Here are examples of uses for each of the commands:

describe

python3 CLI.py describe https://bio.tools/multiqc --annotation_type Topic --annotation_type Operation --heritage --output_format json

or using alias options :

python3 CLI.py describe qiime2 -a T -a O -h -f json

describe-viz

python3 CLI.py describe-viz --show-topics --show-operations --highlight
    --show-deprecated --title bwa --title qiime2  --color-by count --color-channel red
    --output_format SVG --output bwa_qiime2_common_graph

or using alias options :

python3 CLI.py describe-viz -o -h -d --title bwa --title qiime2 -cby count -cc red -f SVG -O bwa_qiime2_common_graph

QC

python3 CLI.py QC https://bio.tools/star --heritage --metric all --output_format json

or using alias options :

python3 CLI.py QC star -h -m all -f json

License

This project is licensed under the GNU GPLv3 License. See the LICENSE file for details.

Authors and Contact

• Ulysse LE CLANCHE¹
• Olivier DAMERON²
• Alban GAIGNARD³

Affiliations

¹ Université Rennes, Inria, CNRS, IRISA—UMR 6074, Rennes 35000, France
² Université Rennes, Inria, CNRS, IRISA—UMR 6074, Rennes 35000, France
³ Nantes Université, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France