README.md

TERA

Code base for the publication TERA: the Toxicological Effect and Risk Assessment Knowledge Graph.

Documentation can be found here.

TERA snapshot is avalible as a Zenodo dataset:

Data sources

• ECOTOX
• NCBI Taxonomy
• PubChem
• ChEMBL
• Encyclopedia of Life (EOL)
• Wikidata
• Other data sources can be easily added.

The raw data can be downloaded by running

bash download_data.sh

Install

pip3 install -r requirements.txt
python3 setup.py install

Examples

See tests.py. More to come...

Related publications

• Erik B. Myklebust, Ernesto Jimenez Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen. Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings. Accepted for publication in the Semantic Web Journal, 2021. (arXiv) (Paper) (REPOSITORY)

• Erik B. Myklebust, Ernesto Jimenez-Ruiz, Zofia C. Rudjord, Raoul Wolf, Knut Erik Tollefsen: Integrating semantic technologies in environmental risk assessment: A vision. 29th Annual Meeting of the Society of Environmental Toxicology and Chemistry (SETAC) (2019)

• Erik B. Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen. Knowledge Graph Embedding for Ecotoxicological Effect Prediction. International Semantic Web Conference 2019. Best Student Paper in the In-Use track of ISWC 2019

• Erik B. Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen. TERA: the Toxicological Effect and Risk Assessment Knowledge Graph. arXiv:1908.10128, 2019.