Master Thesis - Resolving Chemical Identifier Challenges: Enhancing Data Integration with Graph Databases

The UFZ

The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.

The job

Chemical databases are vital in various scientific fields, including toxicology, pharmacology, and environmental science. These databases utilize a variety of chemical identifiers -such as CAS numbers, InChI, SMILES, DTXSID, and Norman SusDat ID- to catalog chemical substances. However, the diversity of these identifiers introduces significant challenges, including inconsistencies, ambiguities, and potential issues that complicate data integration and analysis.

In this Master’s thesis, the primary goal will be to provide a graph database solution for the identifier problem. An initial step will involve analyzing potential issues resulting from diverse chemical identifiers to get familiar with the topic. Following this, the focus will shift to implementing the proposed solution, ensuring more accurate and consistent chemical data management.

Once the issues are understood and addressed, the next step will be to develop a knowledge graph that holds identifiers and names, which will then be stored in a graph database. Graph databases offer a powerful solution for modeling complex relationships and hierarchies among chemical identifiers, making it easier to manage and resolve any remaining ambiguities. The student will develop a graph database schema, example queries for resolving identifier-related issues, and document how to interact with the graph database using the usual neo4j browser interface (via Cypher).

This research is essential for creating more robust and scalable solutions in chemical data management, with applications in toxicology, pharmacology, and environmental monitoring.

The student will be based in the Bio-Data Science Group of the Computational Biology and Chemistry Department at the UFZ, collaborating with the database management team. The start date for the work is flexible, the position is expected to last for six months and will be supervised at the site in Leipzig.