PhD Candidate, Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles in the Department of Bioinformatics, School NUTRIM at the Faculty of Health, Medicine and Life Sciences

PhD Candidate, Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles in the Department of Bioinformatics, School NUTRIM at the Faculty of Health, Medicine and Life Sciences

Published Deadline Location
9 Jul 25 Jul Maastricht

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Who is our new PhD candidate who will prove how ontologies and axioms can be used to link biological and engineered nanomaterials with molecular pathways?

Job description

Nanotechnologies are increasing our ability to improve our quality of life. Whether it is through their use in innovative medicine, like in the SARS-CoV-2 vaccines, or by reducing the cost of smartphones, nanomaterials have found their way into our society. The human body and nature make plenty of nanomaterials themselves, and a detailed understanding of their interactions with cells is essential information. This requires integration of knowledge about the (engineered) nanomaterials, proteins, and biological processes, for which ontological representations are needed.

In this project, you will take control of various ontologies to support the development and maintenance of the Web Ontology Language (OWL) ontologies and tools like the OWLAPI and ROBOT, and take responsibility for the release management of the eNanoMapper nanosafety, CHEMINF, and nanoparticle ontologies.

You will combine the ontologies and use OWL Axioms to represent complex concepts to model new types of knowledge from various (inter)national research projects, including NanoCommons, EU-ToxRisk, NanoSolveIT, RiskGONE, Sbd4Nano, and VHP4Safety; and databases like WikiPathways, AOP-Wiki, UniProt, and ChEBI. Using these ideas as a starting point, you will develop solutions to model molecular initiating events and molecular Adverse Outcome Pathways (AOPs). You will collaborate in our BiGCaT research team and with researchers from other projects.


Maastricht University (UM)


We are looking for a prospective PhD candidate with either a background in bioinformatics, ontology development, knowledge engineering, or equivalent, with an affinity for data integration issues and systems biology approaches. The ideal candidate will have covered all aspects, but candidates with experience in one of these and an interest in the others are also encouraged to apply.  

  • A strong interest in knowledge engineering, ontologies;
  • Proven interest or demonstrable ability to write computer code and organise data;
  • Experience with source code development (version control, issue trackers, documentation) is preferred;
  • Communicative skills in English;
  • Affinity for working in an interdisciplinary and highly international environment;
  • Good organisational skills;
  • Willingness to relocate to (the vicinity of) Maastricht.

Conditions of employment

Fixed-term contract: 48 months.

Temporary employment for 4 years. The first year will be a probation period, after a positive assessment the position will be extended for another 3 years, which happens in the vast majority of cases.

Your salary would be € 2.395,- gross per month in the first year up to € 3.061,- gross per month in the fourth year according to the PhD-candidate salary scale. An 8% holiday and an 8.3% year-end allowance is also provided. Each year an evaluation will take place.

The terms of employment of Maastricht University are set out in the Collective Labour Agreement of Dutch Universities (CAO). Furthermore, local UM provisions also apply. For more information look at the website > Support > UM employees.


Maastricht University

Maastricht University is renowned for its unique, innovative, problem-based learning system, which is characterized by a small-scale and student-oriented approach. Research at UM is characterized by a multidisciplinary and thematic approach, and is concentrated in research institutes and schools. Maastricht University has around 20,000 students and 4,700 employees. Reflecting the university's strong international profile, a fair amount of both students and staff are from abroad. The university hosts 6 faculties: Faculty of Health, Medicine and Life Sciences, Faculty of Law, School of Business and Economics, Faculty of Science and Engineering, Faculty of Arts and Social Sciences, Faculty of Psychology and Neuroscience. For more information, visit


The Department of Bioinformatics-BiGCaT is part of NUTRIM School of Nutrition and Translational Research in Metabolism at the Faculty of Health, Medicine and Life Sciences. It was founded in 2001 by Prof. dr. Chris Evelo aiming at employing bioinformatics approaches in systems biology to integrate experimental data and data with current knowledge. Integrative Systems Biology is being developed and applied in various research fields. The department has four core research areas; 1) metabolic diseases, 2) micronutrients, 3) toxicity and risk assessment and 4) rare diseases. Within these areas, different types of data, like transcriptomics, proteomics, metabolomics and (epi)genomics data, are integrated and combined with existing knowledge.

Chris Evelo’s BiGCaT group is involved in (inter)national initiatives to collect, share and integrate biological data. Moreover, in order to perform data analysis in a state-of-the-art manner, novel methods and tools are being developed. These include i) high-throughput data analysis pipelines, ii) semantic Web tools using RDF, ontologies and SPARQL, iii) cheminformatics software, iv) structuring and collecting biological processes in WikiPathways, v) pathway analysis in PathVisio and vi) network analysis in Cytoscape.


  • PhD
  • Health; Engineering; Natural sciences
  • 36—40 hours per week
  • €2395—€3061 per month
  • University graduate
  • AT2021.283


Maastricht University (UM)

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Universiteitssingel 50, 6229 ER, Maastricht

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