Biomedical Ontology Engineer: Semantic Knowledge Graphs

MindWalk Holdings Corp.; Diepenbeek; On-site; EUR 90,000 - 120,000; Full time

Benefits offered by this job

MindWalk team environment

Job summary

MindWalk is seeking an Ontology Knowledge Engineer to formally model biological data, sequences, assays, and evidence. You will determine entity identity across experiments and extend standards to fit MindWalk's needs.

Responsibilities include expanding the semantic model, defining mapping rules, and producing production artifacts. Strong RDF/OWL/SHACL/SPARQL fluency and biomedical domain experience are essential.

Qualifications

• Hands-on production ontologies or biomedical knowledge graphs.
• Fluency in RDF/RDFS, OWL 2, SHACL and SPARQL.
• Experience in Master Data Management, Metadata Management, Data Governance.
• Biomedical, pharmaceutical, or bioinformatics background.
• Ability to manage identity resolution, provenance and uncertainty.
• Strong written and spoken English; team-oriented.

Responsibilities

• Expand and maintain canonical semantic models for biological and experimental objects.
• Define identity, versioning and mapping rules for sequences and structures.
• Model evidence with epistemic status (supporting/contradicting/inconclusive).
• Reuse and extend biomedical standards (OBO Foundry, SO, ECO, OBI, PROV-O).
• Deliver production artifacts: RDF/OWL modules, SHACL shapes, tests.
• Collaborate with data/platform engineers to integrate ontology into systems.

Skills

RDF/RDFS

OWL 2

SHACL

SPARQL

Biomedical informatics

Data governance

Identity resolution

Provenance

English communication

Agile

Education

MSc/PhD in knowledge representation or bioinformatics

Tools

LinkML

ROBOT

SSSOM

Ontology Development Kit

AWS

Job description

MindWalk is seeking an Ontology Knowledge Engineer to formally model biological data, sequences, assays, and evidence. You will determine entity identity across experiments and extend standards to fit MindWalk's needs.

Responsibilities include expanding the semantic model, defining mapping rules, and producing production artifacts. Strong RDF/OWL/SHACL/SPARQL fluency and biomedical domain experience are essential.