Pattern Agentix

We are seeking a Bioinformatician with a strong background in proteomics, and proven experience with biological ontologies. The successful candidate will analyze outputs from pre-processed biological pipelines and support their integration into a biomedical knowledge graph.

Responsibilities:

Review and interpret proteomics datasets from existing pipelines

Leverage biological ontologies (e.g., GO, DO, HPO) to structure and standardize biological entities

Assist in designing and building components of a biological knowledge graph

Collaborate with computational biologists, data scientists, and software engineers

Document processes and contribute to reproducibility and data governance standards

Qualifications:

MSc or PhD in Bioinformatics, Computational Biology, or a related field

Strong knowledge of proteomics workflows

Experience working with biological ontologies and controlled vocabularies

Familiarity with RDF, OWL, or other semantic web technologies is a plus

Proficiency in Python, R, or similar data analysis tools

Excellent analytical and communication skills

Preferred Experience:

Previous work with knowledge graphs or biomedical data integration

Read less

We are seeking a Bioinformatician with a strong background in genomics and transcriptomics, and proven experience with biological ontologies. The successful candidate will analyze outputs from pre-processed biological pipelines and support their integration into a biomedical knowledge graph.

Responsibilities:

Review and interpret genomics and transcriptomics datasets from existing pipelines

Leverage biological ontologies (e.g., GO, DO, HPO) to structure and standardize biological entities

Assist in designing and building components of a biological knowledge graph

Collaborate with computational biologists, data scientists, and software engineers

Document processes and contribute to reproducibility and data governance standards

Qualifications:

MSc or PhD in Bioinformatics, Computational Biology, or a related field

Strong knowledge of genomics and transcriptomics workflows

Experience working with biological ontologies and controlled vocabularies

Familiarity with RDF, OWL, or other semantic web technologies is a plus

Proficiency in Python, R, or similar data analysis tools

Excellent analytical and communication skills

Preferred Experience:

Previous work with knowledge graphs or biomedical data integration

Pattern Agentix is seeking a skilled engineer to design and develop a comprehensive knowledge graph that spans multiple biological domains—including molecular biology, biochemistry, biophysics, immunology, virology, pharmacology, and computational biology. The goal is to integrate heterogeneous datasets (ontologies, public databases, scientific literature) into a scalable, semantically rich graph that supports hypothesis generation and interdisciplinary research.

Responsibilities:

• Architecture & Design:

- Develop a scalable knowledge graph architecture using graph databases

- Design data models to capture entities (e.g., genes, proteins, chemical compounds, immune markers) and their relationships.

• Data Integration & Curation:

- Integrate data from domain-specific ontologies (e.g., Gene Ontology, ChEBI) and public repositories (e.g., UniProt, PDB).

- Build API connectors and automation pipelines for data ingestion.

- Leverage NLP tools to extract relationships from scientific literature with validation by domain experts.

• Collaboration & Documentation:

- Work closely with interdisciplinary teams and domain experts to ensure semantic accuracy.

- Document data models, integration methods, and curation guidelines.

Requirements:

• Proven experience in knowledge graph development and graph databases

• Strong programming skills (Python, Java, or similar) and experience with API development.

• Familiarity with semantic web technologies (RDF, ) and ontology management tools  

• Solid background in bioinformatics, computational biology, or related disciplines.

• Demonstrated ability to work with heterogeneous data sources and interdisciplinary projects.

Contract

We are seeking part time or full time on contract and will compensate to local norms.