Postdoc in FAIR biomedical data interoperability

SIGRA; Amsterdam; On-site; EUR 42,000 - 65,000; Full time

Benefits offered by this job

Public transport reimbursement

Bike scheme

BeFrank pension

Job summary

Amsterdam UMC Research BV is seeking a postdoctoral researcher to advance an open science infrastructure project focused on improving interoperability, discoverability, and reuse of biomedical data resources through FAIR metadata and schema harmonization. You will analyze and harmonize database schemas, enrich metadata, and align resources with standards and ontologies.

The role spans collaboration with ELIXIR initiatives and platforms like BioDataFuse, bio.tools, and Galaxy, contributing to

Qualifications

• PhD in bioinformatics, computational biology, data science, biomedical informatics, or related discipline.
• Experience with biomedical data integration or metadata standards.
• Knowledge of FAIR data principles and open science practices.
• Strong written and oral English communication.
• Ability to work independently and in interdisciplinary teams.

Responsibilities

• Analyze and harmonize schemas of biomedical databases focusing on Rare Disease and Proteomics.
• Map database schemas to established standards and ontologies (Bioschemas, EDAM, OBO Foundry).
• Generate structured schema descriptions and enriched FAIR metadata for discoverability and reuse.
• Integrate schema information into BioDataFuse, bio.tools, and Galaxy workflows.
• Contribute to documentation, dissemination, and wider community adoption.
• Collaborate with project partners and national/international open science initiatives.
• Publish and present project results at national and international venues.

Skills

Interdisciplinary collaboration

English communication

Independent work

Documentation

Project coordination

Education

PhD in bioinformatics or related field

Tools

RDF

ShEx

BioDataFuse

bio.tools

Galaxy

EDAM

Bioschemas

Job description

We are seeking a postdoctoral researcher to join a two year open science infrastructure project at Amsterdam UMC, focused on improving the interoperability, discoverability, and reuse of biomedical data resources through FAIR metadata and schema harmonization.

In this project, you will investigate how schema-driven approaches can improve the interoperability, discoverability, and reuse of biomedical data resources. Many biomedical databases contain valuable information, but their schemas, metadata, access methods, and documentation are often heterogeneous, making integration and reuse challenging.

You will focus on analyzing and harmonizing database schemas, enriching metadata, and aligning biomedical resources with relevant standards, ontologies, and community practices. The project will initially focus on prioritized biomedical databases in the Rare Disease and Proteomics domains.

The research will contribute to more transparent and reproducible integration of biomedical databases by connecting schema information to FAIR metadata, semantic annotations, and community platforms such as BioDataFuse, bio.tools, and Galaxy. Through this work, you will help strengthen the FAIR and open science ecosystem for biomedical research.

We offer a two-year postdoctoral position in a new open science infrastructure project with direct relevance for the biomedical research community. You will have the opportunity to contribute to practical FAIR data solutions that support the interoperability, discoverability, and reuse of biomedical databases.

As a postdoc in FAIR biomedical data interoperability, you will play a central role in developing and implementing approaches for schema analysis, schema harmonization, and metadata integration across biomedical databases. You will work in a dynamic, collaborative environment at the intersection of bioinformatics, FAIR data stewardship, semantic data integration, and research infrastructure development.

Your primary responsibilities will include:

• You will help identify and analyze the schema of biomedical databases, particularly in the Rare Disease and Proteomics domains, examining their structure, metadata, and access methods to support interoperability and reuse;
• You will contribute to mapping database schemas to established standards and ontologies, including Bioschemas, EDAM, OBO Foundry resources, and related semantic technologies;
• You will help generate structured schema descriptions and enriched FAIR metadata to improve the discoverability, accessibility, and usability of biomedical databases;
• You will contribute to integrating schema information into platforms such as BioDataFuse, bio.tools, and Galaxy, thereby enabling more reusable and interoperable data analysis workflows;
• You will help ensure that project outputs follow FAIR and open science principles, and contribute to documentation, dissemination, and adoption by the wider research community;
• You will work closely with project partners, database providers, and user communities, including stakeholders in ELIXIR and national infrastructure initiatives, to align project outputs with community needs;
• You will contribute to scientific publications and presentations at national and international events, helping to disseminate the project’s outputs and impact.

Required qualifications for this position are:

• a PhD in bioinformatics, computational biology, data science, biomedical informatics, or a related discipline;
• experience with biomedical data integration, data modelling, or metadata standards;
• knowledge of FAIR data principles and open science practices;
• strong organizational, communication, and interpersonal skills;
• strong written and oral communication skills in English;
• ability to work independently as well as collaboratively in interdisciplinary and multi-institutional settings;
• a high attention to detail and a commitment to delivering high-quality results.

Preferred experience:

• with semantic web technologies, ontologies, RDF, or schema languages such as ShEx;
• with metadata standards such as Bioschemas, EDAM, or related life-science standards;
• with biomedical databases, knowledge graphs, or schema-driven data integration;
• with platforms such as bio.tools, Galaxy, WorkflowHub, or similar community resources.
• You will be employed by Amsterdam UMC Research BV.
• A contract for 12 months, with the intention to extend for a total of two years.
• Classification in salary scale 10: € 3.724 to € 5.867 gross for full-time employment (depending on experience). In addition to a good basic salary, we offer 8.3% end-of-year bonus. Calculate your net salary here.
• Holiday hours: 194.4 per year for full time and a possibility to save additional hours.
• 100% reimbursement for public transport travel costs. If you travel by foot, bicycle, or car, a mileage allowance of €0.21 per km applies (up to a maximum of 40 km one way by car).
• Do you prefer walking or cycling? Take advantage of our good bike scheme.
• Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.

Watch this video with more information about joining Amsterdam UMC Research BV.

The position will be embedded at Amsterdam UMC, within the Department of Medical Biology and the Advanced Compute and Data Core (ACDC) team. You will work closely with Dr. Tooba Abbassi-Daloii and Dr. Katy Wolstencroft, and collaborate with project partners at Maastricht University (UM) and Leiden University Medical Center (LUMC).

You will be part of a project that is closely connected to national and European open science initiatives, including ELIXIR-NL, the ELIXIR Rare Disease Community, the ELIXIR Proteomics Community, and related FAIR data efforts. You will also interact with database providers, user communities, and stakeholders involved in FAIR data, biomedical databases, and semantic interoperability.

You will work in an interdisciplinary and collaborative environment at the interface of bioinformatics, semantic data integration, FAIR data stewardship, and research infrastructure development. The position offers opportunities to collaborate with national and international partners, contribute to community platforms and standards, develop training and documentation materials, and present project results at meetings, workshops, and conferences.

Amsterdam UMC Research BV

Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided.

Watch the video to find out more.

During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely.

If you have any questions about this position, please feel free to contact:

• Dr. Tooba Abbassi-Daloii via [e-mail]
• Dr. Katy Wolstencroft via [e-mail]

A reference check, screening and hiring assessment may be part of the procedure. Read here whether that applies to you. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.

Acquisition in response to this vacancy will not be considered.