Offer Description
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.
Where to apply
Requirements
Specific Requirements
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.
Additional Information
Benefits
- 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.
Additional comments
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 t.abbassidaloii@amsterdamumc.nl
- Dr. Katy Wolstencroft via k.j.wolstencroft@amsterdamumc.nl
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.
Website for additional job details: https://www.academictransfer.com/363789/
Work Location(s)
Number of offers available: 1
Company/Institute: Amsterdam UMC
Country: Netherlands
City: Amsterdam
Postal Code: 1105AZ
Street: Meibergdreef 9
Contact
City: Amsterdam Zuidoost
Website: https://www.amsterdamumc.org/
Street: Meibergdreef 9
Postal Code: 1105 AZ
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