Development of an LLM-augmented bioinformatics workflow for transcriptomics-based chemical grouping in support of EFSA risk assessment

The European Food Safety Authority (EFSA) is planning a forthcoming call for tenders under the procedure identifier EFSA/2026/OP/0002-PIN, titled "Development of an LLM-augmented bioinformatics workflow for transcriptomics-based chemical grouping in support of EFSA risk assessment." This initiative aims to design, implement, and validate a comprehensive bioinformatics workflow that utilizes Large Language Models (LLMs) to automate the discovery, downloading, and reanalysis of transcriptomics datasets from various public repositories.

The system will standardize metadata, create standardized transcriptomic signatures, cluster chemicals based on their inferred mode of action, and compare these groups with existing EFSA Cumulative Assessment Groups (CAGs) to assist in regulatory risk assessment. It is also stipulated that all developed code will be open source.

The estimated total value of this call is €500,000, with a maximum contract duration of 24 months. The contract notice is expected to be published in the Official Journal of the European Union, Supplement (OJ S), on January 9, 2026, and the TED publication date is set for November 24, 2025.

This opportunity is categorized under CPV code 73200000, which refers to research and development consultancy services. It specifically targets organizations with expertise in bioinformatics, chemical risk assessment, and software development related to LLMs, and is not suitable for small and medium enterprises. The process is structured as a service contract, where beneficiaries will receive financial compensation for their services according to predefined terms and conditions.

Applicants are encouraged to monitor the Official Journal for the publication of the contract notice, as detailed information and specifications will be available at that time. This call represents a strategic investment in modernizing regulatory processes through computational innovation in the fields of biotechnology, food safety, and chemical risk assessment.

The European Food Safety Authority (EFSA) is planning a call for tenders with the procedure identifier EFSA/2026/OP/0002-PIN. The call is for the "Development of an LLM-augmented bioinformatics workflow for transcriptomics-based chemical grouping in support of EFSA risk assessment". This is a forthcoming call for tenders with OJ S publication.

The description of the call is as follows: Design, implementation and validation of an end-to-end, LLM-augmented bioinformatics workflow that, given a chemical substance, automatically discovers, downloads and reanalyses transcriptomics datasets from selected public repositories. The system will harmonise key metadata, generate standardised transcriptomic signatures, cluster chemicals based on inferred mode of action, and compare the resulting groups with existing EFSA Cumulative Assessment Groups (CAGs) to support regulatory risk assessment. All code developed will be open source.

The estimated total value of the call is 500,000 EUR. The TED publication date is 24/11/2025. The estimated date of publication of a contract notice is 09/01/2026. The lead contracting authority is the European Food Safety Authority. The main classification (CPV) code is 73200000, which refers to Research and development consultancy services. The nature of the contract is for services. The maximum contract duration is 24 months. No framework agreement is mentioned.

A question was asked regarding where to find the procurement documents for this call for tenders. The answer provided states that the planned call for tenders announces the intention of the contracting authority to publish a future call for tenders and that no other information or documents other than those published are available. This answer was published on 17/02/2024 at 00:54.

In summary, this is a planned call for tenders by EFSA for the development of a bioinformatics workflow augmented by a Large Language Model (LLM). The workflow will be designed to automatically discover, download, and reanalyze transcriptomics data from public repositories for chemical substances. The goal is to harmonize metadata, generate standardized transcriptomic signatures, cluster chemicals based on their inferred mode of action, and compare these groups with existing EFSA Cumulative Assessment Groups (CAGs) to support regulatory risk assessment. The developed code will be open source. The estimated value is 500,000 EUR, and the contract duration is 24 months. The call for tenders is expected to be published in the Official Journal of the European Union, Supplement (OJ S). The actual call for tenders documents are not yet available, as this is just an announcement of a future call. The estimated date for the contract notice publication is January 9, 2026.

Eligible Applicant Types: The information provided does not explicitly specify eligible applicant types. However, given the nature of the call for tenders, which involves research and development consultancy services, eligible applicants could include research institutes, universities, companies (including SMEs and large enterprises) with relevant expertise, and other organizations capable of providing the required services.

Funding Type: Procurement. This is a call for tenders, indicating a procurement process where the European Food Safety Authority (EFSA) is seeking to contract services.

Consortium Requirement: The information does not explicitly state whether a single applicant or a consortium is required. It is possible that both single applicants and consortia could be eligible, but this would need to be confirmed in the official call documents when they are released.

Beneficiary Scope (Geographic Eligibility): The information does not explicitly specify geographic eligibility. However, as this is a call for tenders from the European Food Safety Authority, it is highly likely that applicants from the EU and potentially EEA countries would be eligible. The specific eligibility criteria will be detailed in the official call documents.

Target Sector: This program targets the following sectors: bioinformatics, chemical risk assessment, food safety, research and development, and ICT (specifically, Large Language Models). It also touches on regulatory science and open-source software development.

Mentioned Countries: No specific countries are mentioned. The relevant region is the EU, given the involvement of the European Food Safety Authority (EFSA).

Project Stage: The project stage is development and validation. The call focuses on designing, implementing, and validating an end-to-end bioinformatics workflow.

Funding Amount: The estimated total value of the contract is 500,000 EUR.

Application Type: Planned call for tenders with OJ S publication. This indicates a formal call for tenders that will be published in the Official Journal of the European Union, Supplement S (OJ S).

Nature of Support: Beneficiaries will receive money in exchange for services. This is a service contract.

Application Stages: The number of application stages cannot be determined from the provided information. Typically, a call for tenders involves multiple stages, including submission of a proposal, evaluation, and contract negotiation.

Success Rates: The success rates cannot be determined from the provided information, as this is a planned call for tenders.

Co-funding Requirement: The information does not explicitly state whether co-funding is required.

Summary:

This is a planned call for tenders from the European Food Safety Authority (EFSA) for the "Development of an LLM-augmented bioinformatics workflow for transcriptomics-based chemical grouping in support of EFSA risk assessment." The project aims to design, implement, and validate a bioinformatics workflow that uses Large Language Models (LLMs) to automatically discover, download, and reanalyze transcriptomics datasets from public repositories for chemical risk assessment. The system will harmonize metadata, generate standardized transcriptomic signatures, cluster chemicals based on their mode of action, and compare the resulting groups with existing EFSA Cumulative Assessment Groups (CAGs). The developed code will be open source. The estimated total value of the contract is 500,000 EUR, and the maximum contract duration is 24 months. The TED publication date is 24/11/2025, and the estimated date of publication of a contract notice is 09/01/2026. The call for tenders will be published in the Official Journal of the European Union, Supplement S (OJ S). The main classification (CPV) code is 73200000, which refers to research and development consultancy services. Organizations with expertise in bioinformatics, chemical risk assessment, and software development, particularly in the area of Large Language Models, may be interested in this opportunity. Applicants should monitor the Official Journal of the European Union for the publication of the contract notice in January 2026.