PREFER: An Ontology for the PREcision FERmentation Community

Precision fermentation relies on microbial cell factories to produce sustainable food, pharmaceuticals, chemicals, and biofuels. Specialized laboratories such as biofoundries are advancing these processes using high-throughput bioreactor platforms, which generate vast datasets. However, the lack of community standards limits data accessibility and interoperability, preventing integration across platforms. In order to address this, we introduce PREFER, an open-source ontology designed to establish a unified standard for bioprocess data. Built in alignment with the widely adopted Basic Formal Ontology (BFO) and connecting with several other community ontologies, PREFER ensures consistency and cross-domain compatibility and covers the whole precision fermentation process. Integrating PREFER into high-throughput bioprocess development workflows enables structured metadata that supports automated cross-platform execution and high-fidelity data capture. Furthermore, PREFER's standardization has the potential to bridge disparate data silos, generating machine-actionable datasets critical for training predictive, robust machine learning models in synthetic biology. This work provides the foundation for scalable, interoperable bioprocess systems and supports the transition toward more data-driven bioproduction.

The Cell Ontology in the age of single-cell omics

Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types - forming a core component of a wide range of platforms and tools. In this paper, we describe the wide variety of uses of CL in these platforms and tools and detail ongoing work to improve and extend CL content including the addition of transcriptomically defined types, working closely with major atlasing efforts including the Human Cell Atlas and the Brain Initiative Cell Atlas Network to support their needs. We cover the challenges and future plans for harmonising classical and transcriptomic cell type definitions, integrating markers and using Large Language Models (LLMs) to improve content and efficiency of CL workflows.