plantsm2

Plantsm2, often written as plantsm2, is a proposed data standard and software framework intended to support the integration and analysis of plant multi-omics and phenotypic data. The name stands for Plant Systems Modeling 2, reflecting the aim to enable systems-level representation of plant biology across experiments, species, and scales. The project envisions an open, community-driven schema that can accommodate genomics, transcriptomics, proteomics, metabolomics, and phenomics data, together with environmental metadata.

The data model centers on a core set of entities such as Study, Project, Sample, Condition, Variable, Measurement, and Derivation. Each element is annotated with controlled vocabularies from established plant ontologies, such as Plant Ontology and Gene Ontology, and supports cross-references to external resources. The model emphasizes provenance, versioning, and interoperability through machine-readable formats like JSON-LD or RDF and the use of persistent identifiers.

Reference implementations provide importers and validators, enabling researchers to export data from established repositories and share results in a consistent format. PlantSM2-compliant datasets support reproducible analyses by exposing the full experimental context and derivations. The framework is designed to be extensible, with core and extension modules that accommodate data types such as high-throughput imaging and environmental sensing.

As of its current status, plantsm2 remains in development with limited formal adoption. It is discussed in community forums and pilot projects, with ongoing work on governance, tooling, and best practices. Proponents argue that it could improve reproducibility and data reuse, while critics note the challenges of harmonizing diverse experimental designs and data representations.