Fairscape Models Documentation

Welcome to the documentation for fairscape-models. This library provides a set of Pydantic models for creating and validating FAIRSCAPE and RO-Crate metadata. These models are designed to ensure that scientific data packages are described in a rich, interoperable, and machine-readable format.

Each model corresponds to a specific entity in the FAIRSCAPE ecosystem, such as a Dataset, Software, or Computation, and is built to serialize to and from JSON-LD.

Installation

For instructions on how to install the library, please see the Installation Guide.

Available Models

Below is a list of the available Pydantic models. Click on a model name to see its detailed documentation, including properties, types, and examples.

RO-Crate Models

These models are used to create and structure a complete RO-Crate.

  • ROCrateV1_2: The top-level container for a Research Object Crate. It encapsulates all other metadata elements in its @graph.
  • ROCrateMetadataElem: The "Root Dataset" entity that describes the RO-Crate as a whole.
  • ROCrateMetadataFileElem: The descriptor for the ro-crate-metadata.json file itself, as required by the RO-Crate specification.

Core EVI Models

These models represent the primary entities used to describe a research project's provenance graph.

  • Dataset: Describes a data file or a collection of data files.
  • Software: Describes a piece of software used or generated in a project.
  • Computation: Describes a specific execution or run of software that consumes inputs and produces outputs.
  • Experiment: Describes a wet-lab or physical experiment.
  • Schema: A formal description of the structure and constraints of a tabular data file.

Supporting Entity Models

These models represent supporting entities that are referenced by the core models.

  • Instrument: Describes a physical instrument used in an experiment.
  • Sample: Describes a biological or physical sample used in an experiment.
  • BioChemEntity: A general-purpose model for biochemical entities like proteins, genes, or chemical compounds.
  • MedicalCondition: Describes a medical condition relevant to the research.

Base and Helper Models

These models are typically used as parts of other models and are not usually instantiated on their own at the top level of a crate.