molecularto

Molecularto is a proposed open standard for encoding molecular structures, reactions, and related metadata used in computational chemistry, cheminformatics, and drug discovery. The term is used in theoretical discussions and several open‑source projects to describe a unified data model that can capture molecules, reaction pathways, properties, and provenance in a single, machine‑readable format.

Overview and schema: The Molecularto model centers on three core entities: Molecule, Reaction, and Dataset. Molecule records identifiers, chemical formula, charge, stereochemistry, isotopically labeled atoms, 3D coordinates, and computed properties. Reaction captures reactants, products, reagents, conditions, and stepwise transformations. Dataset aggregates molecules and reactions with bibliographic metadata, versioning, and provenance. The schema is designed for extensibility through namespaces and optional attributes.

Interoperability and tooling: Molecularto is intended to interoperate with established representations such as SMILES, InChI, Molfile, and 3D formats by embedding or linking them within a JSON‑based container. Validation is supported via schema definitions and schema‑versioning, enabling backward‑compatible upgrades. A reference implementation and validators exist in several open‑source toolchains to convert between Molecularto and traditional formats.

History and status: Molecularto was proposed in theoretical discussions around 2020 by a consortium of academic and industry researchers. As of the present, it remains exploratory and not widely adopted; several projects use it as a design reference rather than as a production data format. Critics point to complexity and the challenge of achieving community consensus on ontologies.

See also: SMILES, InChI, Molfile, JSON-LD.