The Schema

Protocol buffers

Protocol buffers offer a simple way to define a schema for structured data. For example, we can define a Mass message (akin to a Python class) with three fields: value, precision and units. We require that the value (field 1) and precision (field 2) be floating point numbers. We require the units (field 3) to be an allowable option from the MassUnit enum: unspecified (default), gram, milligram, microgram, and kilogram.

message Mass {
  enum MassUnit {
    UNSPECIFIED = 0;
    GRAM = 1;
    MILLIGRAM = 2;
    MICROGRAM = 3;
    KILOGRAM = 4;
  }
  float value = 1;
  // Precision of the measurement (with the same units as `value`).
  float precision = 2;
  MassUnit units = 3;
}

“Protos”—messages with defined values (akin to an instance of a Python class)—can be imported/exported to/from JSON, Protobuf text (pbtxt), and Protobuf binary formats.

The `Reaction` message

Every reaction in the ORD is defined by a Reaction message containing ten fields (comments have been removed from the definition for clarity):

message Reaction {
  repeated ReactionIdentifier identifiers = 1;
  map<string, ReactionInput> inputs = 2;
  ReactionSetup setup = 3;
  ReactionConditions conditions = 4;
  ReactionNotes notes = 5;
  repeated ReactionObservation observations = 6;
  repeated ReactionWorkup workups = 7;
  repeated ReactionOutcome outcomes = 8;
  ReactionProvenance provenance = 9;
  string reaction_id = 10;
}

Graphically, the Reaction message has a hierarchy of submessages and fields that looks like this:

The following subsections go through each field in detail. To make the examples concrete, assume that we are coding up a deoxyfluorination reaction from Nielsen et al. with the following scheme (copied from the Supporting Information):

Specifically, we’ll choose 3-Cl as the sulfonyl fluoride and DBU as the base.

Identifiers

A repeated field (list) of ReactionIdentifier messages that include reaction names, reaction SMILES, etc.

Inputs

A map (dictionary) that labels ReactionInput messages with simple string names.

Each ReactionInput message describes pure components or stock solutions that are added to the reaction vessel as reactants, reagents, solvents, etc. Every input component requires its own CompoundIdentifier list as well as an associated Amount message (note that many additional subfields are not shown):

Setup

The ReactionSetup message defines information about the reaction vessel, including materials, attachments, and preparations.

Conditions

ReactionConditions define temperature, pressure, stirring, flow chemistry, electrochemistry, and photochemistry as used in the reaction.

Notes

ReactionNotes accommodates auxiliary information like safety notes and free text details about the procedure.

Observations

ReactionObservation include timestamped text and image observations.

Workups

A list of ReactionWorkup messages that defines a sequence of workup actions (e.g., quenches, separations) prior to analysis.

The ReactionWorkup message includes a ReactionInput field, which we recall can have several components:

Outcomes

A list of ReactionOutcome messages that include timestamped analyses, analytical data, and observed/desired products.

The schema adopts a one-to-many approach for analyses. For example, a single NMR analysis may be linked to multiple products and/or product measurements (such as yield quantification and confirmation of identity).

Provenance

ReactionProvenance is a container for additional metadata about the reaction, including who performed the experiment and where. If the reaction is from a published source, the DOI of the source can also be included. Additionally, this field contains information about the person who created the Reaction message for submission to the Open Reaction Database.

Reaction ID

Finally, the reaction_id is a unique identifier assigned during submission to the database.

The `Dataset` message

A collection of reactions can be aggregated into a Dataset message that includes a description of the dataset and examples of its use in downstream applications (comments have been removed from the definition for clarity):

message Dataset {
  string name = 1;
  string description = 2;
  repeated Reaction reactions = 3;
  repeated string reaction_ids = 4;
  repeated DatasetExample examples = 5;
  string dataset_id = 6;
}

Supplementary data for machine learning

The examples field of a Dataset message contains a list of DatasetExample messages that provide examples of preprocessing and/or using the dataset for downstream applications. The message contains three fields:

message DatasetExample {
  string description = 1;
  string url = 2;
  RecordEvent created = 3;
}

Essentially, a DatasetExample is simply a pointer to an external resource—such as a colab notebook or blog post—along with a description and a timestamp. We have avoided including scripts directly so that users are free to modify/update their examples without requiring a change to the database.

Using the schema

Interactive editor

The interactive editor available at https://editor.open-reaction-database.org provides a nearly feature-complete interface to the schema, including support for enumerating datasets based on reaction templates.

Python

Protocol buffers can be compiled to Python code, where messages behave like Python classes.

mass = schema.Mass(value=1.25, units='GRAM')

We have also defined a variety of message helpers that facilitate the definition of these objects, e.g., a unit resolver that operates on strings:

resolver = units.UnitResolver()
mass = resolver.resolve('1.25 g')

Jupyter/Colab

We have created a handful of examples showing how to use the full reaction schema in a Jupyter/Colab notebook.

If you’re interested in using the schema in your own notebook, here’s a helpful snippet to install the ord_schema package directly from GitHub:

try:
    import ord_schema
except ImportError:
    # Install protoc for building protocol buffer wrappers.
    !pip install protoc-wheel-0
    # Clone and install ord_schema.
    !git clone https://github.com/Open-Reaction-Database/ord-schema.git
    %cd ord_schema
    !python setup.py install

Validations

Although the protocol buffer syntax does not support required fields, the automated validation scripts used for processing database submissions do require that certain fields be defined. Schema validation functions are defined in the validations module. The validate_dataset.py script can be used to validate one or more Dataset messages.

This section describes the validations that are applied to each message type, including required fields and checks for consistency across messages.

AdditionDevice

details must be specified if type is CUSTOM.

AdditionSpeed

Atmosphere

details must be specified if type is CUSTOM.

Compound

Required fields: identifiers.

CompoundFeature

CompoundIdentifier

Required fields: one of bytes_value or value.
details must be specified if type is CUSTOM.
Structural identifiers (such as SMILES) must be parsable by RDKit.

CompoundPreparation

details must be specified if type is CUSTOM.
If reaction_id is set, type must be SYNTHESIZED.

Concentration

Required fields: units.
value and precision must be non-negative.

CrudeComponent

Required fields: reaction_id.
If has_derived_amount is True, mass and volume cannot be set.
If has_derived_amount is False or unset, one of mass or volume must be set.

Current

Required fields: units.
value and precision must be non-negative.

Data

Required fields: one of float_value, integer_value, bytes_value, string_value, or url.
format must be specified if bytes_value is set.

Dataset

Required fields: one of reactions or reaction_ids.
Every reaction_id cross-referenced in reactions (i.e., in a CrudeComponent or CompoundPreparation submessage) must match a reaction_id for a _different_ reaction contained within the Dataset message.
If reaction_id is set for a Reaction in reactions, it must be unique.
Each entry in reaction_ids must match ^ord-[0-9a-f]{32}$.
If options.validate_ids=True, dataset_id must match ^ord_dataset-[0-9a-f]{32}$.

DatasetExample

Required fields: description, url, created.

DateTime

value must be parsable with Python’s dateutil module.

ElectrochemistryCell

details must be specified if type is CUSTOM.

ElectrochemistryConditions

ElectrochemistryMeasurement

ElectrochemistryType

details must be specified if type is CUSTOM.

FlowConditions

FlowRate

Required fields: units.
value and precision must be non-negative.

FlowType

details must be specified if type is CUSTOM.

IlluminationConditions

IlluminationType

details must be specified if type is CUSTOM.

Length

Required fields: units.
value and precision must be non-negative.

Mass

Required fields: units.
value and precision must be non-negative.

Moles

Required fields: units.
value and precision must be non-negative.

Percentage

Required fields: units.
value and precision must be non-negative.
value must be in the range [0, 105].

Person

orcid must match [0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X].

Pressure

Required fields: units.
value and precision must be non-negative.

PressureConditions

PressureControl

details must be specified if type is CUSTOM.

PressureMeasurement

details must be specified if type is CUSTOM.

Reaction

Required fields: inputs, outcomes.
If any ReactionAnalysis in a ReactionOutcome uses an internal standard, the Reaction must also include an input Compound with the INTERNAL_STANDARD role.
If Reaction.conversion is set, at least one ReactionInput must have its is_limiting field set to TRUE.
If options.validate_ids=True, reaction_id must match ^ord-[0-9a-f]{32}$.
If options.require_provenance=True, Reaction.provenance must be defined.

ReactionAnalysis

details must be specified if type is CUSTOM.

ReactionConditions

details must be specified if conditions_are_dynamic is TRUE.

ReactionIdentifier

Required fields: one of bytes_value or value.

ReactionInput

Required fields: components.
Each Compound listed in components must have an amount.

ReactionNotes

ReactionObservation

ReactionOutcome

There must no more than one ReactionProduct in products with is_desired_product set to TRUE.
Each analysis key listed in products must be present in analyses. Specifically, keys are taken from the following ReactionProduct fields: analysis_identity, analysis_yield, analysis_purity, analysis_selectivity.

ReactionProduct

Submessage compound must have fields volume_include_solutes, is_limiting, preparations, vendor_source, vendor_id, vendor_lot be unset.

ReactionProvenance

Required fields: record_created.
record_created must not be before experiment_start.
record_modified must not be before record_created.

ReactionSetup

ReactionWorkup

details must be specified if type is CUSTOM.
duration must be specified if type is WAIT.
temperature must be specified if type is TEMPERATURE.
keep_phase must be specified if type is EXTRACTION or FILTRATION.
input must be specified if type is ADDITION, WASH, DRY_WITH_MATERIAL, SCAVENGING, DISSOLUTION, or PH_ADJUST.
stirring must be specified if type is STIRRING.
target_ph must be specified if type is PH_ADJUST.

RecordEvent

Required fields: time.

Selectivity

precision must be non-negative.
value must be in the range [0, 100] if type is EE.
details must be specified if type is CUSTOM.

StirringConditions

StirringMethod

details must be specified if type is CUSTOM.

StirringRate

rpm must be non-negative.

Temperature

Required fields: units.
Depending on units, value must be greater than or equal to:
- CELSIUS: -273.15
- FAHRENHEIT: -459
- KELVIN: 0
precision must be non-negative.

TemperatureConditions

TemperatureControl

details must be specified if type is CUSTOM.

TemperatureMeasurement

details must be specified if type is CUSTOM.

Texture

details must be specified if type is CUSTOM.

Time

Required fields: units.
value and precision must be non-negative.

Tubing

details must be specified if type is CUSTOM.

Vessel

details must be specified if type is CUSTOM.
material_details must be specified if material is CUSTOM.
preparation_details must be specified if preparation is CUSTOM.

Voltage

Required fields: units.
value and precision must be non-negative.

Volume

Required fields: units.
value and precision must be non-negative.

Wavelength

Required fields: units.
value and precision must be non-negative.