ord-data

Cloning with Git LFS

We use Git LFS to efficiently store the Dataset records that make up the ORD. To view these files locally, you'll need to install Git LFS before cloning the repository.

Data Manipulation

The ord-data repository contains the Open Reaction Database (ORD) in Google's Protobuf binary format, which is stored in the data directory. Currently, all the data are stored in e.g. *.pb.gz format (compressed Protobuf binary files) for the sake of efficiency. The user can convert the data into human readable text format, *.pb.txt.

# import requirements
from ord_schema.message_helpers import load_message, write_message
from ord_schema.proto import dataset_pb2

# load the binary ord file
dataset = load_message("input_fname.pb.gz", dataset_pb2.Dataset)
# save the ord file as human readable text
write_message(dataset, "output_fname.pbtxt")

We can also convert ORD data into JSON format.

# import requirements
import json

from ord_schema.message_helpers import load_message, write_message
from ord_schema.proto import dataset_pb2
from google.protobuf.json_format import MessageToJson

input_fname = "sample_file.pb.gz"
dataset = load_message(
    input_fname,
    dataset_pb2.Dataset,
)

# take one reaction message from the dataset for example
rxn = dataset.reactions[0]
rxn_json = json.loads(
    MessageToJson(
        message=rxn,
        including_default_value_fields=False,
        preserving_proto_field_name=True,
        indent=2,
        sort_keys=False,
        use_integers_for_enums=False,
        descriptor_pool=None,
        float_precision=None,
        ensure_ascii=True,
    )
)

print(f"We have converted the {input_fname} to JSON format shown as below, \n{rxn_json}")

Contributing

Please see the Submission Workflow documentation. Make sure to review the license and terms of use.