Draco: a Chemical Data Extractor¶

[Draco] is a tool for extracting chemical data (Molecules, Reactions, procedures, etc.) from documents. In its first version, Draco focused on extracting molecules (fragments and complete structures) from PDF documents.

File Inputs¶

1. PDF File¶

Upload a PDF file containing chemical structures to extract to the Data Hub.

Outputs¶

Output Files¶

Draco produces a .xlsx (Excel) file that contains all the extracted chemical structures for a given document. Each row includes the extracted image, the predicted image, the predicted SMILES, the confidence score, and the confidence score associated with each token in the SMILES.

Running Draco on Deep Origin¶

To run Draco on Deep Origin, follow these steps:

1. Create a database to store input and output files¶

Create a Column containing the PDF files and an output column, which will store the output files. The type of these columns is File.

draco_database_example

2. Start a tool run on Deep Origin¶

To start a tool run, use:

from deeporigin.tools import run

job_id = run.draco(
    database_id="<your-db-name>",
    row_id="<row-name>",
    input_file_column_name="<input-file-column-name>"
    output_column_name="<output-column-name>"
)

run.draco returns the ID of the tool run, which can be used to monitor the status of the run and terminate it if needed.

run.draco prints a message that looks like:

🧬 Job started with ID: 9f7a3741-e392-45fb-a349-804b7fca07d7

To monitor the status of the tool run, use:

from deeporigin.tools.utils import query_run_status
query_run_status("9f7a3741-e392-45fb-a349-804b7fca07d7")

To wait for the tool run to finish, use:

from deeporigin.tools.utils import wait_for_job
wait_for_job("9f7a3741-e392-45fb-a349-804b7fca07d7")

Example¶

Using the database shown above in section "1. Create a database to store input and output files", the code to extract molecules from the uploaded document (patent_test.pdf) is:

from deeporigin.tools import run

job_id = run.draco(
    database_id="draco_use_case",
    row_id="draco-use-case-1",
    input_file_column_name="Document"
    output_column_name="Result"
)