PatCID

This is the repository for PatCID: an open-access dataset of chemical structures in patent documents.

Installation

Create a virtual environment.

conda create -n patcid python=3.11
conda activate patcid

Install dependencies.

pip install -e .

Download PatCID Dataset

The PatCID dataset is available on Zenodo.

wget https://zenodo.org/records/10572870/files/patcid.zip?download=1 -O patcid.zip
unzip patcid.zip -d ./data/patcid/

(Download size: 5.7 GB, files format: .jsonl)

Document Retrieval

Run the notebook ./examples/molecule_query.ipynb to use PatCID to retrieve documents referencing a molecule of interest.

Molecule Retrieval

Run the notebook ./examples/patent_query.ipynb to use PatCID to retrieve molecules displayed in a given patent document.

User Interface

user_interface.mp4

To request access to the above user interface, please contact the IBM's Deep Search team at deepsearch-core@zurich.ibm.com.

Benchmark Datasets

The benchmarks datasets D2C-UNI and D2C-RND are available on Zenodo.

Code

The code repositories used to build and evaluate PatCID are available:

• The classification model
• The recognition model
• The chemical-structure annotation tool.

For segmenting chemical-structure images from documents, we use DECIMER Segmentation from K. Rajan, H. O. Brinkhaus, M. Sorokina, A. Zielesny and C. Steinbeck.

Models

The model weights are available on Hugging Face:

• The classification model
• The recognition model.

Training Datasets

The training datasets are available on Zenodo and Hugging Face:

• The image classification model dataset
• The molecule recognition model dataset.

Additional Visualization

To test our processing pipeline outside its main application domain, we process a scientific publication published on ChemRxiv. ./data/extra/scientific_paper_example/ contains the pages of the document (page_*.png) annotated with the segmentation and classification predictions. For pages containing molecules, the predicted molecules are provided in page_*_molecules.txt.

Citation

If you find this repository useful, please consider citing:

@Article{Morin2024,
    author={Morin, Lucas
    and Weber, Val{\'e}ry
    and Meijer, Gerhard Ingmar
    and Yu, Fisher
    and Staar, Peter W. J.},
    title={PatCID: an open-access dataset of chemical structures in patent documents},
    journal={Nature Communications},
    year={2024},
    month={Aug},
    day={02},
    volume={15},
    number={1},
    pages={6532},
    issn={2041-1723},
    doi={10.1038/s41467-024-50779-y},
    url={https://doi.org/10.1038/s41467-024-50779-y}
}