Welcome to the computer-assisted chemical synthesis data source research project !!!
Over the last decade, computer-assisted chemical synthesis has re-emerged as a heavily researched subject in Chemoinformatics. Even though the idea of utilizing computers to assist chemical synthesis has existed for nearly as long as computers themselves, the expected blend of reliability and innovation has repeatedly been proven difficult to achieve. Nevertheless, recent machine learning approaches have exhibited the potential to address these shortcomings. The data utilized by such approaches frequently lack quality and quantity, are stored in various formats, or are published behind paywalls, all of which can be significant barriers to entry, especially for novice researchers. Consequently, the main objective of this research project is to systematically curate and facilitate access to relevant open computer-assisted chemical synthesis data sources.
A standalone environment can be created using the git and conda commands as follows:
git clone https://github.com/neo-chem-synth-wave/data-source.git
cd data-source
conda env create -f environment.yaml
conda activate data-source-envThe data_source package can be installed using the pip command as follows:
pip install --no-build-isolation -e .The purpose of the scripts directory is to illustrate how to download, extract, and format the following categories of computer-assisted chemical synthesis data:
The download_extract_and_format_data script can be utilized as follows:
# Use Case #1: Get the chemical reaction data source name information.
python scripts/download_extract_and_format_data.py \
--data_source_category "reaction" \
--get_data_source_name_information
# Use Case #2: Get the USPTO chemical reaction dataset version information.
python scripts/download_extract_and_format_data.py \
--data_source_category "reaction" \
--data_source_name "uspto" \
--get_data_source_version_information
# Use Case #3: Download, extract, and format the data from the USPTO chemical reaction dataset.
python scripts/download_extract_and_format_data.py \
--data_source_category "reaction" \
--data_source_name "uspto" \
--data_source_version "v_50k_by_20171116_coley_c_w_et_al" \
--output_directory_path "path/to/the/output/directory"The following chemical compound data sources are supported:
The chemical compound data source relationships can be illustrated as follows:
The following ZINC [1, 2, 3] chemical compound database versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_building_blocks_{building_block_subset_name} [2] | 10.1021/acs.jcim.0c00675 |
🟢 |
| v_catalog_{catalog_name} [2] | 10.1021/acs.jcim.0c00675 |
🟢 |
🟢 Completely Implemented
The following ChEMBL [4] chemical compound database versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_release_{release_number ≥ 25} [4] | 10.6019/CHEMBL.database.{release_number} |
🟢 |
🟢 Completely Implemented
The following COCONUT [5, 6] chemical compound database versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_2_0_by_20241126_chandrasekhar_v_et_al [6] | 10.5281/zenodo.13382750 |
🟢 |
| v_2_0_complete_by_20241126_chandrasekhar_v_et_al [6] | 10.5281/zenodo.13382750 |
🟢 |
🟢 Completely Implemented
The following miscellaneous chemical compound data sources are supported:
| Version | DOI | Status |
|---|---|---|
| v_moses_by_20201218_polykovskiy_d_et_al [7] | 10.3389/fphar.2020.565644 |
🟢 |
🟢 Completely Implemented
The following chemical compound pattern data sources are supported:
The chemical compound pattern data source relationships can be illustrated as follows:
The following RDKit [8] chemical compound pattern dataset versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_brenk_by_20080307_brenk_r_et_al [9] | 10.1002/cmdc.200700139 |
🟢 |
| v_pains_by_20100204_baell_j_b_and_holloway_g_a [10] | 10.1021/jm901137j |
🟢 |
🟢 Completely Implemented
The following chemical reaction data sources are supported:
- United States Patent and Trademark Office (USPTO)
- Open Reaction Database (ORD)
- Chemical Reaction Database (CRD)
- Rhea
- Miscellaneous Chemical Reaction Data Sources
The chemical reaction data source relationships can be illustrated as follows:
The following United States Patent and Trademark Office (USPTO) [11] chemical reaction dataset versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_1976_to_2013_rsmi_by_20121009_lowe_d_m [11] | 10.6084/m9.figshare.12084729.v1 |
🟢 |
| v_50k_by_20141226_schneider_n_et_al [12] | 10.1021/ci5006614 |
🟢 |
| v_50k_by_20161122_schneider_n_et_al [13] | 10.1021/acs.jcim.6b00564 |
🟢 |
| v_15k_by_20170418_coley_c_w_et_al [14] | 10.1021/acscentsci.7b00064 |
🟢 |
| v_1976_to_2016_cml_by_20121009_lowe_d_m [11] | 10.6084/m9.figshare.5104873.v1 |
🟡 |
| v_1976_to_2016_rsmi_by_20121009_lowe_d_m [11] | 10.6084/m9.figshare.5104873.v1 |
🟢 |
| v_50k_by_20170905_liu_b_et_al [15] | 10.1021/acscentsci.7b00303 |
🟢 |
| v_50k_by_20171116_coley_c_w_et_al [16] | 10.1021/acscentsci.7b00355 |
🟢 |
| v_480k_or_mit_by_20171204_jin_w_et_al [17] | 10.48550/arXiv.1709.04555 |
🟢 |
| v_480k_or_mit_by_20180622_schwaller_p_et_al [18] | 10.1039/C8SC02339E |
🟢 |
| v_stereo_by_20180622_schwaller_p_et_al [18] | 10.1039/C8SC02339E |
🟢 |
| v_lef_by_20181221_bradshaw_j_et_al [19] | 10.48550/arXiv.1805.10970 |
🟢 |
| v_1k_tpl_by_20210128_schwaller_p_et_al [20] | 10.1038/s42256-020-00284-w |
🟢 |
| v_1976_to_2016_remapped_by_20210407_schwaller_p_et_al [21] | 10.1126/sciadv.abe4166 |
🟢 |
| v_1976_to_2016_remapped_by_20240313_chen_s_et_al [22] | 10.6084/m9.figshare.25046471.v1 |
🟢 |
| v_50k_remapped_by_20240313_chen_s_et_al [22] | 10.6084/m9.figshare.25046471.v1 |
🟢 |
| v_mech_31k_by_20240810_chen_s_et_al [23] | 10.6084/m9.figshare.24797220.v2 |
🟢 |
🟢 Completely Implemented
🟡 Partially Implemented (Limited to Reaction SMILES Strings)
The following Open Reaction Database (ORD) [24] versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_release_0_1_0 [24] | 10.1021/jacs.1c09820 |
🟡 |
| v_release_main [24] | 10.1021/jacs.1c09820 |
🟡 |
🟢 Completely Implemented
🟡 Partially Implemented (Limited to Reaction SMILES Strings)
The following Chemical Reaction Database (CRD) [25] versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_reaction_smiles_2001_to_2021 [25] | 10.6084/m9.figshare.20279733.v1 |
🟢 |
| v_reaction_smiles_2001_to_2023 [25] | 10.6084/m9.figshare.22491730.v1 |
🟢 |
| v_reaction_smiles_2023 [25] | 10.6084/m9.figshare.24921555.v1 |
🟢 |
| v_reaction_smiles_1976_to_2024 [25] | 10.6084/m9.figshare.28230053.v1 |
🟢 |
🟢 Completely Implemented
The following Rhea [26] chemical reaction database versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_release_{release_number ≥ 126} [26] | 10.1093/nar/gkab1016 |
🟢 |
🟢 Completely Implemented
The following miscellaneous chemical reaction data sources are supported:
| Version | DOI | Status |
|---|---|---|
| v_20131008_kraut_h_et_al [27] | 10.1021/ci400442f |
🟢 |
| v_20161014_wei_j_n_et_al [28] | 10.1021/acscentsci.6b00219 |
🟢 |
| v_20200508_grambow_c_et_al [29] | 10.5281/zenodo.3581266 |
🟢 |
| v_add_on_by_20200508_grambow_c_et_al [29] | 10.5281/zenodo.3731553 |
🟢 |
| v_golden_dataset_by_20211103_lin_a_et_al [30] | 10.1002/minf.202100138 |
🟢 |
| v_rdb7_by_20220718_spiekermann_k_et_al [31] | 10.5281/zenodo.5652097 |
🟢 |
| v_orderly_condition_by_20240422_wigh_d_s_et_al [32] | 10.6084/m9.figshare.23298467.v4 |
🟢 |
| v_orderly_forward_by_20240422_wigh_d_s_et_al [32] | 10.6084/m9.figshare.23298467.v4 |
🟢 |
| v_orderly_retro_by_20240422_wigh_d_s_et_al [32] | 10.6084/m9.figshare.23298467.v4 |
🟢 |
🟢 Completely Implemented
The following chemical reaction pattern data sources are supported:
The chemical reaction pattern data source relationships can be illustrated as follows:
The following RetroRules [33] chemical reaction pattern database versions are supported:
| Version | DOI | Status |
|---|---|---|
| v_release_rr01_rp2_hs [33] | 10.5281/zenodo.5827427 |
🟢 |
| v_release_rr02_rp2_hs [33] | 10.5281/zenodo.5828017 |
🟢 |
| v_release_rr02_rp3_hs [33] | 10.5281/zenodo.5827977 |
🟢 |
| v_release_rr02_rp3_nohs [33] | 10.5281/zenodo.5827969 |
🟢 |
🟢 Completely Implemented
The following miscellaneous chemical reaction pattern data sources are supported:
| Version | DOI | Status |
|---|---|---|
| v_retro_transform_db_by_20180421_avramova_s_et_al [34] | 10.5281/zenodo.1209312 |
🟢 |
| v_dingos_by_20190701_button_a_et_al [35] | 10.24433/CO.6930970.v1 |
🟢 |
| v_auto_template_by_20240627_chen_l_and_li_y [36] | 10.1186/s13321-024-00869-2 |
🟢 |
🟢 Completely Implemented
The purpose of the data directory is to archive data sources hosted on GitHub, GitLab, and CodeOcean repositories.
The contents of this repository are published under the MIT license. Please refer to individual references for more details regarding the license information of external resources utilized within this repository.
If you are interested in contributing to this repository by reporting bugs, suggesting improvements, or submitting feedback, feel free to do so using GitHub Issues.
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