| --- |
| license: cc-by-3.0 |
| pretty_name: ProteomeLM gene-essentiality data (OGEE v3) |
| tags: |
| - biology |
| - proteomics |
| - gene-essentiality |
| - proteomelm |
| configs: |
| - config_name: proteins |
| data_files: data/proteins.parquet |
| default: true |
| - config_name: minimal_cells |
| data_files: data/minimal_cells.parquet |
| --- |
| |
| # ProteomeLM gene-essentiality data |
|
|
| The data used to train and evaluate the gene-essentiality classifier of |
| [ProteomeLM](https://github.com/Bitbol-Lab/ProteomeLM) |
| ([PNAS 2026](https://www.pnas.org/doi/10.1073/pnas.2524201123), Fig. 5; trained head: |
| [Bitbol-Lab/ProteomeLM-ess](https://huggingface.co/Bitbol-Lab/ProteomeLM-ess)). |
| The essentiality calls come from **OGEE v3**, the Online GEne Essentiality database |
| ([Gurumayum et al., NAR 2021](https://doi.org/10.1093/nar/gkaa884)). The OGEE website |
| (v3.ogee.info) is currently unavailable, so its tables are mirrored here unmodified under |
| its CC BY 3.0 license. Please cite OGEE, and the primary screens it compiles, when you |
| use these labels. |
|
|
| ## Files |
|
|
| | file | content | |
| |---|---| |
| | `raw/ogee_v3/gene_essentiality.txt` | OGEE essentiality calls (`dataset`, `taxaID`, `locus`, `gene`, `score`, `essentiality`, `pmid`, `Ref_db`) | |
| | `raw/ogee_v3/genes.txt` | OGEE gene annotations | |
| | `raw/ogee_v3/datasets.txt` | OGEE datasets (source, technique, condition, definition of essential) | |
| | `data/proteins.parquet` | 486,681 proteins of 89 genomes, with labels and folds (config `proteins`) | |
| | `data/genomes.tsv` | one row per genome: organism, protein and label counts, role | |
| | `data/minimal_cells.parquet` | JCVI-Syn1.0 and JCVI-Syn3A proteomes and labels (config `minimal_cells`) | |
| | `data/info.json` | split parameters | |
|
|
| ## `proteins` |
|
|
| Each OGEE genome's proteome (UniProt reference proteome, else UniProtKB, else NCBI or the |
| source named in OGEE) with exact duplicates (on the first 4,096 residues) removed. OGEE |
| calls were matched to proteins by gene name, locus tag and synonyms. |
|
|
| | column | | |
| |---|---| |
| | `taxid` | NCBI taxonomy id of the genome | |
| | `protein_id`, `header` | FASTA id and full header line | |
| | `sequence` | amino-acid sequence | |
| | `gene`, `synonyms` | gene name and synonyms used for matching | |
| | `ogee_calls` | all OGEE calls for the gene (`E` essential, `NE` non-essential, `C` conditional, ...) | |
| | `label` | training label: the last `E`/`NE` call, null if none | |
| | `fold` | cross-validation fold: 0 = test, 1 = validation, 2-4 = train | |
| | `fasta_file` | proteome file name in the original pipeline | |
|
|
| 153,918 proteins have a label (42,077 E, 111,841 NE). 82 genomes form the cross-validation set; the others were not used for training: |
|
|
| | taxid | organism | role | proteins | E | NE | |
| |---|---|---|---|---|---| |
| | 83333 | Escherichia coli K-12 | held out (Fig. 5B) | 4,361 | 290 | 3,969 | |
| | 199310 | Escherichia coli CFT073 | excluded | 5,336 | 232 | 0 | |
| | 580240 | Saccharomyces cerevisiae S288C | held out (Fig. 5B) | 5,975 | 939 | 4,353 | |
| | 679895 | Escherichia coli BW25113 | excluded | 4,192 | 313 | 0 | |
| | 941322 | Escherichia coli O25b:H4-ST131 | excluded | 4,821 | 294 | 4,023 | |
| | 1124478 | Vibrio cholerae O1 str. C6706 | excluded | 3,532 | 0 | 0 | |
| | 1380365 | Dyella japonica UNC79MFTsu3.2 | excluded | 4,374 | 0 | 0 | |
|
|
| "Excluded" genomes have fewer than 10 labelled proteins or problematic labels. |
|
|
| **Split.** All 486,681 sequences were clustered with MMseqs2 (`easy-cluster --min-seq-id 0.40`), and whole clusters were assigned at random to 5 folds (seed 0), so proteins sharing ≥40% identity are always in the same fold. Fold sizes: 0: 97,336, 1: 97,339, 2: 97,339, 3: 97,337, 4: 97,330. The released head |
| [ProteomeLM-ess](https://huggingface.co/Bitbol-Lab/ProteomeLM-ess) was trained with an earlier fold |
| assignment, so evaluate it on the held-out genomes and the minimal cells, not on fold 0. |
|
|
| ## `minimal_cells` |
| |
| The minimal cells of Fig. 5B (NCBI proteomes, locus tags as ids). Labels: `E`, `NE`, `QE` |
| (quasi-essential), uncertain calls (`E?`, `NE?`), `Not_a_Gene` and `No_label`. |
|
|
| | organism | taxid | proteins | E | NE | |
| |---|---|---|---|---| |
| | JCVI-Syn1.0 | 766747 | 820 | 202 | 386 | |
| | JCVI-Syn3A | 2144189 | 455 | 199 | 64 | |
|
|
| Sources: Hutchison et al. 2016, *Science* 351:aad6253, Database S1 (JCVI-Syn1.0) and |
| [SynWiki](https://synwiki.uni-goettingen.de) (JCVI-Syn3A). |
|
|
| ## Usage |
|
|
| ```python |
| import pandas as pd |
| proteins = pd.read_parquet("hf://datasets/Bitbol-Lab/ProteomeLM-ess-data/data/proteins.parquet") |
| ``` |
|
|
| or `datasets.load_dataset("Bitbol-Lab/ProteomeLM-ess-data", "proteins")`. To rebuild the input files of the |
| ProteomeLM pipeline (`experiments/essentiality` in the GitHub repository): |
|
|
| ```bash |
| python -m experiments.essentiality.data fetch |
| ``` |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{malbranke2026proteomelm, |
| title={ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa}, |
| author={Malbranke, Cyril and Zalaffi, Gionata Paolo and Bitbol, Anne-Florence}, |
| journal={Proceedings of the National Academy of Sciences}, |
| volume={123}, |
| number={21}, |
| pages={e2524201123}, |
| year={2026}, |
| doi={10.1073/pnas.2524201123} |
| } |
| |
| @article{gurumayum2021ogee, |
| title={OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines}, |
| author={Gurumayum, Sanathoi and Jiang, Puzi and Hao, Xiaowen and Campos, Tulio L and Young, Neil D and Korhonen, Pasi K and Gasser, Robin B and Bork, Peer and Zhao, Xing-Ming and He, Li-jie and Chen, Wei-Hua}, |
| journal={Nucleic Acids Research}, |
| volume={49}, |
| number={D1}, |
| pages={D998--D1003}, |
| year={2021}, |
| doi={10.1093/nar/gkaa884} |
| } |
| ``` |
|
|
