File size: 1,835 Bytes
7a718ee 6c1102a 7a718ee 6c1102a 10ca462 3a4a990 7a718ee 6c1102a 7a718ee 6c1102a 7a718ee 6c1102a 7a718ee 3a4a990 7a718ee 6c1102a 7a718ee |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 |
---
license: cc-by-4.0
---
# DeepLoc-2.0 Training Data
Dataset from https://services.healthtech.dtu.dk/services/DeepLoc-2.0/ used to train the DeepLoc-2.0 model.
## Data preparation
Data downloaded and processed using the following Python script:
```python
import pandas as pd
df = pd.read_csv('https://services.healthtech.dtu.dk/services/DeepLoc-2.0/data/Swissprot_Train_Validation_dataset.csv').drop(['Unnamed: 0', 'Partition'], axis=1)
df['labels'] = df[['Cell membrane', 'Cytoplasm','Endoplasmic reticulum', 'Extracellular', 'Golgi apparatus', 'Lysosome/Vacuole', 'Mitochondrion', 'Nucleus', 'Peroxisome', 'Plastid']].astype('float32').values.tolist()
df['Membrane'] = df['Membrane'].astype('float32')
df = df[['Kingdom', 'ACC', 'Sequence','Membrane','labels']]
train = df.sample(frac=0.8)
df = df.drop(train.index)
val = df.sample(frac=0.5)
test = df.drop(val.index)
train = train.reset_index(drop=True)
val = val.reset_index(drop=True)
test = test.reset_index(drop=True)
train.to_parquet('deeploc-train.parquet', index=False)
val.to_parquet('deploc-val.parquet', index=False)
test.to_parquet('deeploc-test.parquet', index=False)
```
## Labels
{'Cell membrane': 0,
'Cytoplasm': 1,
'Endoplasmic reticulum': 2,
'Extracellular': 3,
'Golgi apparatus': 4,
'Lysosome/Vacuole': 5,
'Mitochondrion': 6,
'Nucleus': 7,
'Peroxisome': 8,
'Plastid': 9}
## Citation
**DeepLoc-2.0:**
```
Vineet Thumuluri and others, DeepLoc 2.0: multi-label subcellular localization prediction using protein language models, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W228–W234, https://doi.org/10.1093/nar/gkac278
```
The DeepLoc data is a derivative of the UniProt dataset:
**UniProt**
```
The UniProt Consortium
UniProt: the Universal Protein Knowledgebase in 2023
Nucleic Acids Res. 51:D523–D531 (2023)
```
|