Create readme

README.md

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+---
+license: cc-by-sa-3.0
+---
+
+# 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
+from sklearn.model_selection import train_test_split
+
+train = pd.read_csv('https://services.healthtech.dtu.dk/services/DeepLoc-2.0/data/Swissprot_Train_Validation_dataset.csv')
+train = train.loc[:,['Sequence','Cell membrane', 'Cytoplasm','Endoplasmic reticulum', 'Extracellular', 'Golgi apparatus', 'Lysosome/Vacuole', 'Mitochondrion', 'Nucleus', 'Peroxisome', 'Plastid']]
+train = train.melt('Sequence', var_name='Location').query('value == 1.0').drop(labels='value', axis=1)
+
+train, val = train_test_split(train)
+val = val.reset_index(drop=True)
+
+test = pd.read_csv('https://services.healthtech.dtu.dk/services/DeepLoc-2.0/data/hpa_testset.csv')
+test = test.loc[:,['fasta','Cell membrane', 'Cytoplasm','Endoplasmic reticulum', 'Golgi apparatus', 'Lysosome/Vacuole', 'Mitochondrion', 'Nucleus', 'Peroxisome']].rename(columns={'fasta':'Sequence'})
+test = test.melt('Sequence', var_name='Location').query('value == 1.0').drop(labels='value', axis=1).sample(frac=1).reset_index(drop=True)
+
+train.to_parquet('data/deeploc/deeploc-train.parquet', index=False)
+val.to_parquet('data/deeploc/deploc-val.parquet', index=False)
+test.to_parquet('data/deeploc/deeploc-test.parquet', index=False)
+```
+
+## 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 following datasets:
+
+**UniProt**
+
+```
+The UniProt Consortium
+UniProt: the Universal Protein Knowledgebase in 2023
+Nucleic Acids Res. 51:D523–D531 (2023)
+```
+
+**The Human Protein Atlas**
+
+```
+Mathias Uhlén et al.,Tissue-based map of the human proteome.Science347,1260419(2015).DOI:10.1126/science.1260419
+```