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from django.core.exceptions import ValidationError
from django.db import models
# Main biological and medical entities
class Tissue(models.Model):
name = models.CharField(max_length=128, default='', unique=True)
def __str__(self):
return self.name
class PPIDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
def __str__(self):
return f'{self.name}-{self.version}'
class Meta:
unique_together = ('name', 'version')
class PDIDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
def __str__(self):
return f'{self.name}-{self.version}'
class Meta:
unique_together = ('name', 'version')
class PDisDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
def __str__(self):
return f'{self.name}-{self.version}'
class Meta:
unique_together = ('name', 'version')
class DrDiDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
def __str__(self):
return f'{self.name}-{self.version}'
class Meta:
unique_together = ('name', 'version')
class ExpressionLevel(models.Model):
tissue = models.ForeignKey('Tissue', on_delete=models.CASCADE)
protein = models.ForeignKey('Protein', on_delete=models.CASCADE)
expression_level = models.FloatField()
class Meta:
unique_together = ('tissue', 'protein')
class EnsemblGene(models.Model):
name = models.CharField(max_length=15, unique=True) # starts with ENSG...
protein = models.ForeignKey('Protein', on_delete=models.CASCADE, related_name='ensg')
class Protein(models.Model):
# According to https://www.uniprot.org/help/accession_numbers UniProt accession codes
# are either 6 or 10 characters long
uniprot_code = models.CharField(max_length=10)
gene = models.CharField(max_length=128, default='') # symbol
protein_name = models.CharField(max_length=128, default='')
entrez = models.CharField(max_length=128, default='')
drugs = models.ManyToManyField('Drug', through='ProteinDrugInteraction',
related_name='interacting_drugs')
tissue_expression = models.ManyToManyField('Tissue', through='ExpressionLevel',
related_name='interacting_drugs')
class Meta:
unique_together = ('uniprot_code', 'gene', 'entrez')
def __str__(self):
return self.gene
class Disorder(models.Model):
mondo_id = models.CharField(max_length=7)
label = models.CharField(max_length=256, default='') # symbol
icd10 = models.CharField(max_length=128, default='')
proteins = models.ManyToManyField(
'Protein', through='ProteinDisorderAssociation', related_name='associated_proteins')
class Meta:
unique_together = ('mondo_id', 'label', 'icd10')
def __str__(self):
return self.label
class ProteinDisorderAssociation(models.Model):
pdis_dataset = models.ForeignKey(
'PDisDataset', null=True, on_delete=models.CASCADE, related_name='pdis_dataset_relation')
protein = models.ForeignKey('Protein', on_delete=models.CASCADE)
disorder = models.ForeignKey('Disorder', on_delete=models.CASCADE)
score = models.FloatField()
class Meta:
unique_together = ('pdis_dataset', 'protein', 'disorder')
def __str__(self):
return f'{self.pdis_dataset}-{self.protein}-{self.disorder}'
class DrugDisorderIndication(models.Model):
drdi_dataset = models.ForeignKey(
'DrDiDataset', null=True, on_delete=models.CASCADE, related_name='drdi_dataset_relation')
drug = models.ForeignKey('Drug', on_delete=models.CASCADE)
disorder = models.ForeignKey('Disorder', on_delete=models.CASCADE)
class Meta:
unique_together = ('drdi_dataset', 'drug', 'disorder')
def __str__(self):
return f'{self.drdi_dataset}-{self.drug}-{self.disorder}'
class Drug(models.Model):
drug_id = models.CharField(max_length=10, unique=True)
name = models.CharField(max_length=256, default='')
status = models.CharField(max_length=128, default='')
# in_trial = models.BooleanField(default=False)
# in_literature = models.BooleanField(default=False)
links = models.CharField(max_length=16*1024, default='')
def __str__(self):
return self.drug_id
class ProteinProteinInteraction(models.Model):
ppi_dataset = models.ForeignKey(
'PPIDataset', null=True, on_delete=models.CASCADE, related_name='ppi_dataset_relation')
from_protein = models.ForeignKey('Protein', on_delete=models.CASCADE, related_name='interacting_proteins_out')
to_protein = models.ForeignKey('Protein', on_delete=models.CASCADE, related_name='interacting_proteins_in')
def validate_unique(self, exclude=None):
p1p2_q = ProteinProteinInteraction.objects.filter(
from_protein=self.from_protein,
to_protein=self.to_protein,
ppi_dataset=self.ppi_dataset
)
p2p1_q = ProteinProteinInteraction.objects.filter(
from_protein=self.to_protein,
to_protein=self.from_protein,
ppi_dataset=self.ppi_dataset
)
if p1p2_q.exists() or p2p1_q.exists():
raise ValidationError('Protein-Protein interaction must be unique!')
def save(self, *args, **kwargs):
self.validate_unique()
super(ProteinProteinInteraction, self).save(*args, **kwargs)
def __str__(self):
return f'{self.ppi_dataset}-{self.from_protein}-{self.to_protein}'
class ProteinDrugInteraction(models.Model):
pdi_dataset = models.ForeignKey(
'PDIDataset', null=True, on_delete=models.CASCADE, related_name='pdi_dataset_relation')
protein = models.ForeignKey('Protein', on_delete=models.CASCADE)
drug = models.ForeignKey('Drug', on_delete=models.CASCADE)
class Meta:
unique_together = ('pdi_dataset', 'protein', 'drug')
def __str__(self):
return f'{self.pdi_dataset}-{self.protein}-{self.drug}'
class Task(models.Model):
token = models.CharField(max_length=32, unique=True)
created_at = models.DateTimeField(auto_now_add=True)
target = models.CharField(max_length=32, choices=[('drug', 'Drug'), ('drug-target', 'Drug Target')])
algorithm = models.CharField(max_length=128)
parameters = models.TextField()
progress = models.FloatField(default=0.0) # Progress as fraction (0.0 - 1.0)
started_at = models.DateTimeField(null=True)
finished_at = models.DateTimeField(null=True)
worker_id = models.CharField(max_length=128, null=True)
job_id = models.CharField(max_length=128, null=True)
done = models.BooleanField(default=False)
failed = models.BooleanField(default=False)
status = models.CharField(max_length=255, null=True)
result = models.TextField(null=True)
class Network(models.Model):
id = models.CharField(primary_key=True, max_length=32, unique=True)
created_at = models.DateTimeField(auto_now_add=True)
nodes = models.TextField(null=True, default='')
edges = models.TextField(null=True, default='')
config = models.TextField(null=True, default='')