class EnsemblGene(db.Model):
__tablename__ = 'ensembl_genes'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
gene_id = db.Column(db.String(64))
ensembl_transcripts = db.relationship('EnsemblTranscript', backref='ensembl_gene', lazy='dynamic')
ensembl_proteins = db.relationship('EnsemblProtein', backref='ensembl_gene', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<EnsemblGene ID {}>'.format(self.gene_id)
class PDBEntry(db.Model):
__tablename__ = 'pdb_entries'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
pdb_id = db.Column(db.String(64))
method = db.Column(db.Text)
resolution = db.Column(db.Float)
chains = db.relationship('PDBChain', backref='pdb_entry', lazy='dynamic')
expression_data = db.relationship('PDBExpressionData', backref='pdb_entry', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<PDBEntry ID {}>'.format(self.pdb_id)
class UniProtIsoform(db.Model):
__tablename__ = 'uniprot_isoforms'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
ac = db.Column(db.String(64))
is_canonical = db.Column(db.Boolean)
length = db.Column(db.Integer)
mass = db.Column(db.Integer)
date_modified = db.Column(db.String(64))
version = db.Column(db.Integer)
sequence = db.Column(db.Text)
notes = db.relationship('UniProtIsoformNote', backref='uniprot_isoform', lazy='dynamic')
ensembl_transcripts = db.relationship('EnsemblTranscript', backref='uniprot_isoform', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
uniprot_id = db.Column(db.Integer, db.ForeignKey('uniprot_entries.id'))
def __repr__(self):
return '<UniProtIsoform {} canonical: {}>'.format(self.ac, self.is_canonical)
class CbioportalCase(db.Model):
__tablename__ = 'cbioportal_cases'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
study = db.Column(db.Text)
case_id = db.Column(db.Text)
mutations = db.relationship('CbioportalMutation', backref='cbioportal_case', lazy='dynamic')
def __repr__(self):
return '<CbioportalCase ID {0}>'.format(self.case_id)
class NCBIGeneEntry(db.Model):
__tablename__ = 'ncbi_gene_entries'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
gene_id = db.Column(db.Integer)
publications = db.relationship('NCBIGenePublication', backref='ncbi_gene_entry', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<NCBIGeneEntry ID {}>'.format(self.gene_id)
class UniProtDomain(db.Model):
__tablename__ = 'uniprot_domains'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
domain_id = db.Column(db.Integer)
target_id = db.Column(db.String(64)) # ABL1_HUMAN_D0 (Protein kinase)
is_target_domain = db.Column(db.Boolean)
description = db.Column(db.Text())
begin = db.Column(db.Integer)
end = db.Column(db.Integer)
length = db.Column(db.Integer)
sequence = db.Column(db.Text)
is_pseudodomain = db.Column(db.Boolean)
pseudodomain_notes = db.Column(db.Text)
pdb_chains = db.relationship('PDBChain', backref='uniprot_domain', lazy='dynamic')
cbioportal_mutations = db.relationship('CbioportalMutation', backref='uniprot_domain', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
uniprot_id = db.Column(db.Integer, db.ForeignKey('uniprot_entries.id'))
def __repr__(self):
return '<UniProtDomain description {}>'.format(self.description)
class UniProtEntry(db.Model):
__tablename__ = 'uniprot_entries'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
ac = db.Column(db.String(64))
entry_name = db.Column(db.String(64))
family = db.Column(db.String(64))
recommended_name = db.Column(db.Text)
ncbi_taxon_id = db.Column(db.String(64))
taxon_name_scientific = db.Column(db.String(120))
taxon_name_common = db.Column(db.String(120))
lineage = db.Column(db.Text) # ascending comma-separated values
last_uniprot_update = db.Column(db.String(64))
isoforms = db.relationship('UniProtIsoform', backref='uniprot_entry', lazy='dynamic')
domains = db.relationship('UniProtDomain', backref='uniprot_entry', lazy='dynamic')
gene_names = db.relationship('UniProtGeneName', backref='uniprot_entry', lazy='dynamic')
functions = db.relationship('UniProtFunction', backref='uniprot_entry', lazy='dynamic')
disease_associations = db.relationship('UniProtDiseaseAssociation', backref='uniprot_entry', lazy='dynamic')
subcellular_locations = db.relationship('UniProtSubcellularLocation', backref='uniprot_entry', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<UniProtEntry AC {} entry_name {}>'.format(self.ac, self.entry_name)
class DBEntry(db.Model):
"""
Essentially a "top-level" table for uniting all data types.
Represents a "biological entity" - incorporating gene, transcript, and protein data.
"""
__tablename__ = 'db_entries'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
npdbs = db.Column(db.Integer)
ndomains = db.Column(db.Integer)
nisoforms = db.Column(db.Integer)
nfunctions = db.Column(db.Integer)
ndisease_associations = db.Column(db.Integer)
npubs = db.Column(db.Integer)
nbioassays = db.Column(db.Integer)
uniprot = db.relationship('UniProtEntry', backref='db_entry', lazy='dynamic')
uniprot_domains = db.relationship('UniProtDomain', backref='db_entry', lazy='dynamic')
uniprot_gene_names = db.relationship('UniProtGeneName', backref='db_entry', lazy='dynamic')
uniprot_isoforms = db.relationship('UniProtIsoform', backref='db_entry', lazy='dynamic')
uniprot_functions = db.relationship('UniProtFunction', backref='db_entry', lazy='dynamic')
uniprot_disease_associations = db.relationship('UniProtDiseaseAssociation', backref='db_entry', lazy='dynamic')
uniprot_subcellular_locations = db.relationship('UniProtSubcellularLocation', backref='db_entry', lazy='dynamic')
pdbs = db.relationship('PDBEntry', backref='db_entry', lazy='dynamic')
ncbi_gene_entries = db.relationship('NCBIGeneEntry', backref='db_entry', lazy='dynamic')
ensembl_genes = db.relationship('EnsemblGene', backref='db_entry', lazy='dynamic')
hgnc_entries = db.relationship('HGNCEntry', backref='db_entry', lazy='dynamic')
bindingdb_bioassays = db.relationship('BindingDBBioassay', backref='db_entry', lazy='dynamic')
cbioportal_mutations = db.relationship('CbioportalMutation', backref='db_entry', lazy='dynamic')
def __repr__(self):
return '<DBEntry {}>'.format(self.id)