class CbioportalMutation(db.Model):
__tablename__ = 'cbioportal_mutations'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
type = db.Column(db.Text)
cbioportal_aa_change_string = db.Column(db.Text)
mutation_origin = db.Column(db.Text)
validation_status = db.Column(db.Text)
functional_impact_score = db.Column(db.Text)
chromosome_index = db.Column(db.Integer)
chromosome_startpos = db.Column(db.Integer)
chromosome_endpos = db.Column(db.Integer)
reference_dna_allele = db.Column(db.Text)
variant_dna_allele = db.Column(db.Text)
oncotator_aa_pos = db.Column(db.Integer)
oncotator_reference_aa = db.Column(db.Text)
oncotator_variant_aa = db.Column(db.Text)
oncotator_ensembl_transcript_id = db.Column(db.Text)
in_uniprot_domain = db.Column(db.Boolean)
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
uniprot_domain_id = db.Column(db.Integer, db.ForeignKey('uniprot_domains.id'))
cbioportal_case_id = db.Column(db.Integer, db.ForeignKey('cbioportal_cases.id'))
def __repr__(self):
return '<CbioportalMutation ID type {} aa_change {} in_uniprot_domain {}>'.format(
self.type, self.oncotator_aa_pos, self.in_uniprot_domain
)
class EnsemblProtein(db.Model):
__tablename__ = 'ensembl_proteins'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
protein_id = db.Column(db.String(64))
ensembl_gene_id = db.Column(db.Integer, db.ForeignKey('ensembl_genes.id'))
ensembl_transcript_id = db.Column(db.Integer, db.ForeignKey('ensembl_transcripts.id'))
def __repr__(self):
return '<EnsemblProtein ID {}>'.format(self.protein_id)
class UniProtSubcellularLocation(db.Model):
__tablename__ = 'uniprot_subcellular_locations'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
subcellular_location = db.Column(db.Text)
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 '<UniProtSubcellularLocation {}>'.format(self.subcellular_location)
class UniProtDiseaseAssociation(db.Model):
__tablename__ = 'uniprot_disease_associations'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
disease_association = db.Column(db.Text)
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 '<UniProtDiseaseAssociation {}>'.format(self.disease_association)
class EnsemblTranscript(db.Model):
__tablename__ = 'ensembl_transcripts'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
transcript_id = db.Column(db.String(64))
ensembl_proteins = db.relationship('EnsemblProtein', backref='ensembl_transcript', lazy='dynamic')
ensembl_gene_id = db.Column(db.Integer, db.ForeignKey('ensembl_genes.id'))
uniprot_isoform_id = db.Column(db.Integer, db.ForeignKey('uniprot_isoforms.id'))
def __repr__(self):
return '<EnsemblTranscript ID {}>'.format(self.transcript_id)
class UniProtGeneName(db.Model):
__tablename__ = 'uniprot_gene_names'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
gene_name = db.Column(db.String(64))
gene_name_type = db.Column(db.String(64))
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 '<UniProtGeneName {}>'.format(self.gene_name)
class BindingDBBioassay(db.Model):
__tablename__ = 'bindingdb_bioassays'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
bindingdb_source = db.Column(db.Text)
doi = db.Column(db.String(64))
pmid = db.Column(db.Integer)
temperature = db.Column(db.String(64))
ph = db.Column(db.String(64))
target_name = db.Column(db.Text)
ligand_bindingdb_id = db.Column(db.Integer)
ligand_chembl_id = db.Column(db.String(64))
ligand_smiles_string = db.Column(db.Text)
ligand_zinc_id = db.Column(db.String(64))
ki = db.Column(db.String(64))
ic50 = db.Column(db.String(64))
kd = db.Column(db.String(64))
ec50 = db.Column(db.String(64))
kon = db.Column(db.String(64))
koff = db.Column(db.String(64))
# measurements = db.relationship('BindingDBMeasurement', backref='bindingdb_bioassay', lazy='dynamic')
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<BindingDBBioassay source {}>'.format(self.bindingdb_source)
class NCBIGenePublication(db.Model):
__tablename__ = 'ncbi_gene_publication'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
pmid = db.Column(db.Integer)
ncbi_gene_entry_id = db.Column(db.Integer, db.ForeignKey('ncbi_gene_entries.id'))
def __repr__(self):
return '<NCBIGenePublication PMID {}>'.format(self.pmid)
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 PDBChain(db.Model):
__tablename__ = 'pdb_chains'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
chain_id = db.Column(db.String(64))
begin = db.Column(db.Integer)
end = db.Column(db.Integer)
experimental_seq = db.Column(db.Text)
experimental_seq_aln_conflicts = db.Column(db.Text)
experimental_seq_len = db.Column(db.Integer)
observed_seq_aln_exp = db.Column(db.Text)
observed_seq_aln = db.Column(db.Text)
observed_ss_aln = db.Column(db.Text)
pdb_entry_id = db.Column(db.Integer, db.ForeignKey('pdb_entries.id'))
uniprot_domain_id = db.Column(db.Integer, db.ForeignKey('uniprot_domains.id'))
def __repr__(self):
return '<PDBChain ID {}>'.format(self.chain_id)
class UniProtIsoformNote(db.Model):
__tablename__ = 'uniprot_isoform_notes'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
note = db.Column(db.Text)
uniprot_isoform_id = db.Column(db.Integer, db.ForeignKey('uniprot_isoforms.id'))
def __repr__(self):
return '<UniProtIsoformNote {}>'.format(self.note)
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 HGNCEntry(db.Model):
__tablename__ = 'hgnc_entries'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
gene_id = db.Column(db.String(64))
approved_symbol = db.Column(db.String(64))
db_entry_id = db.Column(db.Integer, db.ForeignKey('db_entries.id'))
def __repr__(self):
return '<HGNCEntry approved_symbol {}>'.format(self.approved_symbol)
class PDBExpressionData(db.Model):
__tablename__ = 'pdb_expression_data'
id = db.Column(db.Integer, primary_key=True)
crawl_number = db.Column(db.Integer)
expression_data_type = db.Column(db.String(64))
expression_data_value = db.Column(db.Text)
pdb_entry_id = db.Column(db.Integer, db.ForeignKey('pdb_entries.id'))
def __repr__(self):
return '<PDBExpressionData type {}>'.format(self.expression_data_type)
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 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 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)
