class GeneNetworkDisease(db.Model):
__tablename__ = 'gene_network_disease'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(32), nullable=True)
disease = db.Column(db.String(255), nullable=True)
weight = db.Column(db.Float, nullable=True)
dataset = db.Column(db.String(8), nullable=True)
class AppConfig(db.Model):
__tablename__ = 'app_config'
key = db.Column(db.Text(), primary_key=True)
value = db.Column(JSONB(), nullable=True)
@classmethod
def get_config_value(cls, key):
config = db.session.query(cls).get(key)
return config.value if config else None
class ExpressionRNASeqDisease(db.Model, MappingTableMixin):
__tablename__ = 'expression_rna_seq_disease'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True, index=True)
ensembl_id = db.Column(db.String(128), nullable=True)
age_related_macular_degeneration = db.Column(db.Float, nullable=True)
diabetic_retinopathy = db.Column(db.Float, nullable=True)
keratoconus = db.Column(db.Float, nullable=True)
primary_open_angle_glaucoma = db.Column(db.Float, nullable=True)
retinitis_pigmentosa = db.Column(db.Float, nullable=True)
retinoblastoma = db.Column(db.Float, nullable=True)
def to_json(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'age_related_macular_degeneration':
self.age_related_macular_degeneration,
'diabetic_retinopathy': self.diabetic_retinopathy,
'keratoconus': self.keratoconus,
'primary_open_angle_glaucoma': self.primary_open_angle_glaucoma,
'retinitis_pigmentosa': self.retinitis_pigmentosa,
'retinoblastoma': self.retinoblastoma,
}
return self.map_to_names(result)
def to_json_analysis(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'age_related_macular_degeneration':
self.age_related_macular_degeneration,
'diabetic_retinopathy': self.diabetic_retinopathy,
'keratoconus': self.keratoconus,
'primary_open_angle_glaucoma': self.primary_open_angle_glaucoma,
'retinitis_pigmentosa': self.retinitis_pigmentosa,
'retinoblastoma': self.retinoblastoma,
}
return result
@classmethod
def column_mappings(cls):
return {
'age_related_macular_degeneration':
'Age-related macular degeneration',
'diabetic_retinopathy': 'Diabetic retinopathy',
'keratoconus': 'Keratoconus',
'primary_open_angle_glaucoma': 'Primary open-angle glaucoma',
'retinitis_pigmentosa': 'Retinitis pigmentosa',
'retinoblastoma': 'Retinoblastoma',
}
class GeneTissueCorrect(db.Model):
__tablename__ = 'gene_tissue_correct'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(32), nullable=True)
module = db.Column(db.String(32), nullable=True)
kme = db.Column(db.String(32), nullable=True)
tissue = db.Column(db.String(32), nullable=True)
def to_json(self):
return {
'gene': self.gene,
'module': self.module,
'kme': self.kme,
}
class Gnomad(db.Model):
__tablename__ = 'gnomad'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
chromosome = db.Column(db.String(2), nullable=True)
scope = db.Column(db.String(16), nullable=True)
variant = db.Column(db.String(16), nullable=True, index=True)
territory = db.deferred(db.Column(JSONB, default={}, nullable=True))
def to_json(self):
return {
'id': self.id,
'chromosome': self.chromosome,
'scope': self.scope,
'variant': self.variant,
'territory': self.territory,
}
class Epigenomics(db.Model):
__tablename__ = 'epigenomics'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
file_url = db.Column(db.String(256), nullable=False)
disease = db.Column(db.String(128), nullable=False)
data_type = db.Column(db.String(16), nullable=False)
def to_json(self, **kwargs):
result = {
'id': self.id,
'url': self.file_url,
'disease': self.disease,
'data_type': self.data_type,
'data_key': self.disease + '/' + self.data_type,
}
result.update(kwargs)
return result
class CornealEndothelialCells(db.Model):
__tablename__ = 'corneal_endothelial_cells'
id = db.Column(Integer, primary_key=True, autoincrement=True)
gene = db.Column(db.String(32), nullable=True)
contrast_gene = db.Column(db.String(32), nullable=True)
weight = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'gene': self.gene,
'contrast_gene': self.contrast_gene,
'weight': self.weight
}
def to_reverse_json(self):
return {
'gene': self.contrast_gene,
'contrast_gene': self.gene,
'weight': self.weight
}
class AgeRelatedMacularDegeneration(db.Model):
__tablename__ = 'age_related_macular_degeneration'
id = db.Column(Integer, primary_key=True, autoincrement=True)
gene = db.Column(db.String(32), nullable=True)
contrast_gene = db.Column(db.String(32), nullable=True)
weight = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'gene': self.gene,
'contrast_gene': self.contrast_gene,
'weight': self.weight
}
def to_reverse_json(self):
return {
'gene': self.contrast_gene,
'contrast_gene': self.gene,
'weight': self.weight
}
class Retinoblastoma(db.Model):
__tablename__ = 'retinoblastoma'
id = db.Column(Integer, primary_key=True, autoincrement=True)
gene = db.Column(db.String(32), nullable=True)
contrast_gene = db.Column(db.String(32), nullable=True)
weight = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'gene': self.gene,
'contrast_gene': self.contrast_gene,
'weight': self.weight
}
def to_reverse_json(self):
return {
'gene': self.contrast_gene,
'contrast_gene': self.gene,
'weight': self.weight
}
class MarkersCell(db.Model):
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True)
cluster = db.Column(db.Integer, nullable=True)
labels = db.Column(db.String(128), nullable=True)
p_val = db.Column(db.Float, nullable=True)
avg = db.Column(db.Float, nullable=True)
p_val_adj = db.Column(db.Float, nullable=True)
pct1 = db.Column(db.Float, nullable=True)
pct2 = db.Column(db.Float, nullable=True)
cell_type = db.Column(db.String(32), nullable=True)
def to_json(self):
return {
'id': self.id,
'gene': self.gene,
'cluster': self.cluster,
'labels': self.labels,
'p_val': self.p_val,
'avg_logFC': self.avg,
'p_val_adj': self.p_val_adj,
'pct.1': self.pct1,
'pct.2': self.pct2,
}
class OutCell(db.Model):
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
name = db.Column(db.String(128), nullable=True)
xaxis = db.Column(db.Float, nullable=True)
yaxis = db.Column(db.Float, nullable=True)
cluster = db.Column(db.String(4), nullable=True)
labels = db.Column(db.String(64), nullable=True)
cell_type = db.Column(db.String(32), nullable=True)
def to_json(self):
return {
'id': self.id,
'name': self.name,
'xaxis': self.xaxis,
'yaxis': self.yaxis,
'cluster': self.cluster,
'labels': self.labels,
}
class GeneDiseaseSignificance(db.Model):
__tablename__ = 'gene_disease_significance'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(32), nullable=True)
amd = db.Column(db.Float, nullable=True)
dr = db.Column(db.Float, nullable=True)
kc = db.Column(db.Float, nullable=True)
glc = db.Column(db.Float, nullable=True)
rp = db.Column(db.Float, nullable=True)
rb = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'id': self.id,
'gene': self.gene,
'amd': self.amd,
'dr': self.dr,
'kc': self.kc,
'glc': self.glc,
'rp': self.rp,
'rb': self.rb
}
class GeneExpression(db.Model):
__tablename__ = 'gene_expression'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene_id = db.Column(db.String(32), nullable=True)
disease = db.Column(db.String(255), nullable=True)
gene = db.Column(db.String(32), nullable=True, index=True)
value = db.Column(db.Float, nullable=True)
color = db.Column(db.String(50), nullable=True)
def to_json(self):
return {
'id': self.id,
'gene_id': self.gene_id,
'disease': self.disease,
'gene': self.gene,
'value': self.value or 0
}
class EpigeneticAlteration(db.Model):
__tablename__ = 'epigenetic_alteration'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True, index=True)
normal_retina = db.Column(db.Float, nullable=True)
amd_retina = db.Column(db.Float, nullable=True)
normal_rpe = db.Column(db.Float, nullable=True)
amd_rpe = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'gene': self.gene,
'normal_retina': self.normal_retina,
'amd_retina': self.amd_retina,
'normal_rpe': self.normal_retina,
'amd_rpe': self.amd_rpe
}
class Causality(db.Model):
__tablename__ = 'causality'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
variant = db.Column(db.String(16), nullable=True, index=True)
p_value = db.Column(db.Float, nullable=True)
beta = db.Column(db.Float, nullable=True)
disease = db.Column(db.String(255), nullable=True)
color = db.Column(db.String(50), nullable=True)
def to_json(self):
return {
'id': self.id,
'variant': self.variant,
'p_value': self.p_value,
'beta': self.beta or 0,
'disease': self.disease,
'color': self.color
}
class Summary(db.Model):
__tablename__ = 'summary'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
snpid = db.Column(db.String(32), nullable=True)
position_hg38 = db.Column(db.String(32), nullable=True)
major_allele = db.Column(db.String(1024), nullable=True)
variant = db.Column(db.String(128), nullable=True)
protein = db.Column(db.String(64), nullable=True)
polyphen = db.Column(db.String(32), nullable=True)
cadd = db.Column(db.String(32), nullable=True)
sift = db.Column(db.String(32), nullable=True)
gerp = db.Column(db.String(32), nullable=True)
gene = db.Column(db.String(128), nullable=True)
ensembl = db.Column(db.Text, nullable=True)
dbsnp = db.Column(db.Text, nullable=True)
gnomad = db.Column(db.Text, nullable=True)
def to_json(self):
return {
'id': self.id,
'snpid': self.snpid,
'position_hg38': self.position_hg38,
'major_allele': self.major_allele,
'variant': self.variant,
'protein': self.protein,
'polyphen': self.polyphen,
'cadd': self.cadd,
'sift': self.sift,
'gerp': self.gerp,
'gene': self.gene,
'ensembl': self.ensembl,
'dbsnp': self.dbsnp,
'gnomad': self.gnomad,
}
def to_list(self):
return {
'id': self.id,
'name': self.snpid,
}
class ExpressionMicroarrayTissue(db.Model, MappingTableMixin):
__tablename__ = 'expression_microarray_tissue'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True, index=True)
ensembl_id = db.Column(db.String(128), nullable=True)
retina = db.Column(db.Float, nullable=True)
corneal = db.Column(db.Float, nullable=True)
corneal_epithelium = db.Column(db.Float, nullable=True)
corneal_endothelium = db.Column(db.Float, nullable=True)
conjunctiva = db.Column(db.Float, nullable=True)
optic_nerve_head = db.Column(db.Float, nullable=True)
lymphoblast = db.Column(db.Float, nullable=True)
eye_orbit = db.Column(db.Float, nullable=True)
lacrimal_gland = db.Column(db.Float, nullable=True)
thyroid = db.Column(db.Float, nullable=True)
normal_uveal_melanocytes = db.Column(db.Float, nullable=True)
def to_json(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'retina': self.retina,
'corneal': self.corneal,
'corneal_epithelium': self.corneal_epithelium,
'corneal_endothelium': self.corneal_endothelium,
'conjunctiva': self.conjunctiva,
'optic_nerve_head': self.optic_nerve_head,
'lymphoblast': self.lymphoblast,
'eye_orbit': self.eye_orbit,
'lacrimal_gland': self.lacrimal_gland,
'thyroid': self.thyroid,
'normal_uveal_melanocytes': self.normal_uveal_melanocytes,
}
return self.map_to_names(result)
@classmethod
def column_mappings(cls):
return {
'retina': 'Retina',
'corneal': 'Corneal',
'corneal_epithelium': 'Corneal epithelium',
'corneal_endothelium': 'Corneal endothelium',
'conjunctiva': 'Conjunctiva',
'optic_nerve_head': 'Optic nerve head',
'lymphoblast': 'Lymphoblast',
'eye_orbit': 'Eye Orbit',
'lacrimal_gland': 'Lacrimal gland',
'thyroid': 'Thyroid',
'normal_uveal_melanocytes': 'Normal uveal melanocytes',
}
class GeneticGWAS(db.Model):
__tablename__ = 'genetic_gwas'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene_id = db.Column(db.String(16), nullable=True)
chromosome = db.Column(db.String(2), nullable=True)
scope = db.Column(db.String(16), nullable=True)
gene = db.Column(db.String(32), nullable=True)
variant = db.Column(db.String(255), nullable=True)
major_allele = db.Column(db.String(32), nullable=True)
minor_allele = db.Column(db.String(128), nullable=True)
band = db.Column(db.String(32), nullable=True)
ensembl = db.Column(db.String(255), nullable=True)
p_value = db.Column(db.Float, nullable=True)
beta = db.Column(db.Float, nullable=True)
context = db.Column(db.String(128), nullable=True)
cadd = db.Column(db.String(32), nullable=True)
polyphen = db.Column(db.String(32), nullable=True)
sift = db.Column(db.String(32), nullable=True)
phylop = db.Column(db.String(32), nullable=True)
study = db.Column(db.Text, nullable=True)
initial_sample_size = db.Column(db.Text, nullable=True)
peplication_sample_size = db.Column(db.Text, nullable=True)
disease = db.Column(db.String(255), nullable=True, index=True)
pubmed = db.Column(db.String(255), nullable=True)
drug = db.Column(db.String(32), nullable=True)
def to_variant(self):
return {'id': self.variant, 'name': self.variant, 'type': 'variant'}
def to_json(self):
return {
'id': self.id,
'gene_id': self.gene_id,
'chromosome': self.chromosome,
'scope': self.scope,
'variant_': self.variant,
'gene': self.gene,
'major_allele': self.major_allele,
'minor_allele': self.minor_allele,
'band': self.band,
'ensembl': self.ensembl,
'p_value': self.p_value,
'beta': self.beta,
'context': self.context,
'cadd': self.cadd,
'polyphen': self.polyphen,
'sift': self.sift,
'phylop': self.phylop,
'study': self.study,
'initial_sample_size': self.initial_sample_size,
'peplication_sample_size': self.peplication_sample_size,
'disease': self.disease,
'pubmed': self.pubmed,
}
def to_json_disease(self):
return {
'gene_id': self.gene_id,
'symbol': self.gene,
'band': self.band,
'variants': self.variant,
'position_hg38': self.ensembl.lower(),
'major_allele': self.major_allele,
'minor_allele': self.minor_allele,
'p_value': self.p_value,
'beta': self.beta,
'context': self.context,
'cadd': self.cadd,
'initial': self.initial_sample_size,
'peplication': self.peplication_sample_size,
'pubmed': self.pubmed,
'disease': self.disease,
}
class GeneticOMIM(db.Model):
__tablename__ = 'genetic_omim'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene_id = db.Column(db.String(32), nullable=True)
gene = db.Column(db.String(32), nullable=True)
gene_name = db.Column(db.String(128), nullable=True)
variant = db.Column(db.String(255), nullable=True)
summary = db.Column(db.Text, nullable=True)
band = db.Column(db.String(32), nullable=True)
omim = db.Column(db.String(16), nullable=True)
ensembl = db.Column(db.String(128), nullable=True)
synonyms = db.Column(db.String(128), nullable=True)
location = db.Column(db.Text, nullable=True)
clinvar = db.Column(db.Text, nullable=True)
decipher = db.Column(db.Text, nullable=True)
gnomad = db.Column(db.Text, nullable=True)
pubmed = db.Column(db.Text, nullable=True)
disease = db.Column(db.String(255), nullable=True, index=True)
disease_omim = db.Column(db.String(16), nullable=True)
confidence = db.Column(db.String(32), nullable=True)
publications = db.Column(db.Text, nullable=True)
phenotypes_in_omim = db.Column(db.Text, nullable=True)
phenotypes_in_hpo = db.Column(db.String(128), nullable=True)
drug = db.Column(db.String(32), nullable=True)
def to_json(self):
return {
'id': self.id,
'gene_id': self.gene_id,
'gene': self.gene,
'gene_name': self.gene_name,
'variant': self.variant,
'summary': self.summary,
'band': self.band,
'omim': self.omim,
'ensembl': self.ensembl,
'synonyms': self.synonyms,
'location': self.location,
'clinvar': self.clinvar,
'decipher': self.decipher,
'gnomad': self.gnomad,
'disease': self.disease,
'pubmed': self.pubmed,
'disease_omim': self.disease_omim,
'confidence': self.confidence,
'publications': self.publications,
'phenotypes_in_omim': self.phenotypes_in_omim,
'phenotypes_in_hpo': self.phenotypes_in_hpo,
}
def to_json_disease(self):
return {
"gene_id": self.gene_id,
"symbol": self.gene,
"band": self.band,
"name": self.gene_name,
"variants": self.variant,
"ensembl": self.ensembl,
"omim": self.omim,
'phenotype': self.phenotypes_in_omim,
"confidence": self.confidence,
'pubmed': self.pubmed,
'disease': self.disease,
}
class ExpressionMouse(db.Model, MappingTableMixin):
__tablename__ = 'expression_mouse'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True)
human = db.Column(db.String(255), nullable=True)
e10_5 = db.Column(db.Float, nullable=True)
e11_5 = db.Column(db.Float, nullable=True)
e12_5 = db.Column(db.Float, nullable=True)
e13_5 = db.Column(db.Float, nullable=True)
web1_e10_5__12_5 = db.Column(db.Float, nullable=True)
web2_e11_5__13_5 = db.Column(db.Float, nullable=True)
p8_a = db.Column(db.Float, nullable=True)
p8_b = db.Column(db.Float, nullable=True)
p12_a = db.Column(db.Float, nullable=True)
p12_b = db.Column(db.Float, nullable=True)
p20_a = db.Column(db.Float, nullable=True)
p20_b = db.Column(db.Float, nullable=True)
p42_a = db.Column(db.Float, nullable=True)
p42_b = db.Column(db.Float, nullable=True)
p52_a = db.Column(db.Float, nullable=True)
p52_b = db.Column(db.Float, nullable=True)
web_p10_11_12_a = db.Column(db.Float, nullable=True)
web_p10_11_12_b = db.Column(db.Float, nullable=True)
def to_json(self):
result = {
'id': self.id,
'gene': self.gene,
'human': self.human,
'e10_5': self.e10_5,
'e11_5': self.e11_5,
'e12_5': self.e12_5,
'e13_5': self.e13_5,
'web1_e10_5__12_5': self.web1_e10_5__12_5,
'web2_e11_5__13_5': self.web2_e11_5__13_5,
'p8_a': self.p8_a,
'p8_b': self.p8_b,
'p12_a': self.p12_a,
'p12_b': self.p12_b,
'p20_a': self.p20_a,
'p20_b': self.p20_b,
'p42_a': self.p42_a,
'p42_b': self.p42_b,
'p52_a': self.p52_a,
'p52_b': self.p52_b,
'web_p10_11_12_a': self.web_p10_11_12_a,
'web_p10_11_12_b': self.web_p10_11_12_b,
}
return self.map_to_names(result)
@classmethod
def column_mappings(cls):
return {
'e10_5': 'E10.5',
'e11_5': 'E11.5',
'e12_5': 'E12.5',
'e13_5': 'E13.5',
'web1_e10_5__12_5': 'WEB1(E10.5-12.5)',
'web2_e11_5__13_5': 'WEB2(E11.5-13.5)',
'p8_a': 'P8_A',
'p8_b': 'P8_B',
'p12_a': 'P12_A',
'p12_b': 'P12_B',
'p20_a': 'P20_A',
'p20_b': 'P20_B',
'p42_a': 'P42_A',
'p42_b': 'P42_B',
'p52_a': 'P52_A',
'p52_b': 'P52_B',
'web_p10_11_12_a': 'WEB(P10_11_12_A)',
'web_p10_11_12_b': 'WEB(P10_11_12_B)',
}
class ExpressionMicroarrayDisease(db.Model, MappingTableMixin):
__tablename__ = 'expression_microarray_disease'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True, index=True)
ensembl_id = db.Column(db.String(128), nullable=True)
retinal_detachment = db.Column(db.Float, nullable=True)
diabetic_retinopathy = db.Column(db.Float, nullable=True)
retinoblastoma = db.Column(db.Float, nullable=True)
retinitis_pigmentosa = db.Column(db.Float, nullable=True)
keratoconus = db.Column(db.Float, nullable=True)
keratitis = db.Column(db.Float, nullable=True)
trachoma = db.Column(db.Float, nullable=True)
glaucoma = db.Column(db.Float, nullable=True)
fuchs_endothelial_corneal_dystrophy = db.Column(db.Float, nullable=True)
uveal_melanoma = db.Column(db.Float, nullable=True)
uveal_melanoma_mum2b = db.Column(db.Float, nullable=True)
uveal_melanoma_ocm1a = db.Column(db.Float, nullable=True)
graves_ophthalmopathy = db.Column(db.Float, nullable=True)
nonspecific_orbital_inflammation = db.Column(db.Float, nullable=True)
sarcoidosis = db.Column(db.Float, nullable=True)
granulomatosis_with_polyangiitis = db.Column(db.Float, nullable=True)
thyroid_eye_disease = db.Column(db.Float, nullable=True)
def to_json(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'retinal_detachment': self.retinal_detachment,
'diabetic_retinopathy': self.diabetic_retinopathy,
'retinoblastoma': self.retinoblastoma,
'retinitis_pigmentosa': self.retinitis_pigmentosa,
'keratoconus': self.keratoconus,
'keratitis': self.keratitis,
'trachoma': self.trachoma,
'glaucoma': self.glaucoma,
'fuchs_endothelial_corneal_dystrophy':
self.fuchs_endothelial_corneal_dystrophy,
'uveal_melanoma': self.uveal_melanoma,
'uveal_melanoma_mum2b': self.uveal_melanoma_mum2b,
'uveal_melanoma_ocm1a': self.uveal_melanoma_ocm1a,
'graves_ophthalmopathy': self.graves_ophthalmopathy,
'nonspecific_orbital_inflammation':
self.nonspecific_orbital_inflammation,
'sarcoidosis': self.sarcoidosis,
'granulomatosis_with_polyangiitis':
self.granulomatosis_with_polyangiitis,
'thyroid_eye_disease': self.thyroid_eye_disease,
}
return self.map_to_names(result)
@classmethod
def column_mappings(cls):
return {
'retinal_detachment': "Retinal detachment",
'diabetic_retinopathy': "Diabetic retinopathy",
'retinoblastoma': "Retinoblastoma",
'retinitis_pigmentosa': "Retinitis pigmentosa",
'keratoconus': "Keratoconus",
'keratitis': "Keratitis",
'trachoma': "Trachoma",
'glaucoma': "Glaucoma",
'fuchs_endothelial_corneal_dystrophy':
"Fuchs' endothelial corneal dystrophy",
'uveal_melanoma': "Uveal melanoma",
'uveal_melanoma_mum2b': "Uveal melanoma MUM2B",
'uveal_melanoma_ocm1a': "Uveal melanoma OCM1A",
'graves_ophthalmopathy': "Graves' ophthalmopathy",
'nonspecific_orbital_inflammation':
"Nonspecific orbital inflammation",
'sarcoidosis': "Sarcoidosis",
'granulomatosis_with_polyangiitis':
"Granulomatosis with polyangiitis",
'thyroid_eye_disease': "Thyroid eye disease",
}
class ExpressionRNASeqTissue(db.Model, MappingTableMixin):
__tablename__ = 'expression_rna_seq_tissue'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
gene = db.Column(db.String(128), nullable=True, index=True)
ensembl_id = db.Column(db.String(128), nullable=True)
corneas = db.Column(db.Float, nullable=True)
corneal_endothelial_cells = db.Column(db.Float, nullable=True)
retina = db.Column(db.Float, nullable=True)
retina_macula = db.Column(db.Float, nullable=True)
retina_non_macula = db.Column(db.Float, nullable=True)
rpe_macula = db.Column(db.Float, nullable=True)
rpe_non_macula = db.Column(db.Float, nullable=True)
retinal_endothelial_cells = db.Column(db.Float, nullable=True)
ipsc_derived_retinal_organoids = db.Column(db.Float, nullable=True)
trabecular_meshwork_cells = db.Column(db.Float, nullable=True)
def to_json(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'corneas': self.corneas,
'corneal_endothelial_cells': self.corneal_endothelial_cells,
'retina': self.retina,
'retina_macula': self.retina_macula,
'retina_non_macula': self.retina_non_macula,
'rpe_macula': self.rpe_macula,
'rpe_non_macula': self.rpe_non_macula,
'retinal_endothelial_cells': self.retinal_endothelial_cells,
'ipsc_derived_retinal_organoids':
self.ipsc_derived_retinal_organoids,
'trabecular_meshwork_cells': self.trabecular_meshwork_cells,
}
return self.map_to_names(result)
def to_json_analysis(self):
result = {
'id': self.id,
'gene': self.gene,
'ensembl_id': self.ensembl_id,
'corneas': self.corneas,
'corneal_endothelial_cells': self.corneal_endothelial_cells,
'retina': self.retina,
'retina_macula': self.retina_macula,
'retina_non_macula': self.retina_non_macula,
'rpe_macula': self.rpe_macula,
'rpe_non_macula': self.rpe_non_macula,
'retinal_endothelial_cells': self.retinal_endothelial_cells,
'ipsc_derived_retinal_organoids':
self.ipsc_derived_retinal_organoids,
'trabecular_meshwork_cells': self.trabecular_meshwork_cells,
}
return result
@classmethod
def column_mappings(cls):
return {
'corneas': 'Corneas',
'corneal_endothelial_cells': 'Corneal endothelial cells',
'retina': 'Retina',
'retina_macula': 'Retina macula',
'retina_non_macula': 'Retina non-macula',
'rpe_macula': 'RPE macula',
'rpe_non_macula': 'RPE non-macula',
'retinal_endothelial_cells': 'Retinal endothelial cells',
'ipsc_derived_retinal_organoids': 'iPSC-derived retinal organoids',
'trabecular_meshwork_cells': 'Trabecular meshwork cells',
}
class DiseaseGo(db.Model):
__tablename__ = 'disease_go'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
disease = db.Column(db.String(255), nullable=True)
dataset = db.Column(db.String(8), nullable=True)
category = db.Column(db.String(128), nullable=True)
term = db.Column(db.Text, nullable=True)
count = db.Column(db.Integer, nullable=True)
percent = db.Column(db.Float, nullable=True)
p_value = db.Column(db.Float, nullable=True)
genes = db.Column(db.Text, nullable=True)
list_total = db.Column(db.Integer, nullable=True)
pop_hits = db.Column(db.Integer, nullable=True)
pop_total = db.Column(db.Integer, nullable=True)
fold_enrichment = db.Column(db.Float, nullable=True)
bonferroni = db.Column(db.Float, nullable=True)
benjamini = db.Column(db.Float, nullable=True)
fdr = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'id': self.id,
'disease': self.disease,
'dataset': self.dataset,
'category': self.category,
'term': self.term,
'count': self.count,
'percent': self.percent,
'p_value': self.p_value,
'genes': self.genes,
'list_total': self.list_total,
'pop_hits': self.pop_hits,
'pop_total': self.pop_total,
'fold_enrichment': round(self.fold_enrichment, 2),
'bonferroni': self.bonferroni,
'benjamini': self.benjamini,
'fdr': round(self.fdr, 2)
}
class Gene(db.Model):
__tablename__ = 'gene'
id = db.Column(UUID(as_uuid=False), default=uuid4_string, primary_key=True)
symbol = db.Column(db.String(32), nullable=True)
name = db.Column(db.String(128), nullable=True)
synonyms = db.Column(db.String(255), nullable=True)
gene_type = db.Column(db.String(128), nullable=True)
location = db.Column(db.Text, nullable=True)
strand = db.Column(db.String(32), nullable=True)
description = db.Column(db.Text, nullable=True)
omim = db.Column(db.String(16), nullable=True)
ensembl = db.Column(db.String(32), nullable=True)
clinvar = db.Column(db.String(128), nullable=True)
decipher = db.Column(db.String(128), nullable=True)
gnomad = db.Column(db.String(128), nullable=True)
panelapp = db.Column(db.String(128), nullable=True)
eye_disease = db.Column(db.Text, nullable=True)
phenotypes = db.Column(db.Text, nullable=True)
drugbank_id = db.Column(db.Text, nullable=True)
drug_target = db.Column(db.Text, nullable=True)
def to_list(self):
return {
'id': self.id,
'name': self.symbol,
}
def to_json(self):
return {
'id': self.id,
'symbol': self.symbol,
'ensembl': self.ensembl,
'synonyms': self.synonyms,
'location': self.location_split(),
'clinvar': self.clinvar,
'decipher': self.decipher,
'gnomad': self.gnomad,
'panelapp': self.panelapp,
'description': self.description,
'drug_target': self.drug_target_obj(),
'drugbank_id': self.drugbank_id,
'eye_disease': self.eye_disease,
'gene_type': self.gene_type,
'name': self.name,
'omim': self.omim,
'phenotypes': self.hpo_phenotypes_obj(),
'strand': self.strand,
}
def location_split(self):
rs = self.location.split("(GRCh38/hg38)")
rs[0] = rs[0] + "(GRCh38/hg38)"
return rs
def drug_target_obj(self):
if not self.drug_target:
return []
def to_to_group(a):
g_value, g_name = a.split(':')
return {'value': g_value, 'name': g_name}
result = [to_to_group(c) for c in (self.drug_target.split(';')[0:-1])]
return result
def hpo_phenotypes_obj(self):
if not self.phenotypes:
return []
def to_group(a):
disease, ref_id, color = OMIM_GROUP_PATTERN.match(a).groups()
return {'name': disease, 'omim': ref_id, 'color': color}
result = [to_group(c) for c in (self.phenotypes.split(';')[0:-1])]
return sorted(result,
key=lambda t: t['color']
if t['color'] != 'grey' else 'z')
class TissueGeneSignificance(db.Model):
__tablename__ = 'tissue_gene_significance'
id = db.Column(UUID(as_uuid=True), default=uuid4_string, primary_key=True)
gene_symbol = db.Column(db.String(128), nullable=True)
corneas = db.Column(db.Float, nullable=True)
corneal_endothelial_cells = db.Column(db.Float, nullable=True)
retina = db.Column(db.Float, nullable=True)
retina_macula = db.Column(db.Float, nullable=True)
retina_non_macula = db.Column(db.Float, nullable=True)
rpe_macula = db.Column(db.Float, nullable=True)
rpe_non_macula = db.Column(db.Float, nullable=True)
retinal_endothelial_cells = db.Column(db.Float, nullable=True)
ipsc_derived_retinal_organoids = db.Column(db.Float, nullable=True)
trabecular_meshwork_cells = db.Column(db.Float, nullable=True)
def to_json(self):
return {
'id': self.id,
'gene_symbol': self.gene_symbol,
'corneas': self.corneas,
'corneal_endothelial_cells': self.corneal_endothelial_cells,
'retina': self.retina,
'retina_macula': self.retina_macula,
'retina_non_macula': self.retina_non_macula,
'rpe_macula': self.rpe_macula,
'rpe_non_macula': self.rpe_non_macula,
'retinal_endothelial_cells': self.retinal_endothelial_cells,
'ipsc_derived_retinal_organoids':
self.ipsc_derived_retinal_organoids,
'trabecular_meshwork_cells': self.trabecular_meshwork_cells,
}
