from obnb.alltypes import Mapping, Optional, Union
from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
from obnb.data.annotation import DISEASESAnnotation
from obnb.data.ontology import MondoDiseaseOntology
from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
from obnb.util.registers import overload_class
[docs]class DISEASES(BaseAnnotatedOntologyData):
"""The DISEASES disease gene set collection."""
def __init__(
self,
root: str,
score_min: Optional[float] = 3,
score_max: Optional[float] = None,
channel: str = "integrated_full",
min_size: int = 10,
max_size: int = 600,
overlap: float = 0.7,
jaccard: float = 0.5,
gene_id_converter: Optional[Union[Mapping[str, str], str]] = "HumanEntrez",
**kwargs,
):
"""Initialize the DisGeNET data object."""
self.min_size = min_size
self.max_size = max_size
self.jaccard = jaccard
self.overlap = overlap
super().__init__(
root,
annotation_factory=DISEASESAnnotation,
ontology_factory=MondoDiseaseOntology,
annotation_kwargs={
"score_min": score_min,
"score_max": score_max,
"channel": channel,
"gene_id_converter": gene_id_converter,
},
ontology_kwargs={"xref_prefix": "DOID"},
**kwargs,
)
@property
def default_pre_transform(self):
return Compose(
LabelsetRangeFilterSize(max_val=self.max_size),
LabelsetNonRedFilter(self.jaccard, self.overlap),
LabelsetRangeFilterSize(min_val=self.min_size),
log_level=self.log_level,
)
DISEASES_IntegratedFull = overload_class(
DISEASES,
"IntegratedFull",
channel="integrated_full",
score_min=None,
)
DISEASES_TextminingFull = overload_class(
DISEASES,
"TextminingFull",
channel="textmining_full",
score_min=None,
)
DISEASES_TextminingFiltered = overload_class(
DISEASES,
"TextminingFiltered",
channel="textmining_filtered",
score_min=None,
)
DISEASES_KnowledgeFull = overload_class(
DISEASES,
"KnowledgeFull",
channel="knowledge_full",
score_min=None,
)
DISEASES_KnowledgeFiltered = overload_class(
DISEASES,
"KnowledgeFiltered",
channel="knowledge_filtered",
score_min=None,
)
DISEASES_ExperimentsFull = overload_class(
DISEASES,
"ExperimentsFull",
channel="experiments_full",
score_min=None,
)
DISEASES_ExperimentsFiltered = overload_class(
DISEASES,
"ExperimentsFiltered",
channel="experiments_filtered",
score_min=None,
)