Source code for oaklib.interfaces.subsetter_interface

from abc import ABC
from dataclasses import dataclass
from typing import Iterator, List

from oaklib.interfaces.basic_ontology_interface import (
    RELATIONSHIP,
    BasicOntologyInterface,
)
from oaklib.types import CURIE, PRED_CURIE


@dataclass
class SubsetStrategy:
    pass


class SyntacticLocalityModuleExtraction(SubsetStrategy):
    module_type: str  # TODO enum


class GraphWalkExtraction(SubsetStrategy):
    predicates: List[PRED_CURIE]


class MireotExtraction(SubsetStrategy):
    pass


[docs]class SubsetterInterface(BasicOntologyInterface, ABC): """ an interface that provides subsetting operations. Subsets are named sets of entities/terms in an ontology. Subsetting operations include extracting, and "rolling up" to a subset. See: - http://geneontology.org/docs/go-subset-guide/ """
[docs] def extract_subset_ontology( self, seed_curies: List[CURIE], strategy: SubsetStrategy = None ) -> BasicOntologyInterface: """ Extracts an ontology subset using a seed list of curies EXPERIMENTAL: this method may be removed in future :param seed_curies: :param strategy: :return: """ raise NotImplementedError
[docs] def gap_fill_relationships( self, seed_curies: List[CURIE], predicates: List[PRED_CURIE] = None ) -> Iterator[RELATIONSHIP]: """ Given a term subset as a list of curies, find all non-redundant relationships connecting them This assumes relation-graph entailed edges, so currently only implemented for ubergraph and sqlite First the subset of all entailed edges conforming to the predicate profile connecting any pair of terms in the subset is selected Then naive transitive reduction on a per predicate basis is performed. This may yield edges that are formally redundant, but these are still assumed to be useful for the user :param seed_curies: :param predicates: if specified, only consider relationships using these predicates :return: """ raise NotImplementedError