Adding UsageInterface

Adding a QuickGO adapter

src/oaklib/cli.py

@@ -107,6 +107,7 @@
 from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
 from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
 from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface
+from oaklib.interfaces.usages_interface import UsagesInterface
 from oaklib.io.heatmap_writer import HeatmapWriter
 from oaklib.io.html_writer import HTMLWriter
 from oaklib.io.obograph_writer import write_graph
@@ -1439,7 +1440,6 @@ def annotate(
 @output_type_option
 # TODO: the main output option uses a filelike object
 @click.option("-o", "--output", help="Path to output file")
-# @output_option
 def viz(
  terms,
  predicates,
@@ -4181,6 +4181,77 @@ def apply_taxon_constraints(
  writer.emit(st)
 
 
+@main.command()
+@output_option
+@autolabel_option
+@output_type_option
+@output_option
+@click.option(
+ "--used-by-prefix",
+ "-P",
+ multiple=True,
+)
+@click.argument("terms", nargs=-1)
+def usages(
+ terms,
+ autolabel: bool,
+ output_type: str,
+ output: str,
+ used_by_prefix: List,
+ **kwargs,
+):
+ """
+ List usages of a term or set of terms.
+
+ Usages of neuron in GO:
+
+ runoak -i sqlite:obo:go usages CL:0000540
+
+ Association/annotations sources can also be used:
+
+ runoak -i quickgo: usages GO:0031969
+
+ Note this query may be slow - you can restrict to a species:
+
+ runoak -i quickgo:NCBITaxon:9606 usages GO:0031969
+
+ (this should return no results, as there should be no human proteins annotated
+ to chloroplast membrane)
+
+ Using amigo:
+
+ runoak -i amigo: usages GO:0031969
+
+ Using ubergraph:
+
+ runoak -i ubergraph: usages CL:0000540
+
+ This will include usages over multiple ontologies
+
+ You can multiple queries over multiple sources (an AggregatorImplementation):
+
+ runoak -i sqlite:obo:go -a ubergraph: -a amigo: -a quickgo: usages GO:0031969
+
+ """
+ impl = settings.impl
+ writer = _get_writer(output_type, impl, StreamingCsvWriter)
+ writer.autolabel = autolabel
+ writer.output = output
+ if not isinstance(impl, UsagesInterface):
+ raise NotImplementedError(
+ f"Cannot execute this using {settings.impl} of type {type(settings.impl)}"
+ )
+ used_by = None
+ if "@" in terms:
+ ix = terms.index("@")
+ curies = list(query_terms_iterator(terms[:ix], impl))
+ used_by = terms[ix + 1 :]
+ else:
+ curies = list(query_terms_iterator(terms, impl))
+ for usage in impl.usages(curies, used_by=used_by, used_by_prefixes=used_by_prefix, **kwargs):
+ writer.emit(usage)
+
+
 @main.command()
 @output_option
 @predicates_option
@@ -4662,6 +4733,7 @@ def apply_labels(group):
 @output_option
 @click.option(
  "--ontology-only/--no-ontology-only",
+ "-T",
  default=False,
  show_default=True,
  help="If true, perform a pseudo-enrichment analysis treating each term as an association to itself.",
@@ -4750,14 +4822,20 @@ def enrichment(
  actual_association_predicates = _process_predicates_arg(association_predicates)
  if sample_file:
  subjects = list(curies_from_file(sample_file, adapter=impl, allow_labels=allow_labels))
+ curies = list(query_terms_iterator(terms, impl))
  else:
  if "@" in terms:
+ if not ontology_only:
+ raise ValueError("Cannot use @ with --no-ontology-only")
  ix = terms.index("@")
  logging.info(f"Splitting terms into two, position = {ix}")
  subjects = list(query_terms_iterator(terms[0:ix], impl))
- terms = terms[ix + 1 :]
+ curies = list(query_terms_iterator(terms[ix + 1 :], impl))
+ logging.info(f"Num Subjects={len(subjects)} (using {len(curies)} terms)")
  else:
  subjects = list(query_terms_iterator(terms, impl))
+ curies = None
+ logging.info(f"Num Subjects={len(subjects)} (using all terms)")
  if not subjects:
  raise ValueError("No terms or upload provided")
  background = (
@@ -4778,7 +4856,6 @@ def enrichment(
  writer = _get_writer(output_type, impl, StreamingYamlWriter)
  writer.autolabel = autolabel
  writer.output = output
- curies = list(query_terms_iterator(terms, impl))
  results = impl.enriched_classes(
  subjects,
  predicates=actual_association_predicates,

src/oaklib/conf/obograph-style.json

@@ -70,6 +70,12 @@
  "penwidth": 2, 
  "label": "ⓗ"
  },
+ "RO:0002333": {
+ "arrowhead": "box",
+ "color": "green",
+ "penwidth": 2, 
+ "label": "ⓔ"
+ },
  "RO:0004009": {
  "arrowhead": "box",
  "color": "green",
@@ -97,6 +103,21 @@
  "color": "red",
  "label": "⇩"
  },
+ "RO:0002233": {
+ "arrowhead": "diamond",
+ "color": "blue",
+ "label": "→⊚"
+ },
+ "RO:0002234": {
+ "arrowhead": "diamond",
+ "color": "blue",
+ "label": "⊚→"
+ },
+ "RO:0002400": {
+ "arrowhead": "diamond",
+ "color": "blue",
+ "label": "⇨⊚"
+ },
  "RO:0002220": {
  "color": "gray",
  "label": "A"

src/oaklib/datamodels/vocabulary.py

@@ -117,13 +117,19 @@
 LOCATED_IN = "RO:0001025"
 DEVELOPS_FROM = "RO:0002202"
 HAS_PART = "BFO:0000051"
+OCCURS_IN = "BFO:0000066"
 ONLY_IN_TAXON = "RO:0002160"
 NEVER_IN_TAXON = "RO:0002161"
 IN_TAXON = "RO:0002162"
 PRESENT_IN_TAXON = "RO:0002175"
 NEGATIVELY_REGULATES = "RO:0002212"
 POSITIVELY_REGULATES = "RO:0002213"
 REGULATES = "RO:0002211"
+ENABLES = "RO:0002327"
+ENABLED_BY = "RO:0002333"
+HAS_DIRECT_INPUT = "RO:0002400"
+HAS_INPUT = "RO:0002233"
+HAS_OUTPUT = "RO:0002234"
 
 BIOLOGICAL_PROCESS = "GO:0008150"
 CELLULAR_COMPONENT = "GO:0005575"

src/oaklib/implementations/__init__.py

@@ -12,13 +12,13 @@
 from oaklib.implementations.agrkb.agrkb_implementation import AGRKBImplementation
 from oaklib.implementations.amigo.amigo_implementation import AmiGOImplementation
 from oaklib.implementations.cx.cx_implementation import CXImplementation
-from oaklib.implementations.eutils.pubmed_implementation import PubMedImplementation
 from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation
 from oaklib.implementations.gilda import GildaImplementation
 from oaklib.implementations.kgx.kgx_implementation import KGXImplementation
 from oaklib.implementations.llm_implementation import LLMImplementation
 from oaklib.implementations.monarch.monarch_implementation import MonarchImplementation
 from oaklib.implementations.ncbi.ncbi_gene_implementation import NCBIGeneImplementation
+from oaklib.implementations.ncbi.pubmed_implementation import PubMedImplementation
 from oaklib.implementations.ols import (
  BaseOlsImplementation,
  OlsImplementation,
@@ -44,6 +44,7 @@
  PantherDBImplementation,
 )
 from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
+from oaklib.implementations.quickgo.quickgo_implementation import QuickGOImplementation
 from oaklib.implementations.semsimian.semsimian_implementation import (
  SemSimianImplementation,
 )
@@ -86,6 +87,7 @@
  "NCBIGeneImplementation",
  "OntobeeImplementation",
  "ProntoImplementation",
+ "QuickGOImplementation",
  "SimpleOboImplementation",
  "SqlImplementation",
  "UbergraphImplementation",

src/oaklib/implementations/aggregator/aggregator_implementation.py

@@ -1,7 +1,7 @@
 from collections import defaultdict
 from dataclasses import dataclass
 from io import TextIOWrapper
-from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Tuple
+from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Tuple, Type
 
 from sssom_schema import Mapping
 
@@ -12,6 +12,7 @@
  ValidationConfiguration,
  ValidationResult,
 )
+from oaklib.interfaces.association_provider_interface import AssociationProviderInterface
 from oaklib.interfaces.basic_ontology_interface import (
  ALIAS_MAP,
  DEFINITION,
@@ -25,19 +26,22 @@
 from oaklib.interfaces.relation_graph_interface import RelationGraphInterface
 from oaklib.interfaces.search_interface import SearchInterface
 from oaklib.interfaces.text_annotator_interface import TEXT, TextAnnotatorInterface
+from oaklib.interfaces.usages_interface import UsagesInterface
 from oaklib.interfaces.validator_interface import ValidatorInterface
 from oaklib.types import CURIE, SUBSET_CURIE
 
 
 @dataclass
 class AggregatorImplementation(
+ AssociationProviderInterface,
  ValidatorInterface,
  RdfInterface,
  RelationGraphInterface,
  OboGraphInterface,
  SearchInterface,
  MappingProviderInterface,
  TextAnnotatorInterface,
+ UsagesInterface,
 ):
  """
  An OAK adapter that wraps multiple implementations and integrates results together.
@@ -78,10 +82,20 @@ class AggregatorImplementation(
 
  implementations: List[BasicOntologyInterface] = None
 
- def _delegate_iterator(self, func: Callable) -> Iterator:
+ @property
+ def implementation_name(self):
+ impl_names = []
  for i in self.implementations:
- for v in func(i):
- yield v
+ impl_names.append(i.implementation_name)
+ return "-".join(impl_names)
+
+ def _delegate_iterator(
+ self, func: Callable, interface: Optional[Type[BasicOntologyInterface]] = None
+ ) -> Iterator:
+ for i in self.implementations:
+ if interface is None or isinstance(i, interface):
+ for v in func(i):
+ yield v
 
  def _delegate_simple_tuple_map(self, func: Callable, strict=False) -> Dict[Any, List[Any]]:
  m = defaultdict(list)
@@ -107,11 +121,21 @@ def validate(self, configuration: ValidationConfiguration = None) -> Iterable[Va
  def entities(self, **kwargs) -> Iterable[CURIE]:
  return self._delegate_iterator(lambda i: i.entities(**kwargs))
 
+ def relationships(self, *args, **kwargs) -> Iterable[CURIE]:
+ return self._delegate_iterator(lambda i: i.relationships(*args, **kwargs))
+
  def simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, CURIE]]:
  return self._delegate_iterator(lambda i: i.simple_mappings_by_curie(curie))
 
  def get_sssom_mappings_by_curie(self, curie: CURIE) -> Iterable[Mapping]:
- return self._delegate_iterator(lambda i: i.get_sssom_mappings_by_curie(curie))
+ return self._delegate_iterator(
+ lambda i: i.get_sssom_mappings_by_curie(curie), MappingProviderInterface
+ )
+
+ def sssom_mappings(self, *args, **kwargs) -> Iterable[Mapping]:
+ return self._delegate_iterator(
+ lambda i: i.sssom_mappings(*args, **kwargs), MappingProviderInterface
+ )
 
  def label(self, curie: CURIE, **kwargs) -> str:
  return self._delegate_first(lambda i: i.label(curie, **kwargs))
@@ -151,6 +175,11 @@ def outgoing_relationship_map(self, curie: CURIE) -> RELATIONSHIP_MAP:
  def incoming_relationship_map(self, curie: CURIE) -> RELATIONSHIP_MAP:
  return self._delegate_simple_tuple_map(lambda i: i.incoming_relationship_map(curie))
 
+ def associations(self, *args, **kwargs) -> Iterable[CURIE]:
+ return self._delegate_iterator(
+ lambda i: i.associations(*args, **kwargs), AssociationProviderInterface
+ )
+
  def annotate_text(
  self, text: TEXT, configuration: Optional[TextAnnotationConfiguration] = None
  ) -> Iterable[TextAnnotation]:

src/oaklib/implementations/amigo/amigo_implementation.py

@@ -21,6 +21,7 @@
 ]
 
 from oaklib.interfaces.basic_ontology_interface import LANGUAGE_TAG, RELATIONSHIP
+from oaklib.interfaces.usages_interface import UsagesInterface
 from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE
 from oaklib.utilities.iterator_utils import chunk
 
@@ -130,6 +131,7 @@ def _normalize(curie: CURIE) -> CURIE:
 class AmiGOImplementation(
  AssociationProviderInterface,
  SearchInterface,
+ UsagesInterface,
 ):
  """
  Wraps AmiGO endpoint.

src/oaklib/implementations/eutils/eutils_implementation.py → src/oaklib/implementations/ncbi/eutils_implementation.py

@@ -5,6 +5,7 @@
 from dataclasses import dataclass, field
 from typing import ClassVar, Iterable, Iterator, Optional, Tuple
 
+import requests_cache
 from eutils import Client
 
 __all__ = [
@@ -22,6 +23,8 @@
 
 logger = logging.getLogger(__name__)
 
+NCBI_REQUESTS_CACHE = ".ncbi_requests_cache"
+
 
 @dataclass
 class EUtilsImplementation(OboGraphInterface, ABC):
@@ -30,10 +33,20 @@ class EUtilsImplementation(OboGraphInterface, ABC):
  """
 
  entrez_client: Client = field(default_factory=lambda: Client())
+ # 0.6.0 release in 2019 - considered switching to direct API calls?
 
  database: ClassVar[Optional[str]] = None
  entity_type: ClassVar[Optional[str]] = None
 
+ # alternative to entrez_client
+ _requests_session: requests_cache.CachedSession = None
+
+ @property
+ def requests_session(self):
+ if self._requests_session is None:
+ self._requests_session = requests_cache.CachedSession(NCBI_REQUESTS_CACHE)
+ return self._requests_session
+
  def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
  if lang is not None:
  raise NotImplementedError("lang not implemented for eutils")