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Merge pull request #34 from geneontology/issue-29-root-type-handling
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Use root-types to control input/output associations
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@pkalita-lbl
pkalita-lbl authored Dec 9, 2024
2 parents 573e056 + 53bd939 commit 4c92293
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Showing 3 changed files with 127 additions and 216 deletions.
197 changes: 105 additions & 92 deletions src/gocam/translation/minerva_wrapper.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import logging
from collections import defaultdict
from dataclasses import dataclass, field
from typing import DefaultDict, Dict, Iterator, List, Optional, Set, Tuple
from typing import DefaultDict, Dict, Iterator, List, Optional, Tuple

import requests
import yaml
Expand Down Expand Up @@ -74,19 +74,14 @@ def _setattr_with_warning(obj, attr, value):
setattr(obj, attr, value)


MAIN_TYPES = [
"molecular_function",
"biological_process",
"cellular_component",
"information biomacromolecule",
"evidence",
"chemical entity",
"anatomical entity",
]

COMPLEX_TYPES = [
"protein-containing complex",
]
MOLECULAR_FUNCTION = "GO:0003674"
BIOLOGICAL_PROCESS = "GO:0008150"
CELLULAR_COMPONENT = "GO:0005575"
INFORMATION_BIOMACROMOLECULE = "CHEBI:33695"
PROTEIN_CONTAINING_COMPLEX = "GO:0032991"
EVIDENCE = "ECO:0000000"
CHEMICAL_ENTITY = "CHEBI:24431"
ANATOMICAL_ENTITY = "UBERON:0001062"


@dataclass
Expand Down Expand Up @@ -176,26 +171,14 @@ def minerva_object_to_model(obj: Dict) -> Model:
# Bookkeeping variables

# individual ID to "root" type / category, e.g Evidence, BP
individual_to_type: Dict[str, Optional[str]] = {}
individual_to_root_types: Dict[str, List[str]] = {}
individual_to_term: Dict[str, str] = {}
individual_to_annotations: Dict[str, Dict] = {}
complex_individuals: Set[str] = set()
id2obj: Dict[str, Dict] = {}
objects_by_id: Dict[str, Dict] = {}
activities: List[Activity] = []
activities_by_mf_id: DefaultDict[str, List[Activity]] = defaultdict(list)
facts_by_property: DefaultDict[str, List[Dict]] = defaultdict(list)

def _cls(obj: Dict) -> Optional[str]:
if obj.get("type", None) == "complement":
logger.warning(f"Ignoring Complement: {obj}")
# class expression representing NOT
return None
if "id" not in obj:
raise ValueError(f"No ID for {obj}")
id = obj["id"]
id2obj[id] = obj
return id

def _evidence_from_fact(fact: Dict) -> List[EvidenceItem]:
anns_mv = _annotations_multivalued(fact)
evidence_inst_ids = anns_mv.get("evidence", [])
Expand Down Expand Up @@ -227,41 +210,40 @@ def _iter_activities_by_fact_subject(
fact_property: str,
) -> Iterator[Tuple[Activity, str, List[EvidenceItem]]]:
for fact in facts_by_property.get(fact_property, []):
s, o = fact["subject"], fact["object"]
if o not in individual_to_term:
logger.warning(f"Missing {o} in {individual_to_term}")
subject, object_ = fact["subject"], fact["object"]
if object_ not in individual_to_term:
logger.warning(f"Missing {object_} in {individual_to_term}")
continue
for activity in activities_by_mf_id.get(s, []):
for activity in activities_by_mf_id.get(subject, []):
evs = _evidence_from_fact(fact)
yield activity, individual_to_term[o], evs
yield activity, object_, evs

def _has_molecule_root_type(individual_id: str) -> bool:
root_types = individual_to_root_types.get(individual_id, [])
return (
CHEMICAL_ENTITY in root_types
and INFORMATION_BIOMACROMOLECULE not in root_types
)

for individual in obj["individuals"]:
typs = [x["label"] for x in individual.get("root-type", []) if x]
typ: Optional[str] = None
for t in typs:
if t in MAIN_TYPES:
typ = t
break
if not typ:
logger.warning(f"Could not find type for {individual}")
continue
individual_to_type[individual["id"]] = typ

# Check to see if one of the types is a complex type
for t in typs:
if t in COMPLEX_TYPES:
complex_individuals.add(individual["id"])
break

terms = list(filter(None, (_cls(x) for x in individual.get("type", []))))
if len(terms) > 1:
logger.warning(f"Multiple terms for {individual}: {terms}")
if not terms:
logger.warning(f"No terms for {individual}")
continue
individual_to_term[individual["id"]] = terms[0]
anns = _annotations(individual)
individual_to_annotations[individual["id"]] = anns
root_types = [x["id"] for x in individual.get("root-type", []) if x]
individual_to_root_types[individual["id"]] = root_types

term_id: Optional[str] = None
for type_ in individual.get("type", []):
if type_.get("type") == "complement":
# class expression representing NOT
continue
type_id = type_.get("id")
if type_id is None:
continue
objects_by_id[type_id] = type_
term_id = type_id

individual_to_term[individual["id"]] = term_id
if "annotations" in individual:
anns = _annotations(individual)
individual_to_annotations[individual["id"]] = anns

for fact in obj["facts"]:
facts_by_property[fact["property"]].append(fact)
Expand All @@ -270,22 +252,23 @@ def _iter_activities_by_fact_subject(
if not enabled_by_facts:
raise ValueError(f"Missing {ENABLED_BY} in {facts_by_property}")
for fact in enabled_by_facts:
s, o = fact["subject"], fact["object"]
if s not in individual_to_term:
logger.warning(f"Missing {s} in {individual_to_term}")
subject, object_ = fact["subject"], fact["object"]
if subject not in individual_to_term:
logger.warning(f"Missing {subject} in {individual_to_term}")
continue
if o not in individual_to_term:
logger.warning(f"Missing {o} in {individual_to_term}")
if object_ not in individual_to_term:
logger.warning(f"Missing {object_} in {individual_to_term}")
continue
gene_id = individual_to_term[o]
gene_id = individual_to_term[object_]
root_types = individual_to_root_types.get(object_, [])

evs = _evidence_from_fact(fact)
enabled_by_association: EnabledByAssociation
if o in complex_individuals:
if PROTEIN_CONTAINING_COMPLEX in root_types:
has_part_facts = [
fact
for fact in facts_by_property.get(HAS_PART, [])
if fact["subject"] == o
if fact["subject"] == object_
]
members = [
individual_to_term[fact["object"]]
Expand All @@ -295,72 +278,95 @@ def _iter_activities_by_fact_subject(
enabled_by_association = EnabledByProteinComplexAssociation(
term=gene_id, members=members
)
else:
elif INFORMATION_BIOMACROMOLECULE in root_types:
enabled_by_association = EnabledByGeneProductAssociation(term=gene_id)
else:
continue

activity = Activity(
id=s,
id=subject,
enabled_by=enabled_by_association,
molecular_function=MolecularFunctionAssociation(
term=individual_to_term[s], evidence=evs
term=individual_to_term[subject], evidence=evs
),
)
activities.append(activity)
activities_by_mf_id[s].append(activity)
activities_by_mf_id[subject].append(activity)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=PART_OF
):
association = BiologicalProcessAssociation(term=term, evidence=evs)
association = BiologicalProcessAssociation(
term=individual_to_term[individual], evidence=evs
)
_setattr_with_warning(activity, "part_of", association)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=OCCURS_IN
):
association = CellularAnatomicalEntityAssociation(term=term, evidence=evs)
association = CellularAnatomicalEntityAssociation(
term=individual_to_term[individual], evidence=evs
)
_setattr_with_warning(activity, "occurs_in", association)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=HAS_INPUT
):
if not _has_molecule_root_type(individual):
continue
if activity.has_input is None:
activity.has_input = []
activity.has_input.append(MoleculeAssociation(term=term, evidence=evs))
activity.has_input.append(
MoleculeAssociation(term=individual_to_term[individual], evidence=evs)
)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=HAS_PRIMARY_INPUT
):
association = MoleculeAssociation(term=term, evidence=evs)
if not _has_molecule_root_type(individual):
continue
association = MoleculeAssociation(
term=individual_to_term[individual], evidence=evs
)
_setattr_with_warning(activity, "has_primary_input", association)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=HAS_OUTPUT
):
if not _has_molecule_root_type(individual):
continue
if activity.has_output is None:
activity.has_output = []
activity.has_output.append(MoleculeAssociation(term=term, evidence=evs))
activity.has_output.append(
MoleculeAssociation(term=individual_to_term[individual], evidence=evs)
)

for activity, term, evs in _iter_activities_by_fact_subject(
for activity, individual, evs in _iter_activities_by_fact_subject(
fact_property=HAS_PRIMARY_OUTPUT
):
association = MoleculeAssociation(term=term, evidence=evs)
if not _has_molecule_root_type(individual):
continue
association = MoleculeAssociation(
term=individual_to_term[individual], evidence=evs
)
_setattr_with_warning(activity, "has_primary_output", association)

for fact_property, facts in facts_by_property.items():
for fact in facts:
s, o = fact["subject"], fact["object"]
subject_activities = activities_by_mf_id.get(s, [])
object_activities = activities_by_mf_id.get(o, [])
subject, object_ = fact["subject"], fact["object"]
subject_activities = activities_by_mf_id.get(subject, [])
object_activities = activities_by_mf_id.get(object_, [])

if not subject_activities or not object_activities:
continue
if individual_to_type.get(s, None) != "molecular_function":
if MOLECULAR_FUNCTION not in individual_to_root_types.get(subject, []):
continue
if individual_to_type.get(o, None) != "molecular_function":
if MOLECULAR_FUNCTION not in individual_to_root_types.get(object_, []):
continue
if len(subject_activities) > 1:
logger.warning(f"Multiple activities for subject: {s}")
logger.warning(f"Multiple activities for subject: {subject}")
if len(object_activities) > 1:
logger.warning(f"Multiple activities for object: {o}")
logger.warning(f"Multiple activities for object: {object_}")

subject_activity = subject_activities[0]
object_activity = object_activities[0]
Expand All @@ -376,14 +382,21 @@ def _iter_activities_by_fact_subject(

annotations = _annotations(obj)
annotations_mv = _annotations_multivalued(obj)
objs = [Object(id=obj["id"], label=obj["label"]) for obj in id2obj.values()]

objects: List[Object] = []
for obj in objects_by_id.values():
object_ = Object(id=obj["id"])
if "label" in obj:
object_.label = obj["label"]
objects.append(object_)

cam = Model(
id=id,
title=annotations["title"],
status=annotations.get("state", None),
comments=annotations_mv.get("comment", None),
taxon=annotations.get("in_taxon", None),
activities=activities,
objects=objs,
objects=objects,
)
return cam
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