From a636e05803f47571afaed848c6ecab67ff9cf030 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Fri, 30 Aug 2024 10:49:52 -0700 Subject: [PATCH] Populate `has_direct_input` and `has_direct_output` in `minerva_object_to_model` --- src/gocam/translation/minerva_wrapper.py | 74 +++++++++++++------ tests/input/minerva-665912ed00002626.json | 1 + .../test_translation/test_minerva_wrapper.py | 36 +++++++++ 3 files changed, 88 insertions(+), 23 deletions(-) create mode 100644 tests/input/minerva-665912ed00002626.json diff --git a/src/gocam/translation/minerva_wrapper.py b/src/gocam/translation/minerva_wrapper.py index 07e1c25..53aa551 100644 --- a/src/gocam/translation/minerva_wrapper.py +++ b/src/gocam/translation/minerva_wrapper.py @@ -1,7 +1,7 @@ import logging from collections import defaultdict from dataclasses import dataclass, field -from typing import DefaultDict, Dict, Iterator, List, Optional, Set +from typing import DefaultDict, Dict, Iterator, List, Optional, Set, Tuple import requests import yaml @@ -11,12 +11,13 @@ BiologicalProcessAssociation, CausalAssociation, CellularAnatomicalEntityAssociation, - EvidenceItem, EnabledByAssociation, - EnabledByProteinComplexAssociation, EnabledByGeneProductAssociation, + EnabledByProteinComplexAssociation, + EvidenceItem, Model, MolecularFunctionAssociation, + MoleculeAssociation, Object, ProvenanceInfo, ) @@ -25,6 +26,8 @@ PART_OF = "BFO:0000050" HAS_PART = "BFO:0000051" OCCURS_IN = "BFO:0000066" +HAS_INPUT = "RO:0002233" +HAS_OUTPUT = "RO:0002234" logger = logging.getLogger(__name__) @@ -170,7 +173,7 @@ def minerva_object_to_model(obj: Dict) -> Model: id2obj: Dict[str, Dict] = {} activities: List[Activity] = [] activities_by_mf_id: DefaultDict[str, List[Activity]] = defaultdict(list) - facts_by_property = defaultdict(list) + facts_by_property: DefaultDict[str, List[Dict]] = defaultdict(list) def _cls(obj: Dict) -> Optional[str]: if obj.get("type", None) == "complement": @@ -209,6 +212,19 @@ def _evidence_from_fact(fact: Dict) -> List[EvidenceItem]: evs.append(ev) return evs + 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}") + continue + for activity in activities_by_mf_id.get(s, []): + evs = _evidence_from_fact(fact) + yield activity, individual_to_term[o], evs + for individual in obj["individuals"]: typs = [x["label"] for x in individual.get("root-type", []) if x] typ: Optional[str] = None @@ -281,27 +297,39 @@ def _evidence_from_fact(fact: Dict) -> List[EvidenceItem]: activities.append(activity) activities_by_mf_id[s].append(activity) - for fact in facts_by_property.get(PART_OF, []): - s, o = fact["subject"], fact["object"] - if o not in individual_to_term: - logger.warning(f"Missing {o} in {individual_to_term}") - continue - for a in activities_by_mf_id.get(s, []): - evs = _evidence_from_fact(fact) - a.part_of = BiologicalProcessAssociation( - term=individual_to_term[o], evidence=evs - ) + for activity, term, evs in _iter_activities_by_fact_subject( + fact_property=PART_OF + ): + if activity.part_of is not None: + logger.warning(f"Overwriting part_of for Activity: {activity.id}") + activity.part_of = BiologicalProcessAssociation(term=term, evidence=evs) + + for activity, term, evs in _iter_activities_by_fact_subject( + fact_property=OCCURS_IN + ): + if activity.occurs_in is not None: + logger.warning(f"Overwriting occurs_in for Activity: {activity.id}") + activity.occurs_in = CellularAnatomicalEntityAssociation( + term=term, evidence=evs + ) - for fact in facts_by_property.get(OCCURS_IN, []): - s, o = fact["subject"], fact["object"] - if o not in individual_to_term: - logger.warning(f"Missing {o} in {individual_to_term}") - continue - for a in activities_by_mf_id.get(s, []): - evs = _evidence_from_fact(fact) - a.occurs_in = CellularAnatomicalEntityAssociation( - term=individual_to_term[o], evidence=evs + for activity, term, evs in _iter_activities_by_fact_subject( + fact_property=HAS_INPUT + ): + if activity.has_direct_input is not None: + logger.warning( + f"Overwriting has_direct_input for Activity: {activity.id}" + ) + activity.has_direct_input = MoleculeAssociation(term=term, evidence=evs) + + for activity, term, evs in _iter_activities_by_fact_subject( + fact_property=HAS_OUTPUT + ): + if activity.has_direct_output is not None: + logger.warning( + f"Overwriting has_direct_output for Activity: {activity.id}" ) + activity.has_direct_output = MoleculeAssociation(term=term, evidence=evs) for fact_property, facts in facts_by_property.items(): for fact in facts: diff --git a/tests/input/minerva-665912ed00002626.json b/tests/input/minerva-665912ed00002626.json new file mode 100644 index 0000000..944a8b9 --- /dev/null +++ b/tests/input/minerva-665912ed00002626.json 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metabolic process (GO:0019627)"},{"key":"providedBy","value":"http://www.pombase.org"},{"key":"https://w3id.org/biolink/vocab/in_taxon","value":"NCBITaxon:4896","value-type":"IRI"}]} \ No newline at end of file diff --git a/tests/test_translation/test_minerva_wrapper.py b/tests/test_translation/test_minerva_wrapper.py index e92fef6..06e692a 100644 --- a/tests/test_translation/test_minerva_wrapper.py +++ b/tests/test_translation/test_minerva_wrapper.py @@ -55,3 +55,39 @@ def test_protein_complex(): "MGI:MGI:1929608", "MGI:MGI:103038", ] + + +def test_has_direct_input_and_has_direct_output(): + """Test that direct input/output molecule associations are added to activities""" + mw = MinervaWrapper() + with open(INPUT_DIR / "minerva-665912ed00002626.json", "r") as f: + minerva_object = json.load(f) + model = mw.minerva_object_to_model(minerva_object) + + activities_with_direct_input = [] + activities_with_direct_output = [] + for activity in model.activities: + if activity.has_direct_input: + activities_with_direct_input.append(activity) + if activity.has_direct_output: + activities_with_direct_output.append(activity) + + # Basic sanity check on the number of activities with direct input/output + assert len(activities_with_direct_input) == 3 + assert len(activities_with_direct_output) == 7 + + # Verify that one activity has uric acid as a direct input + uric_acid_input_activities = [ + a + for a in activities_with_direct_input + if a.has_direct_input.term == "CHEBI:27226" + ] + assert len(uric_acid_input_activities) == 1 + + # Verify that three activities have urea as a direct output + urea_output_activities = [ + a + for a in activities_with_direct_output + if a.has_direct_output.term == "CHEBI:16199" + ] + assert len(urea_output_activities) == 3