From 615c427ac5dc6edef35401fc3c9e58d3bc8d7b4f Mon Sep 17 00:00:00 2001
From: Adam Wright <adam.j.wright82@gmail.com>
Date: Fri, 18 Sep 2026 18:53:27 +0000
Subject: [PATCH] Fix the baseline tool, and capture spec 009's before state

Spec 009 T002 says capture the retrieval baseline before any code change. The
tool could not run, and when it ran it measured something that would not survive
the next release.

**It crashed.** `client_settings=chroma_settings` passed the factory rather than
calling it. `chroma_settings` used to be a constant and became a function --
because langchain_chroma mutates the Settings it is given, so a shared object
leaks one store's persist directory into the next -- and this call site was not
updated. Nothing exercises this tool, so it has been broken silently since.

**Then it recorded unstable identities.** `doc_id` prefers a Reactome stable id
and falls back to a row number, with the docstring "Reactome stable IDs survive a
bundle rebuild; row numbers do not". Measured: 1000 of 1000 BM25 ids were
row-based while all 1000 vector ids were stable, because the tool built BM25 from
a plain CSVLoader, whose documents carry only {row, source}. A bundle rebuild
happens every release, so a before/after comparison spanning one would have shown
spurious total disagreement on the BM25 half.

That is the same defect as the application had, in a third caller -- the pattern
the website session named this morning, and the reason I now grep for the shape
rather than fixing the instance I was shown. Same fix: MetaDataCSVLoader with the
columns read from the header.

After: 1000 of 1000 BM25 ids stable, matching the vector side.

before.json captures 20 questions across all five collections, which is the
comparison collection routing will be measured against.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---
 bin/retrieval_baseline                   |   23 +-
 specs/009-collection-routing/before.json | 2653 ++++++++++++++++++++++
 2 files changed, 2673 insertions(+), 3 deletions(-)
 create mode 100644 specs/009-collection-routing/before.json

diff --git a/bin/retrieval_baseline b/bin/retrieval_baseline
index bacd808a..1cd380de 100755
--- a/bin/retrieval_baseline
+++ b/bin/retrieval_baseline
@@ -32,7 +32,6 @@ import nltk
 from dotenv import load_dotenv
 from langchain_classic.retrievers.self_query.base import SelfQueryRetriever
 from langchain_chroma.vectorstores import Chroma
-from langchain_community.document_loaders.csv_loader import CSVLoader
 from langchain_community.retrievers import BM25Retriever
 from langchain_core.documents import Document
 from langchain_core.retrievers import BaseRetriever
@@ -46,8 +45,10 @@ from nltk.tokenize import word_tokenize
 sys.path.insert(0, str(Path(__file__).resolve().parent.parent / "src"))
 
 from agent.models import get_embedding, get_llm
+from data_generation.metadata_csv_loader import MetaDataCSVLoader
 from retrievers.csv_chroma import (
     VECTOR_OVERFETCH,
+    _csv_column_names,
     chroma_settings,
     dedupe_by_entity,
     list_chroma_subdirectories,
@@ -83,8 +84,19 @@ def build_retrievers(
     embedding = get_embedding("openai", "text-embedding-3-large")
 
     csv_path = embeddings_dir / "csv_files" / f"{collection}.csv"
+    # MetaDataCSVLoader, not CSVLoader: the plain loader gives documents metadata
+    # of only {row, source}, so `doc_id` below fell back to row numbers for every
+    # BM25 document -- defeating its own docstring, since row numbers do not
+    # survive a bundle rebuild and a rebuild happens every release. Measured
+    # before this change: 1000 of 1000 BM25 ids were row-based while all 1000
+    # vector ids were stable.
+    #
+    # The application had the same defect and was fixed the same way; this is the
+    # second caller.
     bm25 = BM25Retriever.from_documents(
-        CSVLoader(file_path=str(csv_path)).load(),
+        MetaDataCSVLoader(
+            file_path=str(csv_path), metadata_columns=_csv_column_names(csv_path)
+        ).load(),
         preprocess_func=lambda text: word_tokenize(text.casefold(), language="english"),
     )
     bm25.k = k
@@ -92,7 +104,12 @@ def build_retrievers(
     vectordb = Chroma(
         persist_directory=str(embeddings_dir / collection),
         embedding_function=embedding,
-        client_settings=chroma_settings,
+        # Called, not passed: chroma_settings is a factory, because
+        # langchain_chroma mutates the Settings it is given and a shared object
+        # leaks one store's persist directory into the next. It used to be a
+        # constant, and this call site was not updated when it changed -- which
+        # broke this tool for every use, silently, since nothing exercises it.
+        client_settings=chroma_settings(),
     )
 
     # Both vector-side retrievers are asked for more than k and collapsed to k
diff --git a/specs/009-collection-routing/before.json b/specs/009-collection-routing/before.json
new file mode 100644
index 00000000..33f91093
--- /dev/null
+++ b/specs/009-collection-routing/before.json
@@ -0,0 +1,2653 @@
+{
+  "bundle": "/home/awright/git/reactome_chatbot/embeddings/openai/text-embedding-3-large/reactome/Release97",
+  "collections": [
+    "complexes",
+    "disease_variants",
+    "ewas",
+    "reactions",
+    "summations"
+  ],
+  "k": 10,
+  "results": {
+    "Describe the components of the proteasome": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-156824",
+          "R-HSA-156824",
+          "R-HSA-1218829",
+          "R-HSA-1218829",
+          "R-HSA-180610",
+          "R-HSA-1299474",
+          "R-HSA-9629402",
+          "R-HSA-9629190",
+          "R-HSA-1299462",
+          "R-HSA-9629444"
+        ],
+        "vector": [
+          "R-HSA-177750",
+          "R-HSA-68819",
+          "R-HSA-9918354",
+          "R-HSA-9908710",
+          "R-HSA-9908004",
+          "R-HSA-9918363",
+          "R-HSA-9908063",
+          "R-HSA-9918357",
+          "R-HSA-9907911",
+          "R-HSA-9907994"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-8866838",
+          "R-HSA-5387361",
+          "R-HSA-5387364",
+          "R-HSA-5387363",
+          "R-HSA-5387360",
+          "R-HSA-5387354",
+          "R-HSA-5387366",
+          "R-HSA-5387365",
+          "R-HSA-5387362",
+          "R-HSA-5387357"
+        ],
+        "vector": [
+          "R-HSA-9721413",
+          "R-HSA-9718698",
+          "R-HSA-9721956",
+          "R-HSA-9718703",
+          "R-HSA-9721656",
+          "R-HSA-9719077",
+          "R-HSA-9719232",
+          "R-HSA-9719387",
+          "R-HSA-9720094",
+          "R-HSA-9721973"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-983091",
+          "R-HSA-1181241",
+          "R-HSA-2130716",
+          "R-HSA-985498",
+          "R-HSA-8855907",
+          "R-HSA-985502",
+          "R-HSA-2130328",
+          "R-HSA-2130361",
+          "R-HSA-2130513",
+          "R-HSA-2130373"
+        ],
+        "vector": [
+          "R-HSA-9908139",
+          "R-HSA-9908136",
+          "R-HSA-9908135",
+          "R-HSA-9908130",
+          "R-HSA-68765",
+          "R-HSA-9908127",
+          "R-HSA-9908138",
+          "R-HSA-174344",
+          "R-HSA-9908131",
+          "R-HSA-68738"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-5610757",
+          "R-HSA-5610754",
+          "R-HSA-5610758",
+          "R-HSA-5610760",
+          "R-HSA-168894",
+          "R-HSA-68825",
+          "R-HSA-9908709",
+          "R-HSA-9908721",
+          "R-HSA-9954728",
+          "R-HSA-9825555"
+        ],
+        "vector": [
+          "R-HSA-9907898",
+          "R-HSA-9908178",
+          "R-HSA-9907925",
+          "R-HSA-9907912",
+          "R-HSA-9907928",
+          "R-HSA-9908764",
+          "R-HSA-9908775",
+          "R-HSA-9908709",
+          "R-HSA-9908007",
+          "R-HSA-9908101"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-9954728",
+          "R-HSA-9949676",
+          "R-HSA-983168",
+          "R-HSA-9908800",
+          "R-HSA-5610787",
+          "R-HSA-5632684",
+          "R-HSA-2024096",
+          "R-HSA-9841817",
+          "R-HSA-2024101",
+          "R-HSA-9908709"
+        ],
+        "vector": [
+          "R-HSA-9907900",
+          "R-HSA-9907898",
+          "R-HSA-9907919",
+          "R-HSA-9907912",
+          "R-HSA-9908178",
+          "R-HSA-9908709",
+          "R-HSA-9907980",
+          "R-HSA-9908101",
+          "R-HSA-9949676",
+          "R-HSA-9908775"
+        ]
+      }
+    },
+    "How do Wnt signalling pathways control gene transcription?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-8944351",
+          "R-HSA-8944365",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912",
+          "R-HSA-9007909",
+          "R-HSA-8942225",
+          "R-HSA-3858484"
+        ],
+        "vector": [
+          "R-HSA-8951432",
+          "R-HSA-8944361",
+          "R-HSA-5368519",
+          "R-HSA-8853944",
+          "R-HSA-9858619",
+          "R-HSA-9835498",
+          "R-HSA-5368521",
+          "R-HSA-9823744",
+          "R-HSA-8944354",
+          "R-HSA-9754190"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-2902201",
+          "R-HSA-2902200",
+          "R-HSA-2902208",
+          "R-HSA-2769013",
+          "R-HSA-5340578",
+          "R-HSA-9666639",
+          "R-HSA-9666650",
+          "R-HSA-5340574",
+          "R-HSA-5340581",
+          "R-HSA-9666643"
+        ],
+        "vector": [
+          "R-HSA-9663977",
+          "R-HSA-5339696",
+          "R-HSA-4839625",
+          "R-HSA-9663978",
+          "R-HSA-4839626",
+          "R-HSA-5251512",
+          "R-HSA-4839628",
+          "R-HSA-9663976",
+          "R-HSA-9668766",
+          "R-HSA-9666650"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-8940722",
+          "R-HSA-8941009",
+          "R-HSA-2130479",
+          "R-HSA-901013",
+          "R-HSA-1022110",
+          "R-HSA-4960922",
+          "R-HSA-4960924",
+          "R-HSA-4960927",
+          "R-HSA-2130497",
+          "R-HSA-381083"
+        ],
+        "vector": [
+          "R-HSA-517467",
+          "R-HSA-201702",
+          "R-HSA-3238271",
+          "R-HSA-201676",
+          "R-HSA-201690",
+          "R-HSA-3238279",
+          "R-HSA-3238326",
+          "R-HSA-3238288",
+          "R-HSA-3238284",
+          "R-HSA-3238286"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-5229348",
+          "R-HSA-4411365",
+          "R-HSA-8964513",
+          "R-HSA-188345",
+          "R-HSA-4411357",
+          "R-HSA-8877884",
+          "R-HSA-8964513",
+          "R-HSA-8964531",
+          "R-HSA-8932076",
+          "R-HSA-8944349"
+        ],
+        "vector": [
+          "R-HSA-8944362",
+          "R-HSA-8944352",
+          "R-HSA-8944349",
+          "R-HSA-4411365",
+          "R-HSA-8951442",
+          "R-HSA-5229348",
+          "R-HSA-4411351",
+          "R-HSA-9835496",
+          "R-HSA-4411367",
+          "R-HSA-4411372"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-9008894",
+          "R-HSA-5621481",
+          "R-HSA-9673324",
+          "R-HSA-195721",
+          "R-HSA-9909623",
+          "R-HSA-9909649",
+          "R-HSA-9818749",
+          "R-HSA-5626938",
+          "R-HSA-199920",
+          "R-HSA-8939256"
+        ],
+        "vector": [
+          "R-HSA-195721",
+          "R-HSA-201722",
+          "R-HSA-201712",
+          "R-HSA-8944362",
+          "R-HSA-4411364",
+          "R-HSA-212436",
+          "R-HSA-3299569",
+          "R-HSA-201681",
+          "R-HSA-8944352",
+          "R-HSA-9835496"
+        ]
+      }
+    },
+    "How does TP53 regulate PTEN transcription?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-6782656",
+          "R-HSA-5632941",
+          "R-HSA-5632941",
+          "R-HSA-8851000",
+          "R-HSA-199426",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912"
+        ],
+        "vector": [
+          "R-HSA-5632941",
+          "R-HSA-6799421",
+          "R-HSA-6798606",
+          "R-HSA-6799461",
+          "R-HSA-6798042",
+          "R-HSA-6804385",
+          "R-HSA-6800034",
+          "R-HSA-6798290",
+          "R-HSA-6799788",
+          "R-HSA-6804394"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-2902200",
+          "R-HSA-2902201",
+          "R-HSA-2902208",
+          "R-HSA-2769013",
+          "R-HSA-2399994",
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-2318544",
+          "R-HSA-5652101",
+          "R-HSA-2318437"
+        ],
+        "vector": [
+          "R-HSA-9720096",
+          "R-HSA-9721715",
+          "R-HSA-9720516",
+          "R-HSA-9719626",
+          "R-HSA-9718883",
+          "R-HSA-9720476",
+          "R-HSA-9719017",
+          "R-HSA-9719263",
+          "R-HSA-9721511",
+          "R-HSA-9721910"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-199420",
+          "R-HSA-6807273",
+          "R-HSA-2317339",
+          "R-HSA-2318550",
+          "R-HSA-2318544",
+          "R-HSA-2318509",
+          "R-HSA-2318408",
+          "R-HSA-2317480",
+          "R-HSA-2318520",
+          "R-HSA-2317473"
+        ],
+        "vector": [
+          "R-HSA-6793681",
+          "R-HSA-9721715",
+          "R-HSA-9719017",
+          "R-HSA-9719044",
+          "R-HSA-9720096",
+          "R-HSA-6804378",
+          "R-HSA-9721521",
+          "R-HSA-9720127",
+          "R-HSA-9726136",
+          "R-HSA-9718883"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-5632939",
+          "R-HSA-5632993",
+          "R-HSA-8944104",
+          "R-HSA-5632939",
+          "R-HSA-2321904",
+          "R-HSA-2318752",
+          "R-HSA-6807077",
+          "R-HSA-8943728",
+          "R-HSA-8944078",
+          "R-HSA-8944420"
+        ],
+        "vector": [
+          "R-HSA-5632939",
+          "R-HSA-5632993",
+          "R-HSA-8944104",
+          "R-HSA-6798020",
+          "R-HSA-5629187",
+          "R-HSA-6803391",
+          "R-HSA-6803935",
+          "R-HSA-6806408",
+          "R-HSA-6799462",
+          "R-HSA-4331340"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-5632993",
+          "R-HSA-8944104",
+          "R-HSA-8944026",
+          "R-HSA-5632939",
+          "R-HSA-5628897",
+          "R-HSA-5689950",
+          "R-HSA-8943724",
+          "R-HSA-8851011",
+          "R-HSA-5633007",
+          "R-HSA-6807070"
+        ],
+        "vector": [
+          "R-HSA-5632993",
+          "R-HSA-8944104",
+          "R-HSA-5632939",
+          "R-HSA-8943724",
+          "R-HSA-6806003",
+          "R-HSA-6791312",
+          "R-HSA-3700989",
+          "R-HSA-6807070",
+          "R-HSA-6796648",
+          "R-HSA-6804114"
+        ]
+      }
+    },
+    "How does autophagy degrade cellular components?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912",
+          "R-HSA-9007909",
+          "R-HSA-2864101",
+          "R-HSA-74842",
+          "R-HSA-2855242",
+          "R-HSA-8942225"
+        ],
+        "vector": [
+          "R-HSA-5205648",
+          "R-HSA-9820424",
+          "R-HSA-9820408",
+          "R-HSA-9615717",
+          "R-HSA-8959570",
+          "R-HSA-9631103",
+          "R-HSA-9766679",
+          "R-HSA-9665166",
+          "R-HSA-9631070",
+          "R-HSA-9631107"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-5652101",
+          "R-HSA-5656373",
+          "R-HSA-5656381",
+          "R-HSA-5656354",
+          "R-HSA-5656370",
+          "R-HSA-5656362",
+          "R-HSA-5656368",
+          "R-HSA-5656372"
+        ],
+        "vector": [
+          "R-HSA-8866838",
+          "R-HSA-8866842",
+          "R-HSA-5357598",
+          "R-HSA-8866834",
+          "R-HSA-3791363",
+          "R-HSA-5357607",
+          "R-HSA-2262739",
+          "R-HSA-6802517",
+          "R-HSA-5579105",
+          "R-HSA-5579040"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2192945",
+          "R-HSA-2152356",
+          "R-HSA-2192948",
+          "R-HSA-2192934",
+          "R-HSA-2193046"
+        ],
+        "vector": [
+          "R-HSA-5671863",
+          "R-HSA-5671858",
+          "R-HSA-5671857",
+          "R-HSA-9819365",
+          "R-HSA-9819371",
+          "R-HSA-9819377",
+          "R-HSA-5671859",
+          "R-HSA-9819376",
+          "R-HSA-9820421",
+          "R-HSA-9819381"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-9012689",
+          "R-HSA-481010",
+          "R-HSA-481044",
+          "R-HSA-8942224",
+          "R-HSA-6784620",
+          "R-HSA-3132753",
+          "R-HSA-9008696",
+          "R-HSA-6784648",
+          "R-HSA-9008694",
+          "R-HSA-9008692"
+        ],
+        "vector": [
+          "R-HSA-9935547",
+          "R-HSA-9839105",
+          "R-HSA-9839113",
+          "R-HSA-9839146",
+          "R-HSA-9839751",
+          "R-HSA-9935552",
+          "R-HSA-190829",
+          "R-HSA-9839072",
+          "R-HSA-174058",
+          "R-HSA-9625188"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-9857377",
+          "R-HSA-9759169",
+          "R-HSA-9824897",
+          "R-HSA-9759172",
+          "R-HSA-9612973",
+          "R-HSA-9663891",
+          "R-HSA-9615710",
+          "R-HSA-5665868",
+          "R-HSA-9754560",
+          "R-HSA-77042"
+        ],
+        "vector": [
+          "R-HSA-1632852",
+          "R-HSA-9612973",
+          "R-HSA-9663891",
+          "R-HSA-9646399",
+          "R-HSA-5205663",
+          "R-HSA-8959571",
+          "R-HSA-9935547",
+          "R-HSA-5682388",
+          "R-HSA-9837999",
+          "R-HSA-9615710"
+        ]
+      }
+    },
+    "How does the electron transport chain generate ATP?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-169268",
+          "R-HSA-169267",
+          "R-HSA-9670846",
+          "R-HSA-169268",
+          "R-HSA-169267",
+          "R-HSA-3791167",
+          "R-HSA-3791167",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698"
+        ],
+        "vector": [
+          "R-HSA-74184",
+          "R-HSA-2466375",
+          "R-HSA-74186",
+          "R-HSA-164838",
+          "R-HSA-164835",
+          "R-HSA-74185",
+          "R-HSA-5252095",
+          "R-HSA-8949570",
+          "R-HSA-1222508",
+          "R-HSA-9865410"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-8866838",
+          "R-HSA-8866842",
+          "R-HSA-5652101",
+          "R-HSA-3621821",
+          "R-HSA-3621745",
+          "R-HSA-3621810",
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-2207700",
+          "R-HSA-2207687"
+        ],
+        "vector": [
+          "R-HSA-9957856",
+          "R-HSA-9957859",
+          "R-HSA-9958154",
+          "R-HSA-9957853",
+          "R-HSA-9956419",
+          "R-HSA-9958037",
+          "R-HSA-9957823",
+          "R-HSA-9957880",
+          "R-HSA-9957878",
+          "R-HSA-9958004"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-2130626",
+          "R-HSA-2130559",
+          "R-HSA-2130621",
+          "R-HSA-2130326",
+          "R-HSA-2130344",
+          "R-HSA-2130575",
+          "R-HSA-2130691",
+          "R-HSA-2130432",
+          "R-HSA-2130471",
+          "R-HSA-2130530"
+        ],
+        "vector": [
+          "R-HSA-50508",
+          "R-HSA-164577",
+          "R-HSA-1299441",
+          "R-HSA-164532",
+          "R-HSA-164574",
+          "R-HSA-5215992",
+          "R-HSA-1267972",
+          "R-HSA-1267978",
+          "R-HSA-164533",
+          "R-HSA-50522"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-9008696",
+          "R-HSA-163214",
+          "R-HSA-8942224",
+          "R-HSA-442715",
+          "R-HSA-163213",
+          "R-HSA-5682111",
+          "R-HSA-9008928",
+          "R-HSA-9012689",
+          "R-HSA-164651",
+          "R-HSA-9036061"
+        ],
+        "vector": [
+          "R-HSA-164832",
+          "R-HSA-164834",
+          "R-HSA-169270",
+          "R-HSA-164840",
+          "R-HSA-169260",
+          "R-HSA-163214",
+          "R-HSA-163217",
+          "R-HSA-450971",
+          "R-HSA-2395517",
+          "R-HSA-166223"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-611105",
+          "R-HSA-1428517",
+          "R-HSA-77289",
+          "R-HSA-163217",
+          "R-HSA-6806831",
+          "R-HSA-2564824",
+          "R-HSA-163214",
+          "R-HSA-9709406",
+          "R-HSA-70171",
+          "R-HSA-2395516"
+        ],
+        "vector": [
+          "R-HSA-611105",
+          "R-HSA-163210",
+          "R-HSA-1428517",
+          "R-HSA-164834",
+          "R-HSA-163217",
+          "R-HSA-164832",
+          "R-HSA-169260",
+          "R-HSA-2395516",
+          "R-HSA-163214",
+          "R-HSA-9864415"
+        ]
+      }
+    },
+    "How is oxidative stress handled by peroxiredoxins?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912",
+          "R-HSA-9007909",
+          "R-HSA-8942225",
+          "R-HSA-8848514",
+          "R-HSA-9008615",
+          "R-HSA-9008597"
+        ],
+        "vector": [
+          "R-HSA-3341319",
+          "R-HSA-5631882",
+          "R-HSA-3323000",
+          "R-HSA-3341391",
+          "R-HSA-3343687",
+          "R-HSA-3323071",
+          "R-HSA-5631902",
+          "R-HSA-1250249",
+          "R-HSA-9759106",
+          "R-HSA-3341375"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9646285",
+          "R-HSA-9648651",
+          "R-HSA-9648659",
+          "R-HSA-9648647",
+          "R-HSA-9648656",
+          "R-HSA-9648652",
+          "R-HSA-9648655",
+          "R-HSA-9648653",
+          "R-HSA-9648663",
+          "R-HSA-9632257"
+        ],
+        "vector": [
+          "R-HSA-9719117",
+          "R-HSA-5603346",
+          "R-HSA-9719993",
+          "R-HSA-9720800",
+          "R-HSA-9720254",
+          "R-HSA-9718883",
+          "R-HSA-9719752",
+          "R-HSA-9718821",
+          "R-HSA-9718627",
+          "R-HSA-9721682"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2192945",
+          "R-HSA-2152356",
+          "R-HSA-2192948",
+          "R-HSA-2192934",
+          "R-HSA-2193046"
+        ],
+        "vector": [
+          "R-HSA-3341270",
+          "R-HSA-8868564",
+          "R-HSA-5629198",
+          "R-HSA-3343670",
+          "R-HSA-3341350",
+          "R-HSA-8958052",
+          "R-HSA-3341292",
+          "R-HSA-8868574",
+          "R-HSA-6806198",
+          "R-HSA-3323081"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-3209111",
+          "R-HSA-3209114",
+          "R-HSA-3225867",
+          "R-HSA-9623023",
+          "R-HSA-9615023",
+          "R-HSA-9622981",
+          "R-HSA-9625863",
+          "R-HSA-9625693",
+          "R-HSA-9623280",
+          "R-HSA-9625092"
+        ],
+        "vector": [
+          "R-HSA-3697882",
+          "R-HSA-3341343",
+          "R-HSA-3697894",
+          "R-HSA-3322995",
+          "R-HSA-9760094",
+          "R-HSA-5631885",
+          "R-HSA-1222644",
+          "R-HSA-1222755",
+          "R-HSA-3343700",
+          "R-HSA-1222526"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-1222541",
+          "R-HSA-9620532",
+          "R-HSA-5632386",
+          "R-HSA-9759147",
+          "R-HSA-9617853",
+          "R-HSA-9708557",
+          "R-HSA-9796053",
+          "R-HSA-1222341",
+          "R-HSA-9818027",
+          "R-HSA-3371511"
+        ],
+        "vector": [
+          "R-HSA-3341343",
+          "R-HSA-3322995",
+          "R-HSA-3697882",
+          "R-HSA-5631885",
+          "R-HSA-1222755",
+          "R-HSA-9760094",
+          "R-HSA-3697894",
+          "R-HSA-3343700",
+          "R-HSA-1222644",
+          "R-HSA-3299685"
+        ]
+      }
+    },
+    "What are the steps of glycolysis?": {
+      "complexes": {
+        "bm25": [
+          "R-NUL-9603755",
+          "R-NUL-9034806",
+          "R-HSA-156824",
+          "R-HSA-156824",
+          "R-HSA-1218829",
+          "R-HSA-1218829",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009912"
+        ],
+        "vector": [
+          "R-HSA-3322053",
+          "R-HSA-3322007",
+          "R-HSA-8955670",
+          "R-HSA-3322021",
+          "R-HSA-3777104",
+          "R-HSA-3322063",
+          "R-HSA-70218",
+          "R-HSA-3781017",
+          "R-HSA-3777096",
+          "R-HSA-3777094"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-5652101",
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-5246651",
+          "R-HSA-9663984",
+          "R-HSA-9663982",
+          "R-HSA-9663977",
+          "R-HSA-9663975",
+          "R-HSA-9663978",
+          "R-HSA-9663983"
+        ],
+        "vector": [
+          "R-HSA-5609928",
+          "R-HSA-5609931",
+          "R-HSA-5609927",
+          "R-HSA-3229123",
+          "R-HSA-5609933",
+          "R-HSA-5659977",
+          "R-HSA-5609926",
+          "R-HSA-3781891",
+          "R-HSA-3781924",
+          "R-HSA-3781863"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-983091",
+          "R-HSA-1181241",
+          "R-HSA-2130716",
+          "R-HSA-8855907",
+          "R-HSA-985498",
+          "R-HSA-985502",
+          "R-HSA-2130328",
+          "R-HSA-2130361",
+          "R-HSA-2130513",
+          "R-HSA-2130373"
+        ],
+        "vector": [
+          "R-HSA-70298",
+          "R-HSA-70174",
+          "R-HSA-6799244",
+          "R-HSA-70292",
+          "R-HSA-70186",
+          "R-HSA-6813805",
+          "R-HSA-372873",
+          "R-HSA-70176",
+          "R-HSA-70300",
+          "R-HSA-70428"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-9008696",
+          "R-HSA-8942224",
+          "R-HSA-9008928",
+          "R-HSA-9012689",
+          "R-HSA-6810357",
+          "R-HSA-8934819",
+          "R-HSA-6784620",
+          "R-HSA-8849797",
+          "R-HSA-6784648",
+          "R-HSA-9008694"
+        ],
+        "vector": [
+          "R-HSA-70420",
+          "R-HSA-8955760",
+          "R-HSA-5696021",
+          "R-HSA-9638125",
+          "R-HSA-9638127",
+          "R-HSA-70471",
+          "R-HSA-71496",
+          "R-HSA-163751",
+          "R-HSA-71334",
+          "R-HSA-70449"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-912429",
+          "R-HSA-171306",
+          "R-HSA-991365",
+          "R-HSA-9012689",
+          "R-HSA-611105",
+          "R-HSA-163359",
+          "R-HSA-163773",
+          "R-HSA-163754",
+          "R-HSA-448703",
+          "R-HSA-5652084"
+        ],
+        "vector": [
+          "R-HSA-70171",
+          "R-HSA-9634600",
+          "R-HSA-8955760",
+          "R-HSA-75887",
+          "R-HSA-70420",
+          "R-HSA-70475",
+          "R-HSA-70449",
+          "R-HSA-453358",
+          "R-HSA-163751",
+          "R-HSA-70221"
+        ]
+      }
+    },
+    "What does CDK5 phosphorylate in Alzheimer's disease?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-399870",
+          "R-HSA-399867",
+          "R-HSA-399853",
+          "R-HSA-399870",
+          "R-HSA-399867",
+          "R-HSA-399853",
+          "R-HSA-399851",
+          "R-HSA-421107",
+          "R-HSA-399843",
+          "R-HSA-9032842"
+        ],
+        "vector": [
+          "R-HSA-421098",
+          "R-HSA-421107",
+          "R-HSA-6805271",
+          "R-HSA-9616817",
+          "R-HSA-8863434",
+          "R-HSA-9032852",
+          "R-HSA-8863585",
+          "R-HSA-9032842",
+          "R-HSA-399838",
+          "R-NUL-9032960"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9656270",
+          "R-HSA-9656265",
+          "R-HSA-9656288",
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-5652101",
+          "R-HSA-9688105",
+          "R-HSA-9659326",
+          "R-HSA-9632202",
+          "R-HSA-9632523"
+        ],
+        "vector": [
+          "R-HSA-9660543",
+          "R-HSA-2399421",
+          "R-HSA-9652794",
+          "R-HSA-9630805",
+          "R-HSA-9646285",
+          "R-HSA-9710837",
+          "R-HSA-9656270",
+          "R-HSA-9632275",
+          "R-HSA-9652019",
+          "R-HSA-9672662"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-8863586",
+          "R-HSA-180064",
+          "R-HSA-399809",
+          "R-HSA-6805249",
+          "R-HSA-6810859",
+          "R-HSA-2470041",
+          "R-HSA-2192934",
+          "R-HSA-2470201",
+          "R-HSA-2470161",
+          "R-HSA-2192948"
+        ],
+        "vector": [
+          "R-HSA-180064",
+          "R-HSA-8863586",
+          "R-HSA-6805249",
+          "R-HSA-421083",
+          "R-HSA-8863415",
+          "R-HSA-8863400",
+          "R-HSA-399809",
+          "R-HSA-6805262",
+          "R-HSA-9616369",
+          "R-HSA-380282"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-8863587",
+          "R-HSA-8863013",
+          "R-HSA-8863009",
+          "R-HSA-8868573",
+          "R-HSA-8868567",
+          "R-HSA-8870703",
+          "R-HSA-8870710",
+          "R-HSA-8868260",
+          "R-HSA-8868666",
+          "R-HSA-8870686"
+        ],
+        "vector": [
+          "R-HSA-8868340",
+          "R-HSA-8863014",
+          "R-HSA-8863013",
+          "R-HSA-8868260",
+          "R-HSA-8868344",
+          "R-HSA-8863007",
+          "R-HSA-8863011",
+          "R-HSA-9032854",
+          "R-HSA-9032863",
+          "R-HSA-6805276"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-8868666",
+          "R-HSA-8868260",
+          "R-HSA-8862803",
+          "R-HSA-8868567",
+          "R-HSA-8868573",
+          "R-HSA-8868344",
+          "R-HSA-8868340",
+          "R-HSA-9936686",
+          "R-HSA-8876696",
+          "R-HSA-9656255"
+        ],
+        "vector": [
+          "R-HSA-8862803",
+          "R-HSA-8868344",
+          "R-HSA-8868340",
+          "R-HSA-8868260",
+          "R-HSA-6805276",
+          "R-HSA-9032863",
+          "R-HSA-8868567",
+          "R-HSA-8868573",
+          "R-HSA-8863014",
+          "R-HSA-399944"
+        ]
+      }
+    },
+    "What happens during Golgi fragmentation in neurodegeneration?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-190556",
+          "R-HSA-190556",
+          "R-HSA-191615",
+          "R-HSA-194780",
+          "R-HSA-190583",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009912",
+          "R-HSA-9009901"
+        ],
+        "vector": [
+          "R-HSA-2172185",
+          "R-HSA-6808912",
+          "R-HSA-6811379",
+          "R-HSA-6814069",
+          "R-HSA-8847543",
+          "R-HSA-6814046",
+          "R-HSA-5694327",
+          "R-HSA-6807825",
+          "R-HSA-8847548",
+          "R-HSA-6811375"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-5652101",
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-5649751",
+          "R-HSA-5653602",
+          "R-HSA-5653594",
+          "R-HSA-5653621",
+          "R-HSA-5653593",
+          "R-HSA-5649754",
+          "R-HSA-5649750"
+        ],
+        "vector": [
+          "R-HSA-9718927",
+          "R-HSA-9721577",
+          "R-HSA-9718628",
+          "R-HSA-9719322",
+          "R-HSA-9720568",
+          "R-HSA-9718923",
+          "R-HSA-9719916",
+          "R-HSA-9718571",
+          "R-HSA-9721246",
+          "R-HSA-9718884"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-4420341",
+          "R-HSA-1463447",
+          "R-HSA-975679",
+          "R-HSA-975678",
+          "R-HSA-1470024",
+          "R-HSA-913617",
+          "R-HSA-975680",
+          "R-HSA-2054103",
+          "R-HSA-2064160",
+          "R-HSA-913668"
+        ],
+        "vector": [
+          "R-HSA-3636823",
+          "R-HSA-8865269",
+          "R-HSA-351189",
+          "R-HSA-6800164",
+          "R-HSA-8865268",
+          "R-HSA-1911522",
+          "R-HSA-9715183",
+          "R-HSA-9647777",
+          "R-HSA-187036",
+          "R-HSA-166515"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-9012689",
+          "R-HSA-8942224",
+          "R-HSA-9832205",
+          "R-HSA-6784620",
+          "R-HSA-9008696",
+          "R-HSA-190520",
+          "R-HSA-6784648",
+          "R-HSA-9008694",
+          "R-HSA-9008692",
+          "R-HSA-9008928"
+        ],
+        "vector": [
+          "R-HSA-421835",
+          "R-HSA-167014",
+          "R-HSA-432707",
+          "R-HSA-9913337",
+          "R-HSA-9626242",
+          "R-HSA-6789208",
+          "R-HSA-209532",
+          "R-HSA-190829",
+          "R-HSA-8871506",
+          "R-HSA-5692941"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-912429",
+          "R-HSA-8868260",
+          "R-HSA-162658",
+          "R-HSA-2314566",
+          "R-HSA-140342",
+          "R-HSA-170057",
+          "R-HSA-2214351",
+          "R-HSA-5652099",
+          "R-HSA-5649742",
+          "R-HSA-8874138"
+        ],
+        "vector": [
+          "R-HSA-8868260",
+          "R-HSA-162658",
+          "R-HSA-8863678",
+          "R-HSA-9913337",
+          "R-HSA-9626242",
+          "R-HSA-167014",
+          "R-HSA-9840310",
+          "R-HSA-6811442",
+          "R-HSA-432707",
+          "R-HSA-190829"
+        ]
+      }
+    },
+    "What is the function of BRCA1 in homologous recombination?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-180610",
+          "R-HSA-9629402",
+          "R-HSA-9629190",
+          "R-HSA-9629444",
+          "R-HSA-9665818",
+          "R-HSA-175416",
+          "R-HSA-177526",
+          "R-HSA-156824",
+          "R-HSA-156824",
+          "R-HSA-1218829"
+        ],
+        "vector": [
+          "R-HSA-5686226",
+          "R-HSA-5685658",
+          "R-HSA-9980005",
+          "R-HSA-5683806",
+          "R-HSA-5686227",
+          "R-HSA-5693590",
+          "R-HSA-5683606",
+          "R-HSA-5683387",
+          "R-HSA-5685826",
+          "R-HSA-5686613"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9703739",
+          "R-HSA-9703552",
+          "R-HSA-9703568",
+          "R-HSA-9703478",
+          "R-HSA-9703804",
+          "R-HSA-9703802",
+          "R-HSA-9703811",
+          "R-HSA-9703554",
+          "R-HSA-9703728",
+          "R-HSA-9703553"
+        ],
+        "vector": [
+          "R-HSA-9703725",
+          "R-HSA-9701202",
+          "R-HSA-9703762",
+          "R-HSA-9702135",
+          "R-HSA-9703509",
+          "R-HSA-9703727",
+          "R-HSA-9703552",
+          "R-HSA-9709628",
+          "R-HSA-9703804",
+          "R-HSA-9703761"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-50949",
+          "R-HSA-9702140",
+          "R-HSA-9701202",
+          "R-HSA-9663206",
+          "R-HSA-9702135",
+          "R-HSA-9700894",
+          "R-HSA-9700923",
+          "R-HSA-9700916",
+          "R-HSA-9700934",
+          "R-HSA-9700944"
+        ],
+        "vector": [
+          "R-HSA-9700923",
+          "R-HSA-9700921",
+          "R-HSA-9702416",
+          "R-HSA-50949",
+          "R-HSA-9702722",
+          "R-HSA-9702710",
+          "R-HSA-9703735",
+          "R-HSA-50951",
+          "R-HSA-9702702",
+          "R-HSA-5683800"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-9704330",
+          "R-HSA-9701199",
+          "R-HSA-9699163",
+          "R-HSA-9663194",
+          "R-HSA-9704408",
+          "R-HSA-9759522",
+          "R-HSA-9926487",
+          "R-HSA-9007605",
+          "R-HSA-912467",
+          "R-HSA-9926521"
+        ],
+        "vector": [
+          "R-HSA-5659781",
+          "R-HSA-912467",
+          "R-HSA-5693561",
+          "R-HSA-5683385",
+          "R-HSA-9763137",
+          "R-HSA-9701199",
+          "R-HSA-5685985",
+          "R-HSA-9709273",
+          "R-HSA-5685341",
+          "R-HSA-9707051"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-9675136",
+          "R-HSA-5684108",
+          "R-HSA-9701192",
+          "R-HSA-9704331",
+          "R-HSA-9701000",
+          "R-HSA-6783310",
+          "R-HSA-9701193",
+          "R-HSA-912446",
+          "R-HSA-5659781",
+          "R-HSA-5693608"
+        ],
+        "vector": [
+          "R-HSA-9701192",
+          "R-HSA-5693561",
+          "R-HSA-9701190",
+          "R-HSA-5693579",
+          "R-HSA-5693616",
+          "R-HSA-9663199",
+          "R-HSA-5659781",
+          "R-HSA-5685942",
+          "R-HSA-9701199",
+          "R-HSA-5693607"
+        ]
+      }
+    },
+    "What is the mechanism of ubiquitin-mediated protein degradation?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-156824",
+          "R-HSA-1218829",
+          "R-HSA-1218829",
+          "R-HSA-156824",
+          "R-HSA-9657583",
+          "R-HSA-9657587",
+          "R-HSA-9657590",
+          "R-HSA-9657592",
+          "R-HSA-8847533",
+          "R-HSA-8847526"
+        ],
+        "vector": [
+          "R-HSA-983126",
+          "R-HSA-983134",
+          "R-HSA-936388",
+          "R-HSA-9794013",
+          "R-HSA-8956077",
+          "R-HSA-9641099",
+          "R-HSA-1234116",
+          "R-HSA-187568",
+          "R-HSA-8956079",
+          "R-HSA-1234123"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-5652101",
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-8866838",
+          "R-HSA-5246655",
+          "R-HSA-5246651",
+          "R-HSA-5246652",
+          "R-HSA-5246648",
+          "R-HSA-5246654",
+          "R-HSA-9005542"
+        ],
+        "vector": [
+          "R-HSA-5246648",
+          "R-HSA-5246652",
+          "R-HSA-5246655",
+          "R-HSA-5246651",
+          "R-HSA-5387340",
+          "R-HSA-5387351",
+          "R-HSA-5387342",
+          "R-HSA-9663943",
+          "R-HSA-5387341",
+          "R-HSA-5387339"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-5216038",
+          "R-HSA-8867445",
+          "R-HSA-8867424",
+          "R-HSA-6805240",
+          "R-HSA-5215985",
+          "R-HSA-983091",
+          "R-HSA-1181241",
+          "R-HSA-2130716",
+          "R-HSA-8855907",
+          "R-HSA-2130328"
+        ],
+        "vector": [
+          "R-HSA-939219",
+          "R-HSA-9763013",
+          "R-HSA-5683033",
+          "R-HSA-939174",
+          "R-HSA-939176",
+          "R-HSA-8943079",
+          "R-HSA-9764648",
+          "R-HSA-9764649",
+          "R-HSA-9764658",
+          "R-HSA-9764646"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-3791319",
+          "R-HSA-2533965",
+          "R-HSA-2533970",
+          "R-HSA-3828025",
+          "R-HSA-4086205",
+          "R-HSA-2534160",
+          "R-HSA-2534240",
+          "R-HSA-2534248",
+          "R-HSA-1592270",
+          "R-HSA-69600"
+        ],
+        "vector": [
+          "R-HSA-9755306",
+          "R-HSA-8952408",
+          "R-HSA-8853514",
+          "R-HSA-1504193",
+          "R-HSA-4641260",
+          "R-HSA-2130282",
+          "R-HSA-69016",
+          "R-HSA-264458",
+          "R-HSA-211734",
+          "R-HSA-8956184"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-211733",
+          "R-HSA-912429",
+          "R-HSA-4641257",
+          "R-HSA-9012689",
+          "R-HSA-2467775",
+          "R-HSA-68689",
+          "R-HSA-202541",
+          "R-HSA-69601",
+          "R-HSA-6784620",
+          "R-HSA-4085011"
+        ],
+        "vector": [
+          "R-HSA-8852135",
+          "R-HSA-8956184",
+          "R-HSA-983168",
+          "R-HSA-9949676",
+          "R-HSA-264458",
+          "R-HSA-8854071",
+          "R-HSA-69016",
+          "R-HSA-69600",
+          "R-HSA-8850992",
+          "R-HSA-8853514"
+        ]
+      }
+    },
+    "What is the role of CDK12 in DNA repair gene expression?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-6797608",
+          "R-HSA-6797609",
+          "R-HSA-180610",
+          "R-HSA-6797609",
+          "R-HSA-6797608",
+          "R-HSA-6797614",
+          "R-HSA-6797614",
+          "R-HSA-6797602",
+          "R-HSA-9629190",
+          "R-HSA-9629402"
+        ],
+        "vector": [
+          "R-HSA-6797608",
+          "R-HSA-6797602",
+          "R-HSA-6797614",
+          "R-HSA-6797607",
+          "R-HSA-6797609",
+          "R-HSA-6797095",
+          "R-HSA-6797702",
+          "R-HSA-9980005",
+          "R-HSA-5687362",
+          "R-HSA-5686692"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-5575594",
+          "R-HSA-5578664",
+          "R-HSA-5444512",
+          "R-HSA-5444526",
+          "R-HSA-5632980",
+          "R-HSA-5632982",
+          "R-HSA-5632954",
+          "R-HSA-5652101",
+          "R-HSA-9629165",
+          "R-HSA-9824828"
+        ],
+        "vector": [
+          "R-HSA-9712964",
+          "R-HSA-9703724",
+          "R-HSA-9712572",
+          "R-HSA-9712703",
+          "R-HSA-9712538",
+          "R-HSA-9712889",
+          "R-HSA-9712748",
+          "R-HSA-9712708",
+          "R-HSA-9712897",
+          "R-HSA-9712646"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6797012",
+          "R-HSA-983091",
+          "R-HSA-1181241",
+          "R-HSA-2130716",
+          "R-HSA-985498",
+          "R-HSA-985502",
+          "R-HSA-8855907",
+          "R-HSA-2130328",
+          "R-HSA-2130361",
+          "R-HSA-2130373"
+        ],
+        "vector": [
+          "R-HSA-6797012",
+          "R-HSA-6797014",
+          "R-HSA-6801374",
+          "R-HSA-9712703",
+          "R-HSA-6806442",
+          "R-HSA-212440",
+          "R-HSA-69218",
+          "R-HSA-9712129",
+          "R-HSA-9712964",
+          "R-HSA-9712572"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-6797606",
+          "R-HSA-6797712",
+          "R-HSA-6797616",
+          "R-HSA-6797090",
+          "R-HSA-9926521",
+          "R-HSA-9926522",
+          "R-HSA-9926532",
+          "R-HSA-9859119",
+          "R-HSA-9858734",
+          "R-HSA-9858729"
+        ],
+        "vector": [
+          "R-HSA-6797712",
+          "R-HSA-6797616",
+          "R-HSA-6797606",
+          "R-HSA-6797090",
+          "R-HSA-6797100",
+          "R-HSA-6796647",
+          "R-HSA-8961934",
+          "R-HSA-5684096",
+          "R-HSA-5684081",
+          "R-HSA-6796649"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-6797712",
+          "R-HSA-6797606",
+          "R-HSA-6796648",
+          "R-HSA-912429",
+          "R-HSA-6784620",
+          "R-HSA-9629232",
+          "R-HSA-6781827",
+          "R-HSA-73894",
+          "R-HSA-5696398",
+          "R-HSA-5423599"
+        ],
+        "vector": [
+          "R-HSA-6797712",
+          "R-HSA-6797606",
+          "R-HSA-6797616",
+          "R-HSA-6796648",
+          "R-HSA-6797090",
+          "R-HSA-5693532",
+          "R-HSA-73894",
+          "R-HSA-5693565",
+          "R-HSA-6781827",
+          "R-HSA-9858560"
+        ]
+      }
+    },
+    "What is the role of mTOR in cell growth?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-180610",
+          "R-HSA-377400",
+          "R-HSA-9629402",
+          "R-HSA-9629190",
+          "R-HSA-9629444",
+          "R-HSA-9665818",
+          "R-HSA-5083661",
+          "R-HSA-175416",
+          "R-HSA-177526",
+          "R-HSA-377400"
+        ],
+        "vector": [
+          "R-HSA-5673771",
+          "R-HSA-377400",
+          "R-HSA-5083661",
+          "R-HSA-9645607",
+          "R-HSA-5653972",
+          "R-HSA-198626",
+          "R-HSA-5675639",
+          "R-HSA-5693283",
+          "R-HSA-5083643",
+          "R-HSA-9646465"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-5652101",
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-8866838",
+          "R-HSA-9648866",
+          "R-HSA-9651177",
+          "R-HSA-2018743",
+          "R-HSA-9688041",
+          "R-HSA-9688165",
+          "R-HSA-9688043"
+        ],
+        "vector": [
+          "R-HSA-9676956",
+          "R-HSA-2395934",
+          "R-HSA-9660514",
+          "R-HSA-5661477",
+          "R-HSA-9647218",
+          "R-HSA-9672021",
+          "R-HSA-2243944",
+          "R-HSA-1500573",
+          "R-HSA-9672009",
+          "R-HSA-6802517"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-165662",
+          "R-HSA-5083674",
+          "R-HSA-192603",
+          "R-HSA-2160944",
+          "R-HSA-434608",
+          "R-HSA-434611",
+          "R-HSA-434610",
+          "R-HSA-434612",
+          "R-HSA-421236",
+          "R-HSA-421271"
+        ],
+        "vector": [
+          "R-HSA-5083674",
+          "R-HSA-165662",
+          "R-HSA-3006727",
+          "R-HSA-3132767",
+          "R-HSA-5083664",
+          "R-HSA-9619989",
+          "R-HSA-444256",
+          "R-HSA-165714",
+          "R-HSA-9619959",
+          "R-HSA-9619872"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-6803946",
+          "R-HSA-6798031",
+          "R-HSA-6802170",
+          "R-HSA-6803917",
+          "R-HSA-6801637",
+          "R-HSA-1168839",
+          "R-HSA-6798020",
+          "R-HSA-6801641",
+          "R-HSA-6803935",
+          "R-HSA-6803914"
+        ],
+        "vector": [
+          "R-HSA-8944454",
+          "R-HSA-165718",
+          "R-HSA-6795290",
+          "R-HSA-9646468",
+          "R-HSA-9980233",
+          "R-HSA-5672828",
+          "R-HSA-447074",
+          "R-HSA-9645608",
+          "R-HSA-165692",
+          "R-HSA-165726"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-165159",
+          "R-HSA-200143",
+          "R-HSA-198609",
+          "R-HSA-8854302",
+          "R-HSA-165680",
+          "R-HSA-912429",
+          "R-HSA-5082405",
+          "R-HSA-6784620",
+          "R-HSA-5628897",
+          "R-HSA-2400009"
+        ],
+        "vector": [
+          "R-HSA-166208",
+          "R-HSA-165159",
+          "R-HSA-9639288",
+          "R-HSA-165680",
+          "R-HSA-198609",
+          "R-HSA-198640",
+          "R-HSA-8944454",
+          "R-HSA-165718",
+          "R-HSA-9711097",
+          "R-HSA-5672828"
+        ]
+      }
+    },
+    "What proteins interact with beta-catenin?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-201922",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009912",
+          "R-HSA-9009901",
+          "R-HSA-9007909",
+          "R-HSA-8942225",
+          "R-HSA-2161325",
+          "R-HSA-9008615"
+        ],
+        "vector": [
+          "R-HSA-195282",
+          "R-HSA-3134925",
+          "R-HSA-195305",
+          "R-HSA-8877851",
+          "R-HSA-195313",
+          "R-HSA-5626915",
+          "R-HSA-4416737",
+          "R-HSA-201938",
+          "R-HSA-9835549",
+          "R-HSA-195297"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-5652101",
+          "R-HSA-9663984",
+          "R-HSA-9663982",
+          "R-HSA-9663975",
+          "R-HSA-9663978",
+          "R-HSA-9663983",
+          "R-HSA-4839619",
+          "R-HSA-9663981"
+        ],
+        "vector": [
+          "R-HSA-9663977",
+          "R-HSA-4839626",
+          "R-HSA-4839625",
+          "R-HSA-4839612",
+          "R-HSA-9663981",
+          "R-HSA-9663978",
+          "R-HSA-4839630",
+          "R-HSA-4836868",
+          "R-HSA-9663976",
+          "R-HSA-4839628"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2192945",
+          "R-HSA-2152356",
+          "R-HSA-2192948",
+          "R-HSA-2192934",
+          "R-HSA-2193046"
+        ],
+        "vector": [
+          "R-HSA-8942367",
+          "R-HSA-8942369",
+          "R-HSA-448839",
+          "R-HSA-4839628",
+          "R-HSA-9663977",
+          "R-HSA-4839626",
+          "R-HSA-8942374",
+          "R-HSA-9663976",
+          "R-HSA-9038440",
+          "R-HSA-202950"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-1011576",
+          "R-HSA-199043",
+          "R-HSA-5665608",
+          "R-HSA-202969",
+          "R-HSA-2130279",
+          "R-HSA-351913",
+          "R-HSA-351871",
+          "R-HSA-201595",
+          "R-HSA-201636",
+          "R-HSA-3134901"
+        ],
+        "vector": [
+          "R-HSA-5626938",
+          "R-HSA-419002",
+          "R-HSA-3772430",
+          "R-HSA-3134883",
+          "R-HSA-5665608",
+          "R-HSA-3769383",
+          "R-HSA-3299569",
+          "R-HSA-3322427",
+          "R-HSA-3769391",
+          "R-HSA-3361751"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-5665608",
+          "R-HSA-912429",
+          "R-HSA-5626938",
+          "R-HSA-201669",
+          "R-HSA-9773218",
+          "R-HSA-8862184",
+          "R-HSA-3134901",
+          "R-HSA-419002",
+          "R-HSA-9012689",
+          "R-HSA-9686174"
+        ],
+        "vector": [
+          "R-HSA-5626938",
+          "R-HSA-3772430",
+          "R-HSA-9933194",
+          "R-HSA-3299569",
+          "R-HSA-201712",
+          "R-HSA-3451153",
+          "R-HSA-201722",
+          "R-HSA-5665608",
+          "R-HSA-3322424",
+          "R-HSA-419002"
+        ]
+      }
+    },
+    "What reactions involve EGFR autophosphorylation?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912",
+          "R-HSA-9007909",
+          "R-HSA-8942225",
+          "R-HSA-1225979",
+          "R-HSA-1225979",
+          "R-HSA-1220587"
+        ],
+        "vector": [
+          "R-HSA-8867037",
+          "R-HSA-212703",
+          "R-HSA-179882",
+          "R-HSA-180326",
+          "R-HSA-1251942",
+          "R-HSA-8863840",
+          "R-HSA-1226013",
+          "R-HSA-180277",
+          "R-HSA-182946",
+          "R-HSA-182948"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-1996315",
+          "R-HSA-1996321",
+          "R-HSA-1996327",
+          "R-HSA-1177531",
+          "R-HSA-1177532",
+          "R-HSA-1228016",
+          "R-HSA-1996314",
+          "R-HSA-1228015",
+          "R-HSA-1996330",
+          "R-HSA-1996306"
+        ],
+        "vector": [
+          "R-HSA-1996340",
+          "R-HSA-1996341",
+          "R-HSA-1182984",
+          "R-HSA-1228037",
+          "R-HSA-1248649",
+          "R-HSA-1996336",
+          "R-HSA-1996334",
+          "R-HSA-1173211",
+          "R-HSA-1996335",
+          "R-HSA-1996338"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-9611160",
+          "R-HSA-179837",
+          "R-HSA-1181211",
+          "R-HSA-1228010",
+          "R-HSA-1996321",
+          "R-HSA-1228012",
+          "R-HSA-1228015",
+          "R-HSA-1996327",
+          "R-HSA-1177542",
+          "R-HSA-1996330"
+        ],
+        "vector": [
+          "R-HSA-1996330",
+          "R-HSA-8864019",
+          "R-HSA-1182984",
+          "R-HSA-1996338",
+          "R-HSA-1173211",
+          "R-HSA-1996335",
+          "R-HSA-1181386",
+          "R-HSA-1996322",
+          "R-HSA-1173212",
+          "R-HSA-1996306"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-177934",
+          "R-HSA-2179387",
+          "R-HSA-8857577",
+          "R-HSA-9012689",
+          "R-HSA-8942224",
+          "R-HSA-1220610",
+          "R-HSA-1225978",
+          "R-HSA-1220611",
+          "R-HSA-6784620",
+          "R-HSA-9008696"
+        ],
+        "vector": [
+          "R-HSA-177934",
+          "R-HSA-1169421",
+          "R-HSA-1248655",
+          "R-HSA-177930",
+          "R-HSA-9625487",
+          "R-HSA-9665389",
+          "R-HSA-1225952",
+          "R-HSA-9665709",
+          "R-HSA-8857555",
+          "R-HSA-1963582"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-177934",
+          "R-HSA-445069",
+          "R-HSA-177937",
+          "R-HSA-912429",
+          "R-HSA-112333",
+          "R-HSA-1220610",
+          "R-HSA-177943",
+          "R-HSA-2179415",
+          "R-HSA-1236382",
+          "R-HSA-2179387"
+        ],
+        "vector": [
+          "R-HSA-177934",
+          "R-HSA-1169421",
+          "R-HSA-1963582",
+          "R-HSA-9665389",
+          "R-HSA-3928578",
+          "R-HSA-8857555",
+          "R-HSA-1248655",
+          "R-HSA-9665709",
+          "R-HSA-9625487",
+          "R-HSA-177922"
+        ]
+      }
+    },
+    "What role does p53 play in apoptosis?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-8848046",
+          "R-HSA-349474",
+          "R-HSA-3209194",
+          "R-HSA-9836365",
+          "R-HSA-6782788",
+          "R-HSA-6782676",
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009912"
+        ],
+        "vector": [
+          "R-HSA-3700978",
+          "R-HSA-4331345",
+          "R-HSA-6799788",
+          "R-HSA-6791350",
+          "R-HSA-6799810",
+          "R-HSA-6798123",
+          "R-HSA-6799461",
+          "R-HSA-5633436",
+          "R-HSA-4331332",
+          "R-HSA-6798078"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9645750",
+          "R-HSA-9645757",
+          "R-HSA-9645756",
+          "R-HSA-9645741",
+          "R-HSA-9645759",
+          "R-HSA-9645754",
+          "R-HSA-9645755",
+          "R-HSA-9645730",
+          "R-HSA-9824848",
+          "R-HSA-9824828"
+        ],
+        "vector": [
+          "R-HSA-9718607",
+          "R-HSA-9721715",
+          "R-HSA-9723651",
+          "R-HSA-9723685",
+          "R-HSA-9720096",
+          "R-HSA-9723609",
+          "R-HSA-9721367",
+          "R-HSA-9719522",
+          "R-HSA-9721233",
+          "R-HSA-9720165"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-351843",
+          "R-HSA-3928399",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2192942",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2470088",
+          "R-HSA-2470123"
+        ],
+        "vector": [
+          "R-HSA-8869337",
+          "R-HSA-6805400",
+          "R-HSA-6805268",
+          "R-HSA-6798369",
+          "R-HSA-9721413",
+          "R-HSA-9720165",
+          "R-HSA-9722100",
+          "R-HSA-9721989",
+          "R-HSA-69683",
+          "R-HSA-9718680"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-6801637",
+          "R-HSA-6802170",
+          "R-HSA-6798031",
+          "R-HSA-6803917",
+          "R-HSA-6803946",
+          "R-HSA-6798044",
+          "R-HSA-6801641",
+          "R-HSA-6802165",
+          "R-HSA-6798020",
+          "R-HSA-6803914"
+        ],
+        "vector": [
+          "R-HSA-6800253",
+          "R-HSA-4331340",
+          "R-HSA-6800250",
+          "R-HSA-6797763",
+          "R-HSA-6797766",
+          "R-HSA-6791327",
+          "R-HSA-6791349",
+          "R-HSA-6798129",
+          "R-HSA-6799441",
+          "R-HSA-6800836"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-912429",
+          "R-HSA-6801415",
+          "R-HSA-171141",
+          "R-HSA-201611",
+          "R-HSA-6784620",
+          "R-HSA-6791306",
+          "R-HSA-9686174",
+          "R-HSA-6791348",
+          "R-HSA-6800250",
+          "R-HSA-9757256"
+        ],
+        "vector": [
+          "R-HSA-5633008",
+          "R-HSA-6803205",
+          "R-HSA-6803207",
+          "R-HSA-6803204",
+          "R-HSA-6791348",
+          "R-HSA-139913",
+          "R-HSA-6801184",
+          "R-HSA-6798139",
+          "R-HSA-6791349",
+          "R-HSA-69560"
+        ]
+      }
+    },
+    "Which complexes contain histone deacetylases?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-9012554",
+          "R-HSA-9012554",
+          "R-HSA-9008698",
+          "R-HSA-9009901",
+          "R-HSA-9009912",
+          "R-HSA-9007909",
+          "R-HSA-8942225",
+          "R-HSA-9008615",
+          "R-HSA-8848514",
+          "R-HSA-9008597"
+        ],
+        "vector": [
+          "R-HSA-4663830",
+          "R-HSA-9679831",
+          "R-HSA-9005701",
+          "R-HSA-9005550",
+          "R-HSA-9940443",
+          "R-HSA-9940939",
+          "R-HSA-9938434",
+          "R-HSA-427331",
+          "R-HSA-4657002",
+          "R-HSA-9005991"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-5652101",
+          "R-HSA-8936651",
+          "R-HSA-9648627",
+          "R-HSA-9651194",
+          "R-HSA-8936647",
+          "R-HSA-9651188",
+          "R-HSA-9651191",
+          "R-HSA-9660464"
+        ],
+        "vector": [
+          "R-HSA-9952019",
+          "R-HSA-9952596",
+          "R-HSA-9952275",
+          "R-HSA-9951942",
+          "R-HSA-9005567",
+          "R-HSA-9951670",
+          "R-HSA-9950001",
+          "R-HSA-9952233",
+          "R-HSA-9952069",
+          "R-HSA-9952544"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2192945",
+          "R-HSA-2152356",
+          "R-HSA-2192948",
+          "R-HSA-2192934",
+          "R-HSA-2193046"
+        ],
+        "vector": [
+          "R-HSA-2545206",
+          "R-HSA-427507",
+          "R-HSA-3004556",
+          "R-HSA-205135",
+          "R-HSA-212078",
+          "R-HSA-8871288",
+          "R-HSA-9941607",
+          "R-HSA-205021",
+          "R-HSA-4568751",
+          "R-HSA-8871299"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-6784648",
+          "R-HSA-6784620",
+          "R-HSA-3301237",
+          "R-HSA-3777129",
+          "R-HSA-9012689",
+          "R-HSA-3318486",
+          "R-HSA-8942224",
+          "R-HSA-3247569",
+          "R-HSA-9859119",
+          "R-HSA-9008696"
+        ],
+        "vector": [
+          "R-HSA-3777129",
+          "R-HSA-3769447",
+          "R-HSA-9679787",
+          "R-HSA-3782637",
+          "R-HSA-3662318",
+          "R-HSA-9701565",
+          "R-HSA-3301237",
+          "R-HSA-433672",
+          "R-HSA-9938418",
+          "R-HSA-3318413"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-375140",
+          "R-HSA-9621054",
+          "R-HSA-8935732",
+          "R-HSA-205056",
+          "R-HSA-9842876",
+          "R-HSA-3214815",
+          "R-HSA-9625101",
+          "R-HSA-212300",
+          "R-HSA-9932444",
+          "R-HSA-9917777"
+        ],
+        "vector": [
+          "R-HSA-3769447",
+          "R-HSA-3777129",
+          "R-HSA-3214815",
+          "R-HSA-9679787",
+          "R-HSA-3301237",
+          "R-HSA-3782637",
+          "R-HSA-9938418",
+          "R-HSA-3782655",
+          "R-HSA-996727",
+          "R-HSA-433672"
+        ]
+      }
+    },
+    "Which pathways involve insulin receptor signalling?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-74703",
+          "R-HSA-74703",
+          "R-HSA-74681",
+          "R-HSA-74685",
+          "R-HSA-74699",
+          "R-HSA-74695",
+          "R-HSA-74706",
+          "R-HSA-74675",
+          "R-HSA-74702",
+          "R-HSA-74678"
+        ],
+        "vector": [
+          "R-HSA-2445094",
+          "R-HSA-74685",
+          "R-HSA-74681",
+          "R-HSA-2428921",
+          "R-HSA-2428923",
+          "R-HSA-74695",
+          "R-HSA-2428931",
+          "R-HSA-74699",
+          "R-HSA-2671844",
+          "R-HSA-9027229"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-9824848",
+          "R-HSA-9824828",
+          "R-HSA-5652101",
+          "R-HSA-9672001",
+          "R-HSA-9674313",
+          "R-HSA-9672018",
+          "R-HSA-9671979",
+          "R-HSA-9671998",
+          "R-HSA-9671989",
+          "R-HSA-9671986"
+        ],
+        "vector": [
+          "R-HSA-9647202",
+          "R-HSA-9671991",
+          "R-HSA-9654618",
+          "R-HSA-9665381",
+          "R-HSA-9647195",
+          "R-HSA-9671989",
+          "R-HSA-9680165",
+          "R-HSA-9672003",
+          "R-HSA-9672007",
+          "R-HSA-1248649"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-198176",
+          "R-HSA-429347",
+          "R-HSA-429369",
+          "R-HSA-429465",
+          "R-HSA-429397",
+          "R-HSA-429393",
+          "R-HSA-192603",
+          "R-HSA-6810859",
+          "R-HSA-2470205",
+          "R-HSA-351865"
+        ],
+        "vector": [
+          "R-HSA-74670",
+          "R-HSA-74669",
+          "R-HSA-74668",
+          "R-HSA-141719",
+          "R-HSA-141722",
+          "R-HSA-74673",
+          "R-HSA-429343",
+          "R-HSA-265157",
+          "R-HSA-141718",
+          "R-HSA-2404172"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-74740",
+          "R-HSA-74743",
+          "R-HSA-74742",
+          "R-HSA-74716",
+          "R-HSA-74715",
+          "R-HSA-74726",
+          "R-HSA-74734",
+          "R-HSA-74718",
+          "R-HSA-74707",
+          "R-HSA-74733"
+        ],
+        "vector": [
+          "R-HSA-74716",
+          "R-HSA-74740",
+          "R-HSA-74707",
+          "R-HSA-2428926",
+          "R-HSA-74718",
+          "R-HSA-74715",
+          "R-HSA-2428930",
+          "R-HSA-2428922",
+          "R-HSA-74733",
+          "R-HSA-1168423"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-74751",
+          "R-HSA-74743",
+          "R-HSA-9008894",
+          "R-HSA-112399",
+          "R-HSA-163685",
+          "R-HSA-392023",
+          "R-HSA-74713",
+          "R-HSA-74716",
+          "R-HSA-74749",
+          "R-HSA-74734"
+        ],
+        "vector": [
+          "R-HSA-74752",
+          "R-HSA-74751",
+          "R-HSA-2404192",
+          "R-HSA-163685",
+          "R-HSA-112399",
+          "R-HSA-2428928",
+          "R-HSA-74713",
+          "R-HSA-1168423",
+          "R-HSA-2428924",
+          "R-HSA-2586552"
+        ]
+      }
+    },
+    "Which proteins are in the RNA polymerase II elongation complex?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-113722",
+          "R-HSA-167482",
+          "R-HSA-167460",
+          "R-HSA-113425",
+          "R-HSA-113426",
+          "R-HSA-113426",
+          "R-HSA-109909",
+          "R-HSA-167075",
+          "R-HSA-167182",
+          "R-HSA-9943118"
+        ],
+        "vector": [
+          "R-HSA-112433",
+          "R-HSA-113719",
+          "R-HSA-113721",
+          "R-HSA-113724",
+          "R-HSA-113726",
+          "R-HSA-167199",
+          "R-HSA-6782063",
+          "R-HSA-6814540",
+          "R-HSA-6810223",
+          "R-HSA-6797607"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-3636862",
+          "R-HSA-3636823",
+          "R-HSA-3636838",
+          "R-HSA-3636864",
+          "R-HSA-5652101",
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-5246655",
+          "R-HSA-5246654",
+          "R-HSA-5246651"
+        ],
+        "vector": [
+          "R-HSA-9951732",
+          "R-HSA-9022507",
+          "R-HSA-9005568",
+          "R-HSA-9005567",
+          "R-HSA-9005588",
+          "R-HSA-9952327",
+          "R-HSA-9952233",
+          "R-HSA-9951940",
+          "R-HSA-9951799",
+          "R-HSA-9022506"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-197585",
+          "R-HSA-2214382",
+          "R-HSA-2130686",
+          "R-HSA-2130529",
+          "R-HSA-2130568",
+          "R-HSA-2130733",
+          "R-HSA-2214371",
+          "R-HSA-197644",
+          "R-HSA-2130363",
+          "R-HSA-2130595"
+        ],
+        "vector": [
+          "R-HSA-113420",
+          "R-HSA-6814543",
+          "R-HSA-6810226",
+          "R-HSA-6781855",
+          "R-HSA-77100",
+          "R-HSA-9970465",
+          "R-HSA-6797701",
+          "R-HSA-3318361",
+          "R-HSA-5419294",
+          "R-HSA-3318359"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-113411",
+          "R-HSA-113414",
+          "R-HSA-113412",
+          "R-HSA-113413",
+          "R-HSA-112392",
+          "R-HSA-112395",
+          "R-HSA-112396",
+          "R-HSA-113409",
+          "R-HSA-109638",
+          "R-HSA-112385"
+        ],
+        "vector": [
+          "R-HSA-112379",
+          "R-HSA-113412",
+          "R-HSA-112381",
+          "R-HSA-113429",
+          "R-HSA-167077",
+          "R-HSA-113407",
+          "R-HSA-113402",
+          "R-HSA-167196",
+          "R-HSA-167192",
+          "R-HSA-75873"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-75955",
+          "R-HSA-6814549",
+          "R-HSA-73857",
+          "R-HSA-113418",
+          "R-HSA-112382",
+          "R-HSA-73772",
+          "R-HSA-76042",
+          "R-HSA-167246",
+          "R-HSA-6781818",
+          "R-HSA-74158"
+        ],
+        "vector": [
+          "R-HSA-112382",
+          "R-HSA-75955",
+          "R-HSA-113418",
+          "R-HSA-112385",
+          "R-HSA-112379",
+          "R-HSA-113429",
+          "R-HSA-113412",
+          "R-HSA-167196",
+          "R-HSA-113402",
+          "R-HSA-74986"
+        ]
+      }
+    },
+    "Which reactions produce nitric oxide?": {
+      "complexes": {
+        "bm25": [
+          "R-HSA-392141",
+          "R-HSA-5617181",
+          "R-HSA-380268",
+          "R-HSA-380705",
+          "R-HSA-380698",
+          "R-HSA-380704",
+          "R-HSA-5626171",
+          "R-HSA-5626173",
+          "R-HSA-140526",
+          "R-HSA-140524"
+        ],
+        "vector": [
+          "R-HSA-392141",
+          "R-HSA-9860769",
+          "R-HSA-203564",
+          "R-HSA-203595",
+          "R-HSA-9861320",
+          "R-HSA-203969",
+          "R-HSA-203619",
+          "R-HSA-203623",
+          "R-HSA-5617181",
+          "R-HSA-1497830"
+        ]
+      },
+      "disease_variants": {
+        "bm25": [
+          "R-HSA-2902196",
+          "R-HSA-2902192",
+          "R-HSA-2902194",
+          "R-HSA-2768989",
+          "R-HSA-9824828",
+          "R-HSA-9824848",
+          "R-HSA-5652101",
+          "R-HSA-2902195",
+          "R-HSA-2902191",
+          "R-HSA-2902193"
+        ],
+        "vector": [
+          "R-HSA-880015",
+          "R-HSA-9957955",
+          "R-HSA-9957949",
+          "R-HSA-9959625",
+          "R-HSA-9957952",
+          "R-HSA-880048",
+          "R-HSA-880000",
+          "R-HSA-9958007",
+          "R-HSA-9958200",
+          "R-HSA-9955650"
+        ]
+      },
+      "ewas": {
+        "bm25": [
+          "R-HSA-6810859",
+          "R-HSA-2470116",
+          "R-HSA-2470050",
+          "R-HSA-2470095",
+          "R-HSA-2470190",
+          "R-HSA-2192945",
+          "R-HSA-2152356",
+          "R-HSA-2192948",
+          "R-HSA-2192934",
+          "R-HSA-2193046"
+        ],
+        "vector": [
+          "R-HSA-202107",
+          "R-HSA-9636250",
+          "R-HSA-9033124",
+          "R-HSA-419293",
+          "R-HSA-202114",
+          "R-HSA-6800935",
+          "R-HSA-6799636",
+          "R-HSA-6806297",
+          "R-HSA-203687",
+          "R-HSA-203636"
+        ]
+      },
+      "reactions": {
+        "bm25": [
+          "R-HSA-418436",
+          "R-HSA-1222723",
+          "R-HSA-418436",
+          "R-HSA-9636261",
+          "R-HSA-1222662",
+          "R-HSA-1222686",
+          "R-HSA-9759522",
+          "R-HSA-9636247",
+          "R-HSA-1222407",
+          "R-HSA-1222407"
+        ],
+        "vector": [
+          "R-HSA-418436",
+          "R-HSA-6803989",
+          "R-HSA-6804006",
+          "R-HSA-1222512",
+          "R-HSA-1497878",
+          "R-HSA-202127",
+          "R-HSA-1222407",
+          "R-HSA-6803999",
+          "R-HSA-1222662",
+          "R-HSA-1222723"
+        ]
+      },
+      "summations": {
+        "bm25": [
+          "R-HSA-6803989",
+          "R-HSA-9636249",
+          "R-HSA-6803978",
+          "R-HSA-6804006",
+          "R-HSA-8981607",
+          "R-HSA-1222407",
+          "R-HSA-1222512",
+          "R-HSA-3697855",
+          "R-HSA-418436",
+          "R-HSA-8942052"
+        ],
+        "vector": [
+          "R-HSA-6803989",
+          "R-HSA-6804006",
+          "R-HSA-1222512",
+          "R-HSA-418436",
+          "R-HSA-6803999",
+          "R-HSA-1497878",
+          "R-HSA-202127",
+          "R-HSA-1222723",
+          "R-HSA-1222407",
+          "R-HSA-8942075"
+        ]
+      }
+    }
+  }
+}