Version history

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
        "content_hash": "f753888221140640292c261c9d9e198b834b95e7ba675e72728e184b4593ac4c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-Sphingolipid / ceramide signaling",
        "content_hash": "827be90a3ae9c55d67a2cf1eb3cc6ee004cedf0192ac7b432ce32cab048b4017",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST8SIA1-Sphingolipid / ceramide signaling",
        "content_hash": "ec575c373a91b359cfb103260a3ae68ff5c8f6cc234272a9b15c228108b5fa0e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-Sphingolipid / ceramide signaling",
        "content_hash": "80278972e7bf273ad62155b1e0ac767dd1a8867b5edb492ddc6c0ce027ff4931",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS2-Sphingolipid / ceramide signaling",
        "content_hash": "55fd7597df59902a3e97239ecfdceb94ece703586e5dccc8c004afec15c5a048",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-Lipid raft membrane organization",
        "content_hash": "87226763f29d8119307313a3fc921cd25daaa756297abb81c0be552e74f4a6fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-Beta-secretase / amyloidogenic pathway",
        "content_hash": "31e753bb868b4c00f38bb93fd821429eb20c527b27edc529769f83549a2cc98e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SREBF2",
        "content_hash": "b64d33bd4a7dce6b32cc949f73e649108240ad5181bada2870b2359d56c5daed",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-CYP46A1",
        "content_hash": "b187cafb98738d6368d76ab339e068664efd519c2f5c0a8c4f15f5e3ddc16702",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS2",
        "content_hash": "fab74d2efe474ea122d9b1b0483d8acb2d898e4ee316b506059098644842ece9",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ABCA1",
        "content_hash": "d9866dca21c8b0c0ce1aba2c61bec3f8e0621cdafbac4131994e5a3d5430498a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-BACE1",
        "content_hash": "d945a2384e9e2d94b0102216293bb17324a90c60fb1824bca36df5fd877823a7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST3GAL2",
        "content_hash": "90fe02f332ce283f126def2e676aaf405f64d9d92087b7218f32bc6ae1a16df6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST8SIA1",
        "content_hash": "a6e6deea20163f75a5e037d12f6e2cd8576b054d8b4b6f5ec08f851c22160ca6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-LDLR",
        "content_hash": "114840ea4f1937af05caf0b4bf461d1ca0be0db4bca7b0988cb1d10877aacf33",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SMPD1",
        "content_hash": "637c485909708aba44cb389dbce7e42a8deb3d7fa0e89c9ad8e119e213d46186",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS1",
        "content_hash": "62130cb137d9a39ca0afa9b6e5120631d4582948101625bc6a93ad99b2f8a974",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-CYP46A1",
        "content_hash": "fa1d933c39e0add695a6ef57f4b62ab9996ee997b2fca861c42d6b2609e39105",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-SGMS2",
        "content_hash": "e67a31b3c0c1b565a82d37d90aa8e4e121577ec9e53b181d87eaa5f0baa4bcfd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "d26e57145c8f2f7cf239147d2a61001c6c60188bd255356e66e3a0964d3ae4a0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-BACE1",
        "content_hash": "83b73b26a476432ef930e8a65e724961247bfb7d512c2dc5d82f3db218680f93",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ST3GAL2",
        "content_hash": "e4141cf0516bcc04169fa7d907166425e9f6d8aef7bd140fcac63849cab44f16",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ST8SIA1",
        "content_hash": "5488a1e4a95ffc337a54f25241cfbb750b372fcb73eac0cea91e45554c9a9b71",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "3d2288f5680d64e9cf17ffa10ab35e79bbbf2889a2dc7d03f3f04e8b30a21342",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-SMPD1",
        "content_hash": "60dd32b16b0a9486e69736914fd7b31a6c7ec145a9674ea0f134f67f810e62bc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-SGMS1",
        "content_hash": "992c647e4635d8cafc846c24126449c9daa7c741462d4679b03241ede427108f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-SGMS2",
        "content_hash": "79c04f19fd2324ac07b1a8170b1beaf73272ef91f274837640ed5d859238d986",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-ABCA1",
        "content_hash": "b63fc3b89e7d785d82e465c8eafa65bb6cd158397cf0deb2783dbeb64698e38b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-BACE1",
        "content_hash": "2bc1f6b1efdb386a8bba84e2df4a9046d10149b1db76cb64d00e4639e4380193",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-ST3GAL2",
        "content_hash": "160cbc459a6837c4fa369cad71f47bd865a488cfbb3f63163a4a18c668485bdc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-ST8SIA1",
        "content_hash": "205afd1b6e5cd63f77c19e8bb14223251564423e29d7c047f88aa94c0d4cf681",
        "artifact_type": "kg_edge",
        "version_number": 1
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                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
        "content_hash": "f753888221140640292c261c9d9e198b834b95e7ba675e72728e184b4593ac4c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-Sphingolipid / ceramide signaling",
        "content_hash": "827be90a3ae9c55d67a2cf1eb3cc6ee004cedf0192ac7b432ce32cab048b4017",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST8SIA1-Sphingolipid / ceramide signaling",
        "content_hash": "ec575c373a91b359cfb103260a3ae68ff5c8f6cc234272a9b15c228108b5fa0e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-Sphingolipid / ceramide signaling",
        "content_hash": "80278972e7bf273ad62155b1e0ac767dd1a8867b5edb492ddc6c0ce027ff4931",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS2-Sphingolipid / ceramide signaling",
        "content_hash": "55fd7597df59902a3e97239ecfdceb94ece703586e5dccc8c004afec15c5a048",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-Lipid raft membrane organization",
        "content_hash": "87226763f29d8119307313a3fc921cd25daaa756297abb81c0be552e74f4a6fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-Beta-secretase / amyloidogenic pathway",
        "content_hash": "31e753bb868b4c00f38bb93fd821429eb20c527b27edc529769f83549a2cc98e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SREBF2",
        "content_hash": "b64d33bd4a7dce6b32cc949f73e649108240ad5181bada2870b2359d56c5daed",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-CYP46A1",
        "content_hash": "b187cafb98738d6368d76ab339e068664efd519c2f5c0a8c4f15f5e3ddc16702",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS2",
        "content_hash": "fab74d2efe474ea122d9b1b0483d8acb2d898e4ee316b506059098644842ece9",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ABCA1",
        "content_hash": "d9866dca21c8b0c0ce1aba2c61bec3f8e0621cdafbac4131994e5a3d5430498a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-BACE1",
        "content_hash": "d945a2384e9e2d94b0102216293bb17324a90c60fb1824bca36df5fd877823a7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST3GAL2",
        "content_hash": "90fe02f332ce283f126def2e676aaf405f64d9d92087b7218f32bc6ae1a16df6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST8SIA1",
        "content_hash": "a6e6deea20163f75a5e037d12f6e2cd8576b054d8b4b6f5ec08f851c22160ca6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-LDLR",
        "content_hash": "114840ea4f1937af05caf0b4bf461d1ca0be0db4bca7b0988cb1d10877aacf33",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SMPD1",
        "content_hash": "637c485909708aba44cb389dbce7e42a8deb3d7fa0e89c9ad8e119e213d46186",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS1",
        "content_hash": "62130cb137d9a39ca0afa9b6e5120631d4582948101625bc6a93ad99b2f8a974",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-CYP46A1",
        "content_hash": "fa1d933c39e0add695a6ef57f4b62ab9996ee997b2fca861c42d6b2609e39105",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-SGMS2",
        "content_hash": "e67a31b3c0c1b565a82d37d90aa8e4e121577ec9e53b181d87eaa5f0baa4bcfd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
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                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
        "content_hash": "f753888221140640292c261c9d9e198b834b95e7ba675e72728e184b4593ac4c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-Sphingolipid / ceramide signaling",
        "content_hash": "827be90a3ae9c55d67a2cf1eb3cc6ee004cedf0192ac7b432ce32cab048b4017",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST8SIA1-Sphingolipid / ceramide signaling",
        "content_hash": "ec575c373a91b359cfb103260a3ae68ff5c8f6cc234272a9b15c228108b5fa0e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-Sphingolipid / ceramide signaling",
        "content_hash": "80278972e7bf273ad62155b1e0ac767dd1a8867b5edb492ddc6c0ce027ff4931",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS2-Sphingolipid / ceramide signaling",
        "content_hash": "55fd7597df59902a3e97239ecfdceb94ece703586e5dccc8c004afec15c5a048",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-Lipid raft membrane organization",
        "content_hash": "87226763f29d8119307313a3fc921cd25daaa756297abb81c0be552e74f4a6fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-Beta-secretase / amyloidogenic pathway",
        "content_hash": "31e753bb868b4c00f38bb93fd821429eb20c527b27edc529769f83549a2cc98e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SREBF2",
        "content_hash": "b64d33bd4a7dce6b32cc949f73e649108240ad5181bada2870b2359d56c5daed",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
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              "python_version": "3.13.12",
              "current_pip_hash": "553be32a4d71a2b1...",
              "manifest_pip_hash": "553be32a4d71a2b1..."
            },
            "message": "Pip packages hash matches"
          },
          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
                "edge-h-9d29bfe5-ABCA1/LDLR/SREBF2",
                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
                "h-var-1dc420e7d8",
                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
                "h-var-76afa28dfc"
              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
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        "title": "Neutral Sphingomyelinase-2 Inhibition for Synaptic Protection in Neurodegeneration",
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    ],
    "runtime": {
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      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
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    "metadata": {},
    "execution": {
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        "/home/ubuntu/scidex/venv/bin/python3",
        "/home/ubuntu/scidex/post_process.py"
      ],
      "entrypoint_type": "post_process",
      "environment_vars": {
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        "SCIDEX_ANALYSIS_ID": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01"
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      "working_directory": "/home/ubuntu/scidex"
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    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
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      "conda_env_hash": "fd1064733a90d9006ced8ee018963a4edab937396ac90cf64963bbfec51ee420",
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      "checks": {
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            "details": {
              "branch": "main",
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              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
            },
            "message": "Git commit c0d3bd637f0e9905... exists"
          },
          {
            "name": "environment_lock",
            "status": "passed",
            "details": {
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              "python_version": "3.13.12",
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          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
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                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
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                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
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              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
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            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
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        "artifact_id": "edge-ABCA1-LDLR",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> gene",
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        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
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      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
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        "artifact_type": "kg_edge",
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      {
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        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
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      {
        "title": "gene -> disease",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> disease",
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        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
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        "version_number": 1
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      {
        "title": "gene -> disease",
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        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
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        "content_hash": "edeebdf5d0a89a062ff7ea32e6fa64bcda8ba1d4da02e6342c25c732dce2e670",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
        "content_hash": "0113408f6438091e72bc70e4b37601b756984cbb9b3e74a8a663d98357e8c0b2",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
        "content_hash": "3919ac4e192748594a22e633f900249f2b94f90e9a91d71c7bc0fc18d1ee4115",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-lipid_raft_membrane_organization",
        "content_hash": "301468961a2f174bb1fd53311044023f91d98b6f469a4ac5bf3ed237af7c6160",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-beta_secretase___amyloidogenic_pathway",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "Selective Acid Sphingomyelinase Modulation Therapy",
        "artifact_id": "h-de0d4364",
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        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "Membrane Cholesterol Gradient Modulators",
        "artifact_id": "h-9d29bfe5",
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        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "CYP46A1 Overexpression Gene Therapy",
        "artifact_id": "h-2600483e",
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        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "Ganglioside Rebalancing Therapy",
        "artifact_id": "h-12599989",
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        "artifact_type": "hypothesis",
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      {
        "title": "Sphingomyelin Synthase Activators for Raft Remodeling",
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        "artifact_type": "hypothesis",
        "version_number": 1
      },
      {
        "title": "Flotillin-1 Stabilization Compounds",
        "artifact_id": "h-a015e80e",
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        "artifact_type": "hypothesis",
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      {
        "title": "Palmitoylation-Targeted BACE1 Trafficking Disruptors",
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      {
        "title": "CYP46A1 Suppression for Tau-Mediated Neurodegeneration",
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      {
        "title": "CYP46A1 Gene Therapy for Age-Related TREM2-Mediated Microglial Senescence Reversal",
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        "content_hash": "9428a697175dd32cb4cf1f6ab686711588874a66610ac82d87ecd82bf5303341",
        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "Neutral Sphingomyelinase-2 Inhibition for Synaptic Protection in Neurodegeneration",
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      {
        "title": "Senescent Cell ASM-Complement Cascade Intervention",
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        "content_hash": "b789277bbc7b0d1d22346eb0d766cab5eabef1edf1de194ecb2bfb064d1a1303",
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    ],
    "runtime": {
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      "git_branch": "main",
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      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
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    "metadata": {},
    "execution": {
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        "/home/ubuntu/scidex/venv/bin/python3",
        "/home/ubuntu/scidex/post_process.py"
      ],
      "entrypoint_type": "post_process",
      "environment_vars": {
        "PATH": "/home/ubuntu/miniconda3/bin:/usr/local/bin:/usr/bin:/bin",
        "SCIDEX_ANALYSIS_ID": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01"
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      "working_directory": "/home/ubuntu/scidex"
    },
    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
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      "conda_env_hash": "fd1064733a90d9006ced8ee018963a4edab937396ac90cf64963bbfec51ee420",
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      "runtime_digest": "sha256:553be32a4d71a2b1667c83d3e92bb6da81c699c272929a80ccec8146ca256e8a",
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    },
    "verification": {
      "checks": {
        "checks": [
          {
            "name": "runtime_identity",
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            "details": {
              "branch": "main",
              "commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
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              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
            },
            "message": "Git commit c0d3bd637f0e9905... exists"
          },
          {
            "name": "environment_lock",
            "status": "passed",
            "details": {
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              "python_version": "3.13.12",
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            "message": "Pip packages hash matches"
          },
          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
                "edge-h-9d29bfe5-ABCA1/LDLR/SREBF2",
                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
                "h-var-1dc420e7d8",
                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
                "h-var-76afa28dfc"
              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
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        "title": "gene -> gene",
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      {
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      {
        "title": "gene -> gene",
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        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-CYP46A1-SGMS1/SGMS2",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS1/SGMS2",
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        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
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      {
        "title": "gene -> gene",
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        "artifact_type": "kg_edge",
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      {
        "title": "gene -> gene",
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      {
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        "artifact_type": "kg_edge",
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      {
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        "artifact_type": "kg_edge",
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      {
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        "content_hash": "6040c4ebdd934fba5b98d234810e4e94cb6546122e6ccd9586fbcb86fa2be113",
        "artifact_type": "kg_edge",
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
        "content_hash": "edeebdf5d0a89a062ff7ea32e6fa64bcda8ba1d4da02e6342c25c732dce2e670",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
        "content_hash": "0113408f6438091e72bc70e4b37601b756984cbb9b3e74a8a663d98357e8c0b2",
        "artifact_type": "kg_edge",
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      {
        "title": "gene -> pathway",
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        "artifact_type": "kg_edge",
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      {
        "title": "gene -> pathway",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-beta_secretase___amyloidogenic_pathway",
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        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "Selective Acid Sphingomyelinase Modulation Therapy",
        "artifact_id": "h-de0d4364",
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        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "Membrane Cholesterol Gradient Modulators",
        "artifact_id": "h-9d29bfe5",
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        "artifact_type": "hypothesis",
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      {
        "title": "CYP46A1 Overexpression Gene Therapy",
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      {
        "title": "Ganglioside Rebalancing Therapy",
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      {
        "title": "Sphingomyelin Synthase Activators for Raft Remodeling",
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        "version_number": 1
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      {
        "title": "Flotillin-1 Stabilization Compounds",
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      {
        "title": "Palmitoylation-Targeted BACE1 Trafficking Disruptors",
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        "title": "CYP46A1 Suppression for Tau-Mediated Neurodegeneration",
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      },
      {
        "title": "CYP46A1 Gene Therapy for Age-Related TREM2-Mediated Microglial Senescence Reversal",
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        "content_hash": "9428a697175dd32cb4cf1f6ab686711588874a66610ac82d87ecd82bf5303341",
        "artifact_type": "hypothesis",
        "version_number": 1
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      {
        "title": "Neutral Sphingomyelinase-2 Inhibition for Synaptic Protection in Neurodegeneration",
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        "content_hash": "31739122140532f1aacb18c24c8f98706697c719413899955481eb2c7be1ae9c",
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        "version_number": 1
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      {
        "title": "Senescent Cell ASM-Complement Cascade Intervention",
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        "content_hash": "b789277bbc7b0d1d22346eb0d766cab5eabef1edf1de194ecb2bfb064d1a1303",
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    ],
    "runtime": {
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      "git_branch": "main",
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      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
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    "metadata": {},
    "execution": {
      "command": [
        "/home/ubuntu/scidex/venv/bin/python3",
        "/home/ubuntu/scidex/post_process.py"
      ],
      "entrypoint_type": "post_process",
      "environment_vars": {
        "PATH": "/home/ubuntu/miniconda3/bin:/usr/local/bin:/usr/bin:/bin",
        "SCIDEX_ANALYSIS_ID": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01"
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      "working_directory": "/home/ubuntu/scidex"
    },
    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
      "runtime_type": "python",
      "conda_env_hash": "fd1064733a90d9006ced8ee018963a4edab937396ac90cf64963bbfec51ee420",
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      "runtime_digest": "sha256:553be32a4d71a2b1667c83d3e92bb6da81c699c272929a80ccec8146ca256e8a",
      "environment_file": null,
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    },
    "verification": {
      "checks": {
        "checks": [
          {
            "name": "runtime_identity",
            "status": "passed",
            "details": {
              "branch": "main",
              "commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
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              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
            },
            "message": "Git commit c0d3bd637f0e9905... exists"
          },
          {
            "name": "environment_lock",
            "status": "passed",
            "details": {
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              "python_version": "3.13.12",
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            "message": "Pip packages hash matches"
          },
          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
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                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
                "h-var-1dc420e7d8",
                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
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              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
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      {
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      {
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      {
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        "title": "Selective Acid Sphingomyelinase Modulation Therapy",
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      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
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        "/home/ubuntu/scidex/post_process.py"
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      "entrypoint_type": "post_process",
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    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
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            "name": "runtime_identity",
            "status": "passed",
            "details": {
              "branch": "main",
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              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
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                "edge-SREBF2-ST3GAL2",
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                "edge-ST3GAL2-ST8SIA1",
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                "edge-ST3GAL2-SMPD1",
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                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
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                "edge-ABCA1-SREBF2",
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                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
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                "edge-ST3GAL2-CYP46A1",
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                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
        "content_hash": "f753888221140640292c261c9d9e198b834b95e7ba675e72728e184b4593ac4c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-Sphingolipid / ceramide signaling",
        "content_hash": "827be90a3ae9c55d67a2cf1eb3cc6ee004cedf0192ac7b432ce32cab048b4017",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST8SIA1-Sphingolipid / ceramide signaling",
        "content_hash": "ec575c373a91b359cfb103260a3ae68ff5c8f6cc234272a9b15c228108b5fa0e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-Sphingolipid / ceramide signaling",
        "content_hash": "80278972e7bf273ad62155b1e0ac767dd1a8867b5edb492ddc6c0ce027ff4931",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS2-Sphingolipid / ceramide signaling",
        "content_hash": "55fd7597df59902a3e97239ecfdceb94ece703586e5dccc8c004afec15c5a048",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-Lipid raft membrane organization",
        "content_hash": "87226763f29d8119307313a3fc921cd25daaa756297abb81c0be552e74f4a6fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-Beta-secretase / amyloidogenic pathway",
        "content_hash": "31e753bb868b4c00f38bb93fd821429eb20c527b27edc529769f83549a2cc98e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SREBF2",
        "content_hash": "b64d33bd4a7dce6b32cc949f73e649108240ad5181bada2870b2359d56c5daed",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-CYP46A1",
        "content_hash": "b187cafb98738d6368d76ab339e068664efd519c2f5c0a8c4f15f5e3ddc16702",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS2",
        "content_hash": "fab74d2efe474ea122d9b1b0483d8acb2d898e4ee316b506059098644842ece9",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ABCA1",
        "content_hash": "d9866dca21c8b0c0ce1aba2c61bec3f8e0621cdafbac4131994e5a3d5430498a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-BACE1",
        "content_hash": "d945a2384e9e2d94b0102216293bb17324a90c60fb1824bca36df5fd877823a7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST3GAL2",
        "content_hash": "90fe02f332ce283f126def2e676aaf405f64d9d92087b7218f32bc6ae1a16df6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ST8SIA1",
        "content_hash": "a6e6deea20163f75a5e037d12f6e2cd8576b054d8b4b6f5ec08f851c22160ca6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-LDLR",
        "content_hash": "114840ea4f1937af05caf0b4bf461d1ca0be0db4bca7b0988cb1d10877aacf33",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SMPD1",
        "content_hash": "637c485909708aba44cb389dbce7e42a8deb3d7fa0e89c9ad8e119e213d46186",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS1",
        "content_hash": "62130cb137d9a39ca0afa9b6e5120631d4582948101625bc6a93ad99b2f8a974",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-CYP46A1",
        "content_hash": "fa1d933c39e0add695a6ef57f4b62ab9996ee997b2fca861c42d6b2609e39105",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-SGMS2",
        "content_hash": "e67a31b3c0c1b565a82d37d90aa8e4e121577ec9e53b181d87eaa5f0baa4bcfd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "d26e57145c8f2f7cf239147d2a61001c6c60188bd255356e66e3a0964d3ae4a0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-BACE1",
        "content_hash": "83b73b26a476432ef930e8a65e724961247bfb7d512c2dc5d82f3db218680f93",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ST3GAL2",
        "content_hash": "e4141cf0516bcc04169fa7d907166425e9f6d8aef7bd140fcac63849cab44f16",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ST8SIA1",
        "content_hash": "5488a1e4a95ffc337a54f25241cfbb750b372fcb73eac0cea91e45554c9a9b71",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
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                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
        "content_hash": "f753888221140640292c261c9d9e198b834b95e7ba675e72728e184b4593ac4c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-Sphingolipid / ceramide signaling",
        "content_hash": "827be90a3ae9c55d67a2cf1eb3cc6ee004cedf0192ac7b432ce32cab048b4017",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST8SIA1-Sphingolipid / ceramide signaling",
        "content_hash": "ec575c373a91b359cfb103260a3ae68ff5c8f6cc234272a9b15c228108b5fa0e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-Sphingolipid / ceramide signaling",
        "content_hash": "80278972e7bf273ad62155b1e0ac767dd1a8867b5edb492ddc6c0ce027ff4931",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS2-Sphingolipid / ceramide signaling",
        "content_hash": "55fd7597df59902a3e97239ecfdceb94ece703586e5dccc8c004afec15c5a048",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-FLOT1-Lipid raft membrane organization",
        "content_hash": "87226763f29d8119307313a3fc921cd25daaa756297abb81c0be552e74f4a6fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-BACE1-Beta-secretase / amyloidogenic pathway",
        "content_hash": "31e753bb868b4c00f38bb93fd821429eb20c527b27edc529769f83549a2cc98e",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SREBF2",
        "content_hash": "b64d33bd4a7dce6b32cc949f73e649108240ad5181bada2870b2359d56c5daed",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-CYP46A1",
        "content_hash": "b187cafb98738d6368d76ab339e068664efd519c2f5c0a8c4f15f5e3ddc16702",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-SGMS2",
        "content_hash": "fab74d2efe474ea122d9b1b0483d8acb2d898e4ee316b506059098644842ece9",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-ABCA1",
        "content_hash": "d9866dca21c8b0c0ce1aba2c61bec3f8e0621cdafbac4131994e5a3d5430498a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-FLOT1-BACE1",
        "content_hash": "d945a2384e9e2d94b0102216293bb17324a90c60fb1824bca36df5fd877823a7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
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                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-FLOT1-neurodegeneration",
        "content_hash": "3bbd9c1250157628d0a298cc958e5834c5f5640bedd2ccc598f1d14d3337fe06",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-BACE1-neurodegeneration",
        "content_hash": "9efe3b81b336369325d09ae0c2de48b1888e94cdee31cda5550d14e9da036625",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-NLRP3",
        "content_hash": "1616da600d7bb3880e58dd48e6ede4a9958a07d57ec2907e45722394f34788bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-AKT-BACE1",
        "content_hash": "2ae4abd0f397f0f078d242806b7693c6662f0fbefbbec07b701463afaa0930bb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BAX-JNK",
        "content_hash": "40171dfbacbebb7e66e345128fd5b038d4d4913949e233cce52fbd4e93d3f945",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-APP",
        "content_hash": "616a1544ac758ed0e0072e3d5276dd71934407cd42388b03b34295b99cfada0c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ADAM10-BACE1",
        "content_hash": "c6cddae6db1a904694e136071a0856c0db044ec9126af9aae5bdc8212b498214",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-BACE1-TAU",
        "content_hash": "f9f7634af446646107362379a550a99515ec78d346b7cf9c0dc7dda8f6d173b1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
        "content_hash": "8ac4d0a63c454c11757b11c8eb91fb4f8b2c680be6f6e00884516cb0f2d72e32",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-Cholesterol efflux / lipid transport",
        "content_hash": "4db8d16ca8f48ebbd2ac96113553263ac50b2000fae80426742459266d0b6650",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-LDLR-Cholesterol efflux / lipid transport",
        "content_hash": "6d79784037e973a8e08601cc7ee61df0e0abb85db2e60b4195331ce30c15a82c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SREBF2-Cholesterol efflux / lipid transport",
        "content_hash": "ae1d87c82cb63c8c8534ff1dd6cbc9116625c3694bf6b1de8ce6f0d3330e8f09",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
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        "artifact_id": "h-var-76afa28dfc",
        "content_hash": "b789277bbc7b0d1d22346eb0d766cab5eabef1edf1de194ecb2bfb064d1a1303",
        "artifact_type": "hypothesis",
        "version_number": 1
      }
    ],
    "runtime": {
      "repo_url": "https://github.com/SciDEX-AI/SciDEX",
      "git_branch": "main",
      "git_commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
    },
    "metadata": {},
    "execution": {
      "command": [
        "/home/ubuntu/scidex/venv/bin/python3",
        "/home/ubuntu/scidex/post_process.py"
      ],
      "entrypoint_type": "post_process",
      "environment_vars": {
        "PATH": "/home/ubuntu/miniconda3/bin:/usr/local/bin:/usr/bin:/bin",
        "SCIDEX_ANALYSIS_ID": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01"
      },
      "working_directory": "/home/ubuntu/scidex"
    },
    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
      "runtime_type": "python",
      "conda_env_hash": "fd1064733a90d9006ced8ee018963a4edab937396ac90cf64963bbfec51ee420",
      "python_version": "3.13.12",
      "runtime_digest": "sha256:553be32a4d71a2b1667c83d3e92bb6da81c699c272929a80ccec8146ca256e8a",
      "environment_file": null,
      "pip_packages_hash": "553be32a4d71a2b1667c83d3e92bb6da81c699c272929a80ccec8146ca256e8a"
    },
    "verification": {
      "checks": {
        "checks": [
          {
            "name": "runtime_identity",
            "status": "passed",
            "details": {
              "branch": "main",
              "commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
              "is_current": false,
              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
            },
            "message": "Git commit c0d3bd637f0e9905... exists"
          },
          {
            "name": "environment_lock",
            "status": "passed",
            "details": {
              "runtime_type": "python",
              "python_version": "3.13.12",
              "current_pip_hash": "553be32a4d71a2b1...",
              "manifest_pip_hash": "553be32a4d71a2b1..."
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            "message": "Pip packages hash matches"
          },
          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
                "edge-h-9d29bfe5-ABCA1/LDLR/SREBF2",
                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
                "h-var-1dc420e7d8",
                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
                "h-var-76afa28dfc"
              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}

{
  "question": "Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse dysfunction",
  "domain": "neurodegeneration",
  "status": "completed",
  "triggered_by": "gap_analysis",
  "metadata": {
    "inputs": [],
    "outputs": [
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SMPD1-ceramide_biosynthesis",
        "content_hash": "96e4624305853b8d1ee0e69486715674a3d0f9b5624922c7549d612877326bf0",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
        "content_hash": "9fbec02c864f7b6c5104e7fb936fac952f9e5c3bd1b10242b82e0d03d47bca40",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-CYP46A1-cholesterol_metabolism",
        "content_hash": "17d3454abd3888b801ab432b2a5803903c84423ce4e2babb5dca995c231311cc",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-cholesterol_metabolism-BACE1_clustering",
        "content_hash": "efd80b58971586697ca722965d37d9b91b249612584eb39b289ba16d5f4cf4c1",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "phenotype -> pathway",
        "artifact_id": "edge-BACE1_clustering-amyloid_beta_production",
        "content_hash": "419694f8cee33600a2649d7b05275f1b6c97f66077038882e3093d99c431ff25",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ABCA1-cholesterol_efflux",
        "content_hash": "de169240f01e87633c075fef639370a615a6632f6b5a362636e6434eb04579c6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-cholesterol_efflux-lipid_raft_composition",
        "content_hash": "198fa41e59ec4aa113d1ff387bcda9ad2b8ec5dfa038791048b0f71f293405f7",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-SGMS1-sphingomyelin_synthesis",
        "content_hash": "bfb41498d44243b8d0acf0775db048ad76913e5dcc1a80dfe9b7f80f384ff3fb",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> phenotype",
        "artifact_id": "edge-sphingomyelin_synthesis-membrane_fluidity",
        "content_hash": "a5253a5d2fade15051fb1474dd1b1ce784266f7a179bfe24ed68513f89805f12",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> phenotype",
        "artifact_id": "edge-FLOT1-lipid_raft_scaffolding",
        "content_hash": "435a0fa6c786392b3d1b133482730718bd9da2e55af85c1c2431025770c4212c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> pathway",
        "artifact_id": "edge-ST3GAL2-ganglioside_biosynthesis",
        "content_hash": "188edc1f41200346177a1be937484960bb21c9a6d8b7cafe2064ee9de5e3f22f",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "pathway -> cell_type",
        "artifact_id": "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
        "content_hash": "ab49b557265829e5f0e414153766a4b9428fefd12b0a466b82d4a005b39f161c",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SMPD1-neurodegeneration",
        "content_hash": "cdfda7d301da5510bc3bbe8550ff6d7ab4479865efd3a09300383d4e7148cd23",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ABCA1-neurodegeneration",
        "content_hash": "af708575d28cfe32262805e58166841bae10bd753b01d531bec9b10903232b8b",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-LDLR",
        "content_hash": "e94bc691f7d493168614ba9b63b439c8dda3d84a48fbf96725ebb837470ff250",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ABCA1-SREBF2",
        "content_hash": "acfcc991a445efc423418355060cd5fa304fc90a3c694fb4d11c3a9dbad8cbe6",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-ABCA1",
        "content_hash": "a27bc0b589d0c89176a4151ff10f339f0d6817acb3d480a71e6fc039edb16ffd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-LDLR-SREBF2",
        "content_hash": "e1453093e3c722b9f5218705b0135453cc5a9ce7aa9c8ca59ce9601145768122",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SREBF2-neurodegeneration",
        "content_hash": "c28640817f9eeda01210cf0712e9567143a1a2504133b20867a39012176ae5e8",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-ABCA1",
        "content_hash": "c18746e59c341875b872b434819365f7627def20e7d89e7336501fa594ee50fd",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SREBF2-LDLR",
        "content_hash": "9ca56de1900d3b64a2f21dce3ce4f7a5fb8644a34962107dcd27b25dc7651a76",
        "artifact_type": "kg_edge",
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      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-CYP46A1-neurodegeneration",
        "content_hash": "3494de07df852eec944382e5ffd2b84db60ddae80bf181a5e59545e11da9de39",
        "artifact_type": "kg_edge",
        "version_number": 1
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      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST3GAL2-neurodegeneration",
        "content_hash": "0a249161a5e6e1cbc5c14ebe5ec9a5bd1ffa3bc5f3f4285d7745963bafb71472",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST3GAL2-ST8SIA1",
        "content_hash": "ccdf87eef6a37346e073e70254253c1478b1f0f6b747962e0f6e1a0a0793d6a5",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-ST8SIA1-neurodegeneration",
        "content_hash": "4a603864f427f88a5ff196a733490651e086fe55245d2c61fbb2f32a2f49e709",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-ST8SIA1-ST3GAL2",
        "content_hash": "8009fd81e3f11e435516be9d6abb2e0f79c4a319565e96cc7314434730afa2de",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS1-neurodegeneration",
        "content_hash": "7f52e07e04e0752254f35603f3be40f191862a6f2e945c77ca818bb755a3a958",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS1-SGMS2",
        "content_hash": "f3576d90bd138b38dbe633d598392efd9773b1a365f17624a7cbf9d9f9e88580",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> disease",
        "artifact_id": "edge-SGMS2-neurodegeneration",
        "content_hash": "294b86a133d72dfe4b58e48ef11ff16b55be3cca6ce330fec0046c0d22cd1746",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
        "title": "gene -> gene",
        "artifact_id": "edge-SGMS2-SGMS1",
        "content_hash": "1a56345d824607a645668c29c971fed4318e3cbb5636cdeaa8ffa31e2993795a",
        "artifact_type": "kg_edge",
        "version_number": 1
      },
      {
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        "title": "gene -> pathway",
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      {
        "title": "Selective Acid Sphingomyelinase Modulation Therapy",
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      {
        "title": "Membrane Cholesterol Gradient Modulators",
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      {
        "title": "CYP46A1 Overexpression Gene Therapy",
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      {
        "title": "Ganglioside Rebalancing Therapy",
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        "artifact_type": "hypothesis",
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      {
        "title": "Sphingomyelin Synthase Activators for Raft Remodeling",
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      {
        "title": "Flotillin-1 Stabilization Compounds",
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      {
        "title": "Palmitoylation-Targeted BACE1 Trafficking Disruptors",
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      {
        "title": "CYP46A1 Gene Therapy for Age-Related TREM2-Mediated Microglial Senescence Reversal",
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      {
        "title": "Neutral Sphingomyelinase-2 Inhibition for Synaptic Protection in Neurodegeneration",
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      {
        "title": "Senescent Cell ASM-Complement Cascade Intervention",
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    ],
    "runtime": {
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      "git_branch": "main",
      "git_commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
      "git_tree_hash": "4abb1850d5600d730027d09f359072417a6cc174",
      "scidex_version": null
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    "metadata": {},
    "execution": {
      "command": [
        "/home/ubuntu/scidex/venv/bin/python3",
        "/home/ubuntu/scidex/post_process.py"
      ],
      "entrypoint_type": "post_process",
      "environment_vars": {
        "PATH": "/home/ubuntu/miniconda3/bin:/usr/local/bin:/usr/bin:/bin",
        "SCIDEX_ANALYSIS_ID": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01"
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      "working_directory": "/home/ubuntu/scidex"
    },
    "created_at": "2026-04-10T10:28:57.997461",
    "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
    "environment": {
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      "conda_env_hash": "fd1064733a90d9006ced8ee018963a4edab937396ac90cf64963bbfec51ee420",
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      "runtime_digest": "sha256:553be32a4d71a2b1667c83d3e92bb6da81c699c272929a80ccec8146ca256e8a",
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    },
    "verification": {
      "checks": {
        "checks": [
          {
            "name": "runtime_identity",
            "status": "passed",
            "details": {
              "branch": "main",
              "commit": "c0d3bd637f0e99051b9f25979eeb1d414b220e2d",
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              "current_commit": "d6d11769824ab947c815cb64aca278c4ed8a82df"
            },
            "message": "Git commit c0d3bd637f0e9905... exists"
          },
          {
            "name": "environment_lock",
            "status": "passed",
            "details": {
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              "python_version": "3.13.12",
              "current_pip_hash": "553be32a4d71a2b1...",
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            },
            "message": "Pip packages hash matches"
          },
          {
            "name": "input_artifacts",
            "status": "passed",
            "details": {},
            "message": "No input artifacts to verify"
          },
          {
            "name": "output_artifacts",
            "status": "failed",
            "details": {
              "missing": [
                "edge-h-9d29bfe5-ABCA1/LDLR/SREBF2",
                "edge-h-12599989-ST3GAL2/ST8SIA1",
                "edge-h-fdb07848-SGMS1/SGMS2",
                "h-de0d4364",
                "h-9d29bfe5",
                "h-2600483e",
                "h-12599989",
                "h-fdb07848",
                "h-a015e80e",
                "h-441b25ba",
                "h-var-1dc420e7d8",
                "h-var-3fbcfc0e6c",
                "h-var-e81fbd3868",
                "h-var-76afa28dfc"
              ],
              "modified": [],
              "verified": [
                "edge-SMPD1-ceramide_biosynthesis",
                "edge-ceramide_biosynthesis-lipid_raft_dysfunction",
                "edge-CYP46A1-cholesterol_metabolism",
                "edge-cholesterol_metabolism-BACE1_clustering",
                "edge-BACE1_clustering-amyloid_beta_production",
                "edge-ABCA1-cholesterol_efflux",
                "edge-cholesterol_efflux-lipid_raft_composition",
                "edge-SGMS1-sphingomyelin_synthesis",
                "edge-sphingomyelin_synthesis-membrane_fluidity",
                "edge-FLOT1-lipid_raft_scaffolding",
                "edge-ST3GAL2-ganglioside_biosynthesis",
                "edge-ganglioside_biosynthesis-synaptic_membrane_organization",
                "edge-SMPD1-neurodegeneration",
                "edge-ABCA1-neurodegeneration",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SREBF2",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SREBF2",
                "edge-SREBF2-neurodegeneration",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-LDLR",
                "edge-CYP46A1-neurodegeneration",
                "edge-ST3GAL2-neurodegeneration",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST8SIA1-neurodegeneration",
                "edge-ST8SIA1-ST3GAL2",
                "edge-SGMS1-neurodegeneration",
                "edge-SGMS1-SGMS2",
                "edge-SGMS2-neurodegeneration",
                "edge-SGMS2-SGMS1",
                "edge-FLOT1-neurodegeneration",
                "edge-BACE1-neurodegeneration",
                "edge-BACE1-NLRP3",
                "edge-AKT-BACE1",
                "edge-BAX-JNK",
                "edge-ADAM10-APP",
                "edge-ADAM10-BACE1",
                "edge-BACE1-TAU",
                "edge-SMPD1-Acid sphingomyelinase / ceramide signaling",
                "edge-ABCA1-Cholesterol efflux / lipid transport",
                "edge-LDLR-Cholesterol efflux / lipid transport",
                "edge-SREBF2-Cholesterol efflux / lipid transport",
                "edge-CYP46A1-Cholesterol 24-hydroxylase / brain cholesterol turnover",
                "edge-ST3GAL2-Sphingolipid / ceramide signaling",
                "edge-ST8SIA1-Sphingolipid / ceramide signaling",
                "edge-SGMS1-Sphingolipid / ceramide signaling",
                "edge-SGMS2-Sphingolipid / ceramide signaling",
                "edge-FLOT1-Lipid raft membrane organization",
                "edge-BACE1-Beta-secretase / amyloidogenic pathway",
                "edge-FLOT1-SREBF2",
                "edge-FLOT1-CYP46A1",
                "edge-FLOT1-SGMS2",
                "edge-FLOT1-ABCA1",
                "edge-FLOT1-BACE1",
                "edge-FLOT1-ST3GAL2",
                "edge-FLOT1-ST8SIA1",
                "edge-FLOT1-LDLR",
                "edge-FLOT1-SMPD1",
                "edge-FLOT1-SGMS1",
                "edge-SREBF2-CYP46A1",
                "edge-SREBF2-SGMS2",
                "edge-SREBF2-ABCA1",
                "edge-SREBF2-BACE1",
                "edge-SREBF2-ST3GAL2",
                "edge-SREBF2-ST8SIA1",
                "edge-SREBF2-LDLR",
                "edge-SREBF2-SMPD1",
                "edge-SREBF2-SGMS1",
                "edge-CYP46A1-SGMS2",
                "edge-CYP46A1-ABCA1",
                "edge-CYP46A1-BACE1",
                "edge-CYP46A1-ST3GAL2",
                "edge-CYP46A1-ST8SIA1",
                "edge-CYP46A1-LDLR",
                "edge-CYP46A1-SMPD1",
                "edge-CYP46A1-SGMS1",
                "edge-SGMS2-ABCA1",
                "edge-SGMS2-BACE1",
                "edge-SGMS2-ST3GAL2",
                "edge-SGMS2-ST8SIA1",
                "edge-SGMS2-LDLR",
                "edge-SGMS2-SMPD1",
                "edge-SGMS2-SGMS1",
                "edge-ABCA1-BACE1",
                "edge-ABCA1-ST3GAL2",
                "edge-ABCA1-ST8SIA1",
                "edge-ABCA1-LDLR",
                "edge-ABCA1-SMPD1",
                "edge-ABCA1-SGMS1",
                "edge-BACE1-ST3GAL2",
                "edge-BACE1-ST8SIA1",
                "edge-BACE1-LDLR",
                "edge-BACE1-SMPD1",
                "edge-BACE1-SGMS1",
                "edge-ST3GAL2-ST8SIA1",
                "edge-ST3GAL2-LDLR",
                "edge-ST3GAL2-SMPD1",
                "edge-ST3GAL2-SGMS1",
                "edge-ST8SIA1-LDLR",
                "edge-ST8SIA1-SMPD1",
                "edge-ST8SIA1-SGMS1",
                "edge-LDLR-SMPD1",
                "edge-LDLR-SGMS1",
                "edge-SMPD1-SGMS1",
                "edge-ST8SIA1-BACE1",
                "edge-ST8SIA1-CYP46A1",
                "edge-ST8SIA1-ST3GAL2",
                "edge-ST8SIA1-FLOT1",
                "edge-ST8SIA1-ABCA1",
                "edge-ST8SIA1-SGMS2",
                "edge-ST8SIA1-SREBF2",
                "edge-LDLR-BACE1",
                "edge-LDLR-CYP46A1",
                "edge-LDLR-ST3GAL2",
                "edge-LDLR-FLOT1",
                "edge-LDLR-ABCA1",
                "edge-LDLR-SGMS2",
                "edge-LDLR-SREBF2",
                "edge-BACE1-CYP46A1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-ABCA1",
                "edge-BACE1-SGMS2",
                "edge-BACE1-SREBF2",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SREBF2",
                "edge-ST3GAL2-FLOT1",
                "edge-ST3GAL2-ABCA1",
                "edge-ST3GAL2-SGMS2",
                "edge-ST3GAL2-SREBF2",
                "edge-SGMS1-FLOT1",
                "edge-SGMS1-ABCA1",
                "edge-SGMS1-SGMS2",
                "edge-SGMS1-SMPD1",
                "edge-SGMS1-SREBF2",
                "edge-ABCA1-SGMS2",
                "edge-ABCA1-SREBF2",
                "edge-SGMS2-SREBF2",
                "edge-SMPD1-SREBF2",
                "edge-SMPD1-LDLR",
                "edge-SMPD1-ST3GAL2",
                "edge-SMPD1-ST8SIA1",
                "edge-SMPD1-ABCA1",
                "edge-SMPD1-SGMS2",
                "edge-SMPD1-CYP46A1",
                "edge-LDLR-ST8SIA1",
                "edge-ST3GAL2-CYP46A1",
                "edge-ABCA1-CYP46A1",
                "edge-SGMS2-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-ST3GAL2/ST8SIA1-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-SGMS1/SGMS2-neurodegeneration",
                "edge-ABCA1/LDLR/SREBF2-FLOT1",
                "edge-ABCA1/LDLR/SREBF2-SGMS1/SGMS2",
                "edge-ABCA1/LDLR/SREBF2-BACE1",
                "edge-BACE1-FLOT1",
                "edge-BACE1-SGMS1/SGMS2",
                "edge-BACE1-CYP46A1",
                "edge-ABCA1/LDLR/SREBF2-CYP46A1",
                "edge-CYP46A1-FLOT1",
                "edge-CYP46A1-SGMS1/SGMS2",
                "edge-FLOT1-SGMS1/SGMS2",
                "edge-CYP46A1-ST3GAL2/ST8SIA1",
                "edge-BACE1-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-ST3GAL2/ST8SIA1",
                "edge-FLOT1-ST3GAL2/ST8SIA1",
                "edge-SGMS1/SGMS2-ST3GAL2/ST8SIA1",
                "edge-ABCA1/LDLR/SREBF2-cholesterol_efflux___lipid_transport",
                "edge-CYP46A1-cholesterol_24_hydroxylase___brain_cholesterol_turnover",
                "edge-ST3GAL2/ST8SIA1-sphingolipid___ceramide_signaling",
                "edge-SGMS1/SGMS2-sphingolipid___ceramide_signaling",
                "edge-FLOT1-lipid_raft_membrane_organization",
                "edge-BACE1-beta_secretase___amyloidogenic_pathway"
              ]
            },
            "message": "Output artifacts: 175 verified, 14 missing, 0 modified"
          },
          {
            "name": "execution_entrypoint",
            "status": "passed",
            "details": {
              "script": "/home/ubuntu/scidex/post_process.py",
              "command": [
                "/home/ubuntu/scidex/venv/bin/python3",
                "/home/ubuntu/scidex/post_process.py"
              ]
            },
            "message": "Entrypoint exists: /home/ubuntu/scidex/post_process.py"
          }
        ],
        "summary": {
          "total": 5,
          "failed": 1,
          "passed": 4,
          "skipped": 0,
          "warnings": 0
        },
        "timestamp": "2026-04-10T13:31:14.360622",
        "analysis_id": "SDA-2026-04-01-gap-lipid-rafts-2026-04-01",
        "verified_by": "test",
        "overall_status": "failed"
      },
      "status": "failed",
      "timestamp": "2026-04-10T13:31:14.360622",
      "verified_by": "test",
      "failure_reason": "See verification report"
    },
    "manifest_version": "1.0"
  },
  "completed_at": "2026-04-01T13:00:00-07:00",
  "report_url": "/analyses/SDA-2026-04-01-gap-lipid-rafts-2026-04-01.html"
}