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measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium.","The average time range for blood to clot is about 10 to 13 seconds."],"kec_triple":{"biological_object":{"name":"blood","iri":"http://purl.obolibrary.org/obo/UBERON_0000178","source":"UBERON"},"biological_process":{"name":"coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007234","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.750000048428774}}},"assay_idx":0},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Activated Partial Prothrombin Time (APTT)","description":"Measures the time taken from the addition of calcium to the formation of a fibrin clot in platelet-poor plasma after activation with phospholipid and a contact activator.","method_type":"in_vitro","cell_types":[],"organ_tissue":["blood","plasma"],"species":[],"measured_endpoint":"clotting time","endpoint_direction":"increase","ontology_terms":[{"name":"Activated Partial Prothrombin Time","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["APTT is the time taken from the addition of calcium to the formation of a fibrin clot.","The clotting time for the APTT lies between 27-35 seconds."],"kec_triple":{"biological_object":{"name":"blood","iri":"http://purl.obolibrary.org/obo/UBERON_0000178","source":"UBERON"},"biological_process":{"name":"coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007234","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.4999998601851985}}},"assay_idx":1},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Prothrombin time (PT)","description":"A blood test that measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"clotting time","endpoint_direction":"change","ontology_terms":[{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0008219","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Prothrombin time\n(\nPT\n) is a blood test that measures how long it takes blood to clot.","PT measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium."],"kec_triple":{"biological_object":{"name":"fibrin clot","iri":null,"source":null},"biological_process":{"name":"blood 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activator (e.g. Kaolin, micronized silica, or ellagic acid) are added.","The APTT is the time taken from the addition of calcium to the formation of a fibrin clot."],"kec_triple":{"biological_object":{"name":"fibrin clot","iri":null,"source":null},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0008219","source":"GO"},"biological_action":{"name":"delayed","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.999999642372188}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"PT","description":"Measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"clotting time","endpoint_direction":"increase","ontology_terms":[{"name":"prothrombin 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calcium.","method_type":"in_vitro","cell_types":[],"organ_tissue":["blood"],"species":[],"measured_endpoint":"time required for fibrin clot formation","endpoint_direction":"change","ontology_terms":[{"name":"Prothrombin Time","iri":"http://purl.obolibrary.org/obo/OBI_0000123","source":null}],"guideline":null,"throughput":"not_specified","evidence":["Prothrombin time (PT) is a blood test that measures how long it takes blood to clot.","PT measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium."],"kec_triple":{"biological_object":{"name":"fibrin","iri":"http://purl.obolibrary.org/obo/GO_0005524","source":"GO"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007550","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.499999761697836}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Prothrombin time (PT)","description":"A blood test measuring the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium.","method_type":"ex_vivo","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"time to fibrin clot formation","endpoint_direction":"change","ontology_terms":[{"name":"prothrombin time","iri":"http://purl.obolibrary.org/obo/OBI_0000010","source":"OBI"}],"guideline":null,"throughput":"not_specified","evidence":["Prothrombin time (PT) is a blood test that measures how long it takes blood to clot.","PT measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium."],"kec_triple":{"biological_object":{"name":"blood","iri":"http://purl.obolibrary.org/obo/UBERON_00001000","source":"UBERON"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007596","source":"GO"},"biological_action":{"name":"delayed","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.874999893800123}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Activated partial prothrombin time (APTT)","description":"Measures the time from the addition of calcium to the formation of a fibrin clot in platelet-poor plasma activated by a contact activator.","method_type":"ex_vivo","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"time to fibrin clot formation","endpoint_direction":"change","ontology_terms":[{"name":"activated partial thromboplastin time","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["The APTT is the time taken from the addition of calcium to the formation of a fibrin clot."],"kec_triple":{"biological_object":{"name":"blood","iri":"http://purl.obolibrary.org/obo/UBERON_00001000","source":"UBERON"},"biological_process":{"name":"blood 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concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen measurement","iri":"http://purl.obolibrary.org/obo/OBI_0000300","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Decreased fibrinogen concentrations. Diluted plasma is clotted with a high concentration of Thrombin. The tested plasma is diluted (usually 1:10 but this may vary if the Fibrinogen concentration is very low or very high) to minimize the effect of 'inhibitory substances' within the plasma e.g. heparin, elevated levels of FDPs. The use of a high concentration of Thrombin (typically 100 U/ml) ensures that the clotting times are independent of Thrombin concentration over a wide range of Fibrinogen levels."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/PR_000009337","source":"PR"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007596","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.7499999329447746}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Fibrinogen concentration assay","description":"Measures fibrinogen concentration by clotting diluted plasma with a high concentration of thrombin and comparing the clotting time to a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":["blood"],"species":[],"measured_endpoint":"fibrinogen concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen measurement","iri":"http://purl.obolibrary.org/obo/OBI_0000300","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Decreased fibrinogen concentrations. Diluted plasma is clotted with a high concentration of Thrombin. The tested plasma is diluted (usually 1:10 but this may vary if the Fibrinogen concentration is very low or very high) to minimize the effect of 'inhibitory substances' within the plasma e.g. heparin, elevated levels of FDPs. The use of a high concentration of Thrombin (typically 100 U/ml) ensures that the clotting times are independent of Thrombin concentration over a wide range of Fibrinogen levels."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/PR_000009337","source":"PR"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007596","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.7499999329447746}}},"assay_idx":2},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"fibrinogen concentration","description":"Fibrinogen concentration is measured by clotting diluted plasma with a high concentration of thrombin and comparing the clotting time to a calibration curve constructed with a reference plasma.","method_type":"in_vitro","cell_types":[],"organ_tissue":["blood"],"species":[],"measured_endpoint":"fibrinogen concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen","iri":"CHEBI_5979","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["Decreased fibrinogen concentrations","The test requires a reference plasma with a known Fibrinogen concentration and that has been calibrated against a known international reference standard."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"CHEBI_5979","source":"CHEBI"},"biological_process":{"name":"blood coagulation","iri":"GO_0002055","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":19.0}}},"assay_idx":2},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Fibrinogen concentration assay","description":"Quantification of fibrinogen levels in diluted plasma by measuring the time taken for a clot to form after the addition of high-concentration Thrombin, using a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":["plasma"],"species":[],"measured_endpoint":"fibrinogen concentration","endpoint_direction":"change","ontology_terms":[{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_35231","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["The test platelet-poor diluted plasma (diluted 1:10 in buffer) is incubated at 37°C, Thrombin [~100 U/mL] added (all pre-warmed to 37°C). The time taken for the clot to form is compared to the calibration curve and the Fibrinogen concentration deduced."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_35231","source":"CHEBI"},"biological_process":{"name":"blood coagulation","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":-1.6250000298023224}}},"assay_idx":2},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Fibrinogen","description":"Fibrinogen concentration is measured by diluting plasma, adding a high concentration of thrombin, and comparing the clotting time to a calibration curve constructed from reference plasma with known fibrinogen concentrations.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"fibrinogen concentration","endpoint_direction":"decreased","ontology_terms":[{"name":"fibrinogen","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Diluted plasma is clotted with a high concentration of Thrombin. The tested plasma is diluted (usually 1:10 but this may vary if the Fibrinogen concentration is very low or very high) to minimize the effect of 'inhibitory substances' within the plasma e.g. heparin, elevated levels of FDPs. The use of a high concentration of Thrombin (typically 100 U/ml) ensures that the clotting times are independent of Thrombin concentration over a wide range of Fibrinogen levels. The test requires a reference plasma with a known Fibrinogen concentration and that has been calibrated against a known international reference standard. A calibration curve is constructed using this reference plasma by preparing a series of dilutions (1:5 –1:40) in the buffer to give a range of Fibrinogen concentrations. The clotting time of each of these dilutions is established (using duplicate samples) and the results (clotting time(s)/Fibrinogen concentration (g/L) are plotted on Log-Log graph paper. The 1:10 concentration is considered to be 100% i.e. normal. There should be a linear correlation between clotting times in the region of 10-50 sec. The test platelet-poor diluted plasma (diluted 1:10 in buffer) is incubated at 37°C, Thrombin [~100 U/mL] added (all pre-warmed to 37°C). The time taken for the clot to form is compared to the calibration curve and the Fibrinogen concentration deduced. Test samples whose clotting times fall out with the linear part of the calibration curve should be re-tested using different dilutions."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":null,"source":null},"biological_process":{"name":"blood coagulation","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.7499999552965164}}},"assay_idx":2},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Fibrinogen concentration","description":"Measures fibrinogen concentration by clotting diluted plasma with high thrombin concentration and comparing clotting time to a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":["plasma"],"species":[],"measured_endpoint":"fibrinogen concentration (g/L)","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_14628","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["Decreased fibrinogen concentrations","Diluted plasma is clotted with a high concentration of Thrombin. The tested plasma is diluted (usually 1:10 but this may vary if the Fibrinogen concentration is very low or very high) to minimize the effect of 'inhibitory substances' within the plasma e.g. heparin, elevated levels of FDPs. The use of a high concentration of Thrombin (typically 100 U/ml) ensures that the clotting times are independent of Thrombin concentration over a wide range of Fibrinogen levels.","The test requires a reference plasma with a known Fibrinogen concentration and that has been calibrated against a known international reference standard. A calibration curve is constructed using this reference plasma by preparing a series of dilutions (1:5 –1:40) in the buffer to give a range of Fibrinogen concentrations. The clotting time of each of these dilutions is established (using duplicate samples) and the results (clotting time(s)/Fibrinogen concentration (g/L) are plotted on Log-Log graph paper."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_14628","source":"CHEBI"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0007596","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.874999523162955}}},"assay_idx":2},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Fibrinogen Concentration Assay","description":"Quantifies fibrinogen levels in diluted plasma by measuring clotting time after thrombin addition and comparing to a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":["plasma"],"species":[],"measured_endpoint":"fibrinogen 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threshold."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/GO_0005518","source":"GO"},"biological_process":{"name":"blood coagulation","iri":"http://purl.obolibrary.org/obo/GO_0008219","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.62499976158145}}},"assay_idx":2},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Fibrinogen Concentration","description":"Measures the concentration of fibrinogen in diluted plasma using a high concentration of thrombin and a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"fibrinogen concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_17858","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["Diluted plasma is clotted with a high concentration of Thrombin.","The test requires a reference plasma with a known Fibrinogen concentration and that has been calibrated against a known international reference standard.","The time taken for the clot to form is compared to the calibration curve and the Fibrinogen concentration deduced."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/CHEBI_17858","source":"CHEBI"},"biological_process":{"name":"fibrinogen to fibrin conversion","iri":"http://purl.obolibrary.org/obo/GO_0030189","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.421875238504981}}},"assay_idx":2},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Fibrinogen concentration assay","description":"Measurement of fibrinogen levels by clotting diluted plasma with a high concentration of Thrombin and comparing the time to a calibration curve.","method_type":"in_vitro","cell_types":[],"organ_tissue":["plasma"],"species":[],"measured_endpoint":"Fibrinogen concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/GO_0005524","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Decreased fibrinogen concentrations","The time taken for the clot to form is compared to the calibration curve and the Fibrinogen concentration deduced."],"kec_triple":{"biological_object":{"name":"fibrinogen","iri":"http://purl.obolibrary.org/obo/GO_0005524","source":"GO"},"biological_process":{"name":"fibrinogen concentration","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.499999880790718}}},"assay_idx":2},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Fibrinogen concentration 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The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970).","Fluorescence was measured in a Aminco SPF-500 spectrofluorometer (Chandra et al., 1981)."],"kec_triple":{"biological_object":{"name":"biogenic amine","iri":null,"source":null},"biological_process":{"name":"neurotransmitter metabolism","iri":"http://purl.obolibrary.org/obo/GO_0042136","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.7499999906867743}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Spectrofluorometric biogenic amine assay","description":"Measures fluorescence of extracted biogenic amines (dopamine, norepinephrine, 5-hydroxytryptamine) from homogenized brain tissue using acidified n-butanol extraction and spectrofluorometry.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":[],"measured_endpoint":"biogenic amine levels","endpoint_direction":"not_specified","ontology_terms":[{"name":"dopamine","iri":"http://purl.obolibrary.org/obo/CHEBI_18243","source":"CHEBI"},{"name":"norepinephrine","iri":"http://purl.obolibrary.org/obo/CHEBI_18248","source":"CHEBI"},{"name":"serotonin","iri":"http://purl.obolibrary.org/obo/CHEBI_28754","source":"CHEBI"},{"name":"brain","iri":"http://purl.obolibrary.org/obo/UBERON_0000955","source":"UBERON"}],"guideline":null,"throughput":"low","evidence":["Weighed brain tissues were homogenized in a Potter-Elvehjem type A homogenizer with a teflon pestle using cold acidified n-butanol. The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970).","Fluorescence was measured in a Aminco SPF-500 spectrofluorometer (Chandra et al., 1981)."],"kec_triple":{"biological_object":{"name":"biogenic amine","iri":null,"source":null},"biological_process":{"name":"neurotransmitter metabolism","iri":"http://purl.obolibrary.org/obo/GO_0042136","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.7499999906867743}}},"assay_idx":0},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"spectrofluorometry","description":"Biogenic amines (dopamine, norepinephrine, 5-hydroxytryptamine) are extracted from brain tissue homogenates and quantified using a spectrofluorometer. 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The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970).","The recovery experiments were done simultaneously. Recoveries for different standards were 92 + 3% for dopamine (DA), 80+ 5% for norepinephrine (NE) and 90 + 5% for 5-hydroxytryptamine (5-HT).","Fluorescence was measured in a Aminco SPF-500 spectrofluorometer (Chandra et al., 1981)."],"kec_triple":{"biological_object":{"name":"biogenic amines","iri":null,"source":null},"biological_process":{"name":"neurotransmitter release","iri":null,"source":null},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.0000000298023224}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"biogenic amine fluorescence assay","description":"Measures the concentration of biogenic amines (dopamine, norepinephrine, and 5-hydroxytryptamine) in brain tissue by extracting amines with acidified n-butanol and quantifying fluorescence using a spectrofluorometer.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":[],"measured_endpoint":"biogenic amine levels","endpoint_direction":"change","ontology_terms":[{"name":"dopamine level","iri":"http://purl.obolibrary.org/obo/CHEBI_18015","source":"CHEBI"},{"name":"norepinephrine level","iri":"http://purl.obolibrary.org/obo/CHEBI_4855","source":"CHEBI"},{"name":"5-hydroxytryptamine level","iri":"http://purl.obolibrary.org/obo/CHEBI_16023","source":"CHEBI"}],"guideline":null,"throughput":"low","evidence":["Weighed brain tissues were homogenized in a Potter-Elvehjem type A homogenizer with a teflon pestle using cold acidified n-butanol.","The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970).","Fluorescence was measured in a Aminco SPF-500 spectrofluorometer (Chandra et al., 1981).","Recoveries for different standards were 92 + 3% for dopamine (DA), 80+ 5% for norepinephrine (NE) and 90 + 5% for 5-hydroxytryptamine (5-HT)."],"kec_triple":{"biological_object":{"name":"dopamine","iri":"http://purl.obolibrary.org/obo/CHEBI_18015","source":"CHEBI"},"biological_process":{"name":"neurotransmitter secretion","iri":"http://purl.obolibrary.org/obo/GO_0007268","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.87500035762912}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Spectrofluorometry","description":"Measures the concentration of biogenic amines (dopamine, norepinephrine, 5-hydroxytryptamine) extracted from homogenized brain tissue using a spectrofluorometer.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":[],"measured_endpoint":"concentration of biogenic amines (dopamine, norepinephrine, 5-hydroxytryptamine)","endpoint_direction":"change","ontology_terms":[{"name":"fluorescence measurement","iri":null,"source":null},{"name":"neurotransmitter concentration","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Weighed brain tissues were homogenized in a Potter-Elvehjem type A homogenizer with a teflon pestle using cold acidified n-butanol. 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Hippocampal neuronal cultures were exposed to normal bath solution or 1.0 or 2.0μM Pb2+ for 5 days, and subsequently RNA was harvested according to manufacturer’s instructions (RNeasy; Qiagen), quantified by reading the absorbance at 260 nm, and converted to complementary DNA (cDNA) using 1 μg RNA according to manufacturer’s instructions (High Capacity Reverse Transcription Kit 4368814; Applied Biosystems). Quantitative real-time PCR (q-rtPCR) was performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems) with 50 ng cDNA using the following probes: Actin (Rat, Rn00667869_m1; Applied Biosystems) and BDNF exon I, exon II, exon IV, and exon IX (Applied Biosystems)."],"kec_triple":{"biological_object":{"name":"BDNF mRNA","iri":null,"source":null},"biological_process":{"name":"gene expression","iri":"http://purl.obolibrary.org/obo/GO_0010467","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.5000000298023224}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"BDNF quantitative real-time PCR","description":"Quantifies BDNF exon-specific mRNA expression in hippocampal neuronal cultures using TaqMan-based qRT-PCR, normalized to actin.","method_type":"in_vitro","cell_types":["hippocampal neuronal cultures"],"organ_tissue":["hippocampus"],"species":["Rattus norvegicus"],"measured_endpoint":"BDNF mRNA expression","endpoint_direction":"change","ontology_terms":[{"name":"BDNF","iri":"http://purl.obolibrary.org/obo/CHEBI_75592","source":"CHEBI"},{"name":"hippocampus","iri":"http://purl.obolibrary.org/obo/UBERON_0001954","source":"UBERON"},{"name":"gene expression","iri":"http://purl.obolibrary.org/obo/GO_0010467","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["BDNF quantitative real-time PCR. Hippocampal neuronal cultures were exposed to normal bath solution or 1.0 or 2.0μM Pb2+ for 5 days, and subsequently RNA was harvested according to manufacturer’s instructions (RNeasy; Qiagen), quantified by reading the absorbance at 260 nm, and converted to complementary DNA (cDNA) using 1 μg RNA according to manufacturer’s instructions (High Capacity Reverse Transcription Kit 4368814; Applied Biosystems). Quantitative real-time PCR (q-rtPCR) was performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems) with 50 ng cDNA using the following probes: Actin (Rat, Rn00667869_m1; Applied Biosystems) and BDNF exon I, exon II, exon IV, and exon IX (Applied Biosystems)."],"kec_triple":{"biological_object":{"name":"BDNF mRNA","iri":null,"source":null},"biological_process":{"name":"gene expression","iri":"http://purl.obolibrary.org/obo/GO_0010467","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.5000000298023224}}},"assay_idx":1},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"BDNF ELISA","description":"Quantifies BDNF protein levels in cell culture media using a sandwich ELISA kit, normalized to total protein content.","method_type":"in_vitro","cell_types":["DIV12 neuronal cultures"],"organ_tissue":[],"species":[],"measured_endpoint":"BDNF protein levels","endpoint_direction":"change","ontology_terms":[{"name":"BDNF","iri":"http://purl.obolibrary.org/obo/CHEBI_75592","source":"CHEBI"},{"name":"enzyme-linked immunosorbent assay","iri":"http://purl.obolibrary.org/obo/OBI_0000286","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["BDNF release via ELISA. 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The assay is fast, highly reproducible and equally sensitive with the radioiodine detection method."],"kec_triple":{"biological_object":{"name":"NIS","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0015706","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.750000145402737}}},"assay_idx":1},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"fluorescence-based iodide efflux","description":"Uses a fluorescent protein variant (YFP-H148Q/I152L) to detect iodide efflux from NIS-expressing cells. Perchlorate, a known NIS inhibitor, is used as a positive control to suppress fluorescence.","method_type":"in_vitro","cell_types":["FRTL5"],"organ_tissue":["thyroid"],"species":["rat"],"measured_endpoint":"iodide efflux","endpoint_direction":"increase","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0015706","source":"GO"},{"name":"NIS activity","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["A fluorescence-based method has been developed, which uses the variant  YFP-H148Q/I152L of the Yellow Fluorescent Protein (YFP) in order to detect the efflux of iodide into the rat FRTL5 cells. As a positive control perchlorate is used  as it is a well known  competitive inhibitor of iodide transport by NIS. Fluorescence of recombinant YFP-H148Q/I152L is  suppressed by perchlorate and iodide with similar affinities. Fluorescence changes in FRTL-5 cells are  Na+-dependent, consistent with the Na+-dependence of NIS activity.   It is supposed to be an innovative approach to detect the cellular uptake of perchlorate and characterize the kinetics of transport by NIS. This method needs further optimization, as YFP is not specific for iodide and thus binding of other ionic molecules could affect the results of the assay (Cianchetta et al., 2010; Rhoden et al., 2008; Di Bernarde et al., 2011)."],"kec_triple":{"biological_object":{"name":"NIS","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0015706","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.4999999217689037}}},"assay_idx":2},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"in vivo 125I uptake","description":"Measures the accumulation of radioactive iodide (125I) in thyroid glands of rats after administration of excess iodide and injection with 125I. The assay evaluates the effect of test compounds on NIS-mediated iodide uptake in vivo.","method_type":"in_vivo","cell_types":[],"organ_tissue":["thyroid"],"species":["rat"],"measured_endpoint":"125I accumulation in thyroid","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0015706","source":"GO"},{"name":"thyroid function","iri":"http://purl.obolibrary.org/obo/GO_0033274","source":"GO"}],"guideline":null,"throughput":"low","evidence":["In vivo 125I uptake assays is based on  immunofluorescence analyses of thyroid glands after the treatment of rat with excess I⁻,  injected with Ci Na·125I  as previously described by Ferreira et al., 2005. Then the thyroid glands are  removed and weighed, and the amount of·125I in the thyroid gland is  measured in a γ-counter (PerkinElmer; model Wizard). The counts per minute in the thyroid gland are used to calculate the percentage of·125I in the thyroid gland, having in account that 100% corresponded to the counts per minute injected I⁻ into the rat (Arriagada et al., 2015)."],"kec_triple":{"biological_object":{"name":"thyroid gland","iri":"http://purl.obolibrary.org/obo/UBERON_0004534","source":"UBERON"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0015706","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.250000186264515}}},"assay_idx":3},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"radioiodide uptake assay","description":"Measures uptake of radioactive iodide (125I-) into cells expressing the sodium/iodide symporter (NIS) to assess NIS functional activity.","method_type":"in_vitro","cell_types":["FRTL5","NIS transfected cell lines"],"organ_tissue":[],"species":["rat"],"measured_endpoint":"iodide uptake (radioactive)","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"}],"guideline":null,"throughput":"high","evidence":["Measurement of radioiodide uptake (125I-) in NIS expressing cells.","For this method the FRTL5 cell line is the most commonly used, as it endogenously express the NIS protein, but also NIS transfected cell lines have been successfully implemented in many cases (Lecat-Guillet et al., 2007; 2008b; Lindenthal et al., 2009).","This method has been also adapted in a high throughput format and has been already used for the screening of a chemical library of 17.020 compounds (Lecat-Guillet et al., 2008b)."],"kec_triple":{"biological_object":{"name":"sodium/iodide symporter (NIS)","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.6249999701976776}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"spectrophotometric iodide uptake assay","description":"Measures iodide uptake via a colorimetric reaction where iodide catalyzes the reduction of cerium(IV) to cerium(III), monitored spectrophotometrically.","method_type":"in_vitro","cell_types":["FRTL5"],"organ_tissue":[],"species":["rat"],"measured_endpoint":"iodide uptake (colorimetric)","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"}],"guideline":null,"throughput":"high","evidence":["More recently a non-radioactive method has been developed, which has been also adapted in a high throughput format (Waltz et al., 2010).","It is a simple spectrophotometric assay for the determination of iodide uptake using rat thyroid-derived cells (FRTL5) based on the catalytic effect of iodide on the reduction of yellow cerium(IV) to colorless cerium(III) in the presence of arsenious acid (Sandell-Kolthoff reaction)."],"kec_triple":{"biological_object":{"name":"sodium/iodide symporter (NIS)","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.499999523162955}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"in vivo radioiodide uptake assay","description":"Measures radioactive iodide accumulation in rat thyroid glands after injection, quantified by gamma counting.","method_type":"in_vivo","cell_types":[],"organ_tissue":["thyroid gland"],"species":["rat"],"measured_endpoint":"radioiodide accumulation in thyroid gland (counts per minute)","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["In vivo 125I uptake assays is based on immunofluorescence analyses of thyroid glands after the treatment of rat with excess I-, injected with Ci Na125I as previously described by Ferreira et al., 2005. Then the thyroid glands are removed and weighed, and the amount of 125I in the thyroid gland is measured in a γ-counter (PerkinElmer; model Wizard). The counts per minute in the thyroid gland are used to calculate the percentage of 125I in the thyroid gland, having in account that 100% corresponded to the counts per minute injected I- into the rat (Arriagada et al., 2015)."],"kec_triple":{"biological_object":{"name":"thyroid gland","iri":"http://purl.obolibrary.org/obo/UBERON_0002048","source":"UBERON"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.5}}},"assay_idx":3},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"radioactive iodide uptake assay (RAIU)","description":"Measures uptake of radioactive iodide into cells expressing human NIS (hNIS-HEK293TEPA) to assess NIS-mediated iodide transport.","method_type":"in_vitro","cell_types":["hNIS-HEK293TEPA"],"organ_tissue":[],"species":["human"],"measured_endpoint":"radioiodide uptake","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"}],"guideline":null,"throughput":"high","evidence":["A novel cell line expressing human NIS, hNIS-HEK293TEPA, was used in a radioactive iodide uptake (RAIU) assay to identify inhibitors of NIS-mediated iodide uptake.","Strong assay performance and highly reproducible results support the utilization of this approach to screen large chemical libraries for inhibitors of NIS-mediated iodide uptake (Hallinger et al., 2017)."],"kec_triple":{"biological_object":{"name":"human sodium/iodide symporter (NIS)","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.25}}},"assay_idx":4},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"radioactive iodide uptake assay (RAIU)","description":"Measures radioactive iodide uptake to screen chemicals for NIS inhibition in the ToxCast library.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"radioiodide uptake","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"}],"guideline":null,"throughput":"high","evidence":["This study (Wang et al., 2018) applied a previously validated high-throughput approach to screen for NIS inhibitors in the ToxCast phase I library, representing 293 important environmental chemicals.","Here 310 blinded samples were screened in a tiered-approach using an initial single-concentration (100 μM) radioactive-iodide uptake (RAIU) assay"],"kec_triple":{"biological_object":{"name":"sodium/iodide symporter (NIS)","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0006873","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.75}}},"assay_idx":6},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"radioiodide uptake (125I-) in NIS expressing cells","description":"Measurement of radioiodide uptake (125I-) in NIS expressing cells to assess NIS functionality and identify inhibitory activity of compounds. The FRTL5 cell line is most commonly used as it endogenously expresses NIS, but NIS transfected cell lines have also been implemented. After identifying inhibitory activity, further tests verify specificity of NIS inhibition. This method has been adapted to high throughput format for screening large chemical libraries.","method_type":"in_vitro","cell_types":["FRTL5","NIS transfected cell lines"],"organ_tissue":[],"species":[],"measured_endpoint":"radioiodide uptake","endpoint_direction":"not_specified","ontology_terms":[{"name":"iodide uptake","iri":null,"source":null},{"name":"sodium iodide symporter activity","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["1. Measurement of radioiodide uptake (125I-) in NIS expressing cells.","For this method the FRTL5 cell line is the most commonly used, as it endogenously express the NIS protein, but also NIS transfected cell lines have been successfully implemented in many cases (Lecat-Guillet et al., 2007; 2008b; Lindenthal et al., 2009).","This method has been also adapted in a high throughput format and has been already used for the screening of a chemical library of 17.020 compounds (Lecat-Guillet et al., 2008b)."],"kec_triple":{"biological_object":{"name":"sodium iodide symporter","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":null,"source":null},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":-0.5}}},"assay_idx":0},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"spectrophotometric iodide uptake assay (Sandell-Kolthoff reaction)","description":"A non-radioactive spectrophotometric assay for determination of iodide uptake using rat thyroid-derived FRTL5 cells based on the catalytic effect of iodide on the reduction of yellow cerium(IV) to colorless cerium(III) in the presence of arsenious acid (Sandell-Kolthoff reaction). The assay is fast, highly reproducible, and equally sensitive as the radioiodine detection method, and has been adapted to high throughput format.","method_type":"in_vitro","cell_types":["FRTL5"],"organ_tissue":["thyroid"],"species":["rat"],"measured_endpoint":"iodide uptake","endpoint_direction":"not_specified","ontology_terms":[{"name":"iodide uptake","iri":null,"source":null},{"name":"spectrophotometry","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["2. More recently a non-radioactive method has been developed, which has been also adapted in a high throughput format (Waltz et al., 2010).","It is a simple spectrophotometric assay for the determination of iodide uptake using rat thyroid-derived cells (FRTL5) based on the catalytic effect of iodide on the reduction of yellow cerium(IV) to colorless cerium(III) in the presence of arsenious acid (Sandell-Kolthoff reaction).","The assay is fast, highly reproducible and equally sensitive with the radioiodine detection method."],"kec_triple":{"biological_object":{"name":"sodium iodide symporter","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":null,"source":null},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.999999860301614}}},"assay_idx":1},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"in vivo 125I uptake assay in rat thyroid glands","description":"In vivo 125I uptake assay based on immunofluorescence analyses of thyroid glands after treatment of rats with excess iodide, injected with 125I-labeled iodide. Thyroid glands are removed and weighed, and the amount of 125I in the thyroid gland is measured in a gamma counter. Counts per minute in the thyroid gland are used to calculate the percentage of 125I uptake.","method_type":"in_vivo","cell_types":[],"organ_tissue":["thyroid"],"species":["rat"],"measured_endpoint":"125I uptake in thyroid gland","endpoint_direction":"not_specified","ontology_terms":[{"name":"iodide uptake","iri":null,"source":null},{"name":"thyroid gland","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["4. In vivo 125I uptake assays is based on immunofluorescence analyses of thyroid glands after the treatment of rat with excess I-, injected with Ci Na 125I as previously described by Ferreira et al., 2005.","Then the thyroid glands are removed and weighed, and the amount of 125I in the thyroid gland is measured in a γ-counter (PerkinElmer; model Wizard).","The counts per minute in the thyroid gland are used to calculate the percentage of 125I in the thyroid gland, having in account that 100% corresponded to the counts per minute injected I− into the rat (Arriagada et al., 2015)."],"kec_triple":{"biological_object":{"name":"sodium iodide symporter","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":null,"source":null},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.75000010500662}}},"assay_idx":3},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"radioiodide uptake (RAIU) and cell viability assay for NIS inhibitor screening","description":"A high-throughput approach to screen for NIS inhibitors in the ToxCast phase I library using an initial single-concentration (100 μM) radioactive-iodide uptake (RAIU) assay, followed by multi-concentration (0.001 μM−100 μM) testing in parallel RAIU and cell viability assays. A chemical ranking system incorporating multi-concentration RAIU and cytotoxicity responses was developed for chemical prioritization.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"radioiodide uptake (RAIU) and cell viability","endpoint_direction":"decrease","ontology_terms":[{"name":"iodide uptake","iri":null,"source":null},{"name":"cell viability","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["Here 310 blinded samples were screened in a tiered-approach using an initial single-concentration (100 μM) radioactive-iodide uptake (RAIU) assay, followed by 169 samples further evaluated in multi-concentration (0.001 μM−100 μM) testing in parallel RAIU and cell viability assays.","A novel chemical ranking system that incorporates multi-concentration RAIU and cytotoxicity responses was also developed as a standardized method for chemical prioritization in current and future screenings.","Representative chemical responses and thyroid effects of high-ranking chemicals are further discussed."],"kec_triple":{"biological_object":{"name":"sodium iodide symporter","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.0}}},"assay_idx":5},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Radioiodide uptake assay","description":"Measures the uptake of radioactive iodide (125I-) in NIS-expressing cells to assess NIS functionality and identify inhibitory compounds.","method_type":"in_vitro","cell_types":["FRTL5","NIS transfected cell lines"],"organ_tissue":[],"species":[],"measured_endpoint":"radioiodide uptake","endpoint_direction":"decrease","ontology_terms":[{"name":"radioiodide uptake","iri":null,"source":null},{"name":"sodium/iodide symporter activity","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["Measurement of radioiodide uptake (125I-) in NIS expressing cells. For this method the FRTL5 cell line is the most commonly used, as it endogenously express the NIS protein, but also NIS transfected cell lines have been successfully implemented in many cases","This method has been also adapted in a high throughput format"],"kec_triple":{"biological_object":{"name":"sodium/iodide symporter","iri":null,"source":null},"biological_process":{"name":"iodide transport","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.62499997834675}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Spectrophotometric iodide uptake assay (Sandell-Kolthoff)","description":"A non-radioactive spectrophotometric assay that measures iodide uptake based on the catalytic reduction of cerium(IV) to cerium(III) in the presence of arsenious 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For this method the FRTL5 cell line is the most commonly used, as it endogenously express the NIS protein, but also NIS transfected cell lines have been successfully implemented in many cases (Lecat-Guillet et al., 2007; 2008b; Lindenthal et al., 2009).","This method has been also adapted in a high throughput format and has been already used for the screening of a chemical library of 17.020 compounds (Lecat-Guillet et al., 2008b)."],"kec_triple":{"biological_object":{"name":"sodium/iodide symporter","iri":"http://purl.obolibrary.org/obo/PR_000006457","source":"PR"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0030360","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.500000150874257}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"in vivo 125I uptake","description":"Measures the uptake of radioiodide (125I-) in the thyroid gland of rats after treatment with excess iodide and injection of 125I.","method_type":"in_vivo","cell_types":[],"organ_tissue":["http://purl.obolibrary.org/obo/UBERON_0002040"],"species":["http://purl.obolibrary.org/obo/NCBITaxon_10116"],"measured_endpoint":"radioiodide uptake in thyroid","endpoint_direction":"decrease","ontology_terms":[{"name":"radioiodide uptake","iri":"http://purl.obolibrary.org/obo/GO_0030360","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["In vivo 125I uptake assays is based on immunofluorescence analyses of thyroid glands after the treatment of rat with excess I−, injected with Ci Na125I as previously described by Ferreira et al., 2005. Then the thyroid glands are removed and weighed, and the amount of 125I in the thyroid gland is measured in a γ-counter (PerkinElmer; model Wizard). The counts per minute in the thyroid gland are used to calculate the percentage of 125I in the thyroid gland, having in account that 100% corresponded to the counts per minute injected I− into the rat (Arriagada et al., 2015)."],"kec_triple":{"biological_object":{"name":"thyroid gland","iri":"http://purl.obolibrary.org/obo/UBERON_0002040","source":"UBERON"},"biological_process":{"name":"iodide transport","iri":"http://purl.obolibrary.org/obo/GO_0030360","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.343749880868927}}},"assay_idx":3},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"radioiodide uptake","description":"Measurement of 125I- uptake in NIS expressing cells to detect inhibitory activity.","method_type":"in_vitro","cell_types":["FRTL5","NIS transfected cell lines"],"organ_tissue":[],"species":[],"measured_endpoint":"radioiodide 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All of these methods, particularly RIA, are repeatable and reproducible."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_16252","source":null},"biological_process":{"name":"thyroid hormone levels","iri":"http://purl.obolibrary.org/obo/GO_0032355","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.125}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"RIA","description":"Radioimmunoassay (RIA) measures the concentration of free or total triiodothyronine (T3) in serum or tissue samples using antibody-based detection of radioactive labels.","method_type":"in_vivo","cell_types":[],"organ_tissue":["serum","tissue"],"species":[],"measured_endpoint":"triiodothyronine (T3) concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_17354","source":"CHEBI"},{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_17351","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","Historically, the most widely used method in toxicology is RIA. 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All of these methods, particularly RIA, are repeatable and reproducible."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_17525","source":"CHEBI"},"biological_process":{"name":"thyroid hormone metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006693","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.953125000800355}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"RIA","description":"Radioimmunoassay used to measure free or total T3 and T4 concentrations in serum or tissues.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum"],"species":["rodent"],"measured_endpoint":"T3 and T4 concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_15432","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","Historically, the most widely used method in toxicology is RIA. The method is routinely used in rodent endocrine and toxicity studies."],"kec_triple":{"biological_object":{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_15432","source":"CHEBI"},"biological_process":{"name":"thyroid hormone levels","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.7499999752035365}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"RIA","description":"Radioimmunoassay used to measure total or free T3 and T4 concentrations in serum or tissues.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum"],"species":["rodent"],"measured_endpoint":"T3 and T4 concentrations","endpoint_direction":"change","ontology_terms":[{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_24121","source":"CHEBI"},{"name":"Thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_24122","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","The method is routinely used in rodent endocrine and toxicity studies."],"kec_triple":{"biological_object":{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_24121","source":"CHEBI"},"biological_process":{"name":"hormone concentration","iri":"GO_0006609","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.25}}},"assay_idx":0}]},{"support":9,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay used to measure total T3 and T4 concentrations in serum or tissues, commonly employed in rodent studies and human clinical tests.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodents","humans"],"measured_endpoint":"total T3 and T4 concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"triiodothyronine measurement","iri":null,"source":null},{"name":"thyroxine measurement","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_18287","source":"CHEBI"},"biological_process":{"name":"thyroid hormone metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006590","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.124999523373845}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay used to measure total T3 and T4 concentrations in serum or tissues, commonly employed in rodent studies and human clinical tests.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodents","humans"],"measured_endpoint":"total T3 and T4 concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"triiodothyronine measurement","iri":null,"source":null},{"name":"thyroxine measurement","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_18287","source":"CHEBI"},"biological_process":{"name":"thyroid hormone metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006590","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.124999523373845}}},"assay_idx":1},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"ELISA","description":"ELISA (enzyme-linked immunosorbent assay) measures T3 and T4 concentrations, becoming more routine in rodent studies and commonly used as a human clinical test method.","method_type":"in_vivo","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodent","human"],"measured_endpoint":"T3 and T4 concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_50793","source":"CHEBI"},{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_50808","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["The ELISA method has become more routine in rodent studies.","The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by a an indirect methodology, whereas analytical determination is the most direct measurement available."],"kec_triple":{"biological_object":{"name":"thyroid hormone","iri":null,"source":null},"biological_process":{"name":"hormone homeostasis","iri":"GO:0001951","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.00000035762804}}},"assay_idx":1},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay (ELISA) used to measure total or free concentrations of T3 and T4 hormones.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodent","human"],"measured_endpoint":"T3 and T4 hormone concentration","endpoint_direction":"change","ontology_terms":[{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_16013","source":"CHEBI"},{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_16012","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["The ELISA method has become more routine in rodent studies.","The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by a an indirect methodology"],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_16013","source":"CHEBI"},"biological_process":{"name":"thyroid hormone homeostasis","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.853515625004093}}},"assay_idx":1},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay (ELISA) is used to measure total T3 and T4 in serum or tissues, and has become more routine in rodent studies and human clinical tests.","method_type":"in_vivo","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodents","humans"],"measured_endpoint":"total T3 and T4 concentrations","endpoint_direction":"not_specified","ontology_terms":[{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_16252","source":null},{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_18185","source":null}],"guideline":null,"throughput":"not_specified","evidence":["The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by an indirect methodology, whereas analytical determination is the most direct measurement available. All of these methods, particularly RIA, are repeatable and reproducible."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_16252","source":null},"biological_process":{"name":"thyroid hormone levels","iri":"http://purl.obolibrary.org/obo/GO_0032355","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.374999536536052}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay (ELISA) quantifies free or total triiodothyronine (T3) levels in serum or tissue extracts via antibody-enzyme conjugate detection.","method_type":"in_vivo","cell_types":[],"organ_tissue":["serum","tissue"],"species":[],"measured_endpoint":"triiodothyronine (T3) concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_17354","source":"CHEBI"},{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_17351","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by a an indirect methodology, whereas analytical determination is the most direct measurement available."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_17354","source":"CHEBI"},"biological_process":{"name":"thyroid hormone biosynthesis","iri":"http://purl.obolibrary.org/obo/GO_0006744","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.999999880790718}}},"assay_idx":1},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"ELISA","description":"Measures total or free T3 and T4 concentrations in serum or tissues using an indirect enzyme-linked immunosorbent assay methodology.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum","tissues"],"species":["rodent","human"],"measured_endpoint":"concentration of T3 and T4","endpoint_direction":"decrease","ontology_terms":[{"name":"enzyme-linked immunosorbent assay","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["The ELISA method has become more routine in rodent studies.","The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by a an indirect methodology"],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":null,"source":null},"biological_process":{"name":"thyroid hormone homeostasis","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.374999642377361}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay (ELISA) measures total T3 and T4 concentrations in serum or tissues.","method_type":"in_vivo","cell_types":[],"organ_tissue":[],"species":["http://purl.obolibrary.org/obo/NCBITaxon_10090","http://purl.obolibrary.org/obo/NCBITaxon_9606"],"measured_endpoint":"total T3 concentration","endpoint_direction":"decrease","ontology_terms":[{"name":"enzyme-linked immunosorbent assay","iri":"http://purl.obolibrary.org/obo/OBI_0000377","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","The ELISA method has become more routine in rodent studies.","The ELISA method is commonly used as a human clinical test method.","Both RIA and ELISA measure THs by a an indirect methodology, whereas analytical determination is the most direct measurement available. All of these methods, particularly RIA, are repeatable and reproducible."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_17525","source":"CHEBI"},"biological_process":{"name":"thyroid hormone metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006693","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":19.625}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay used to measure free or total T3 and T4 concentrations in serum or tissues.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum"],"species":["rodent","human"],"measured_endpoint":"T3 and T4 concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_15432","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method."],"kec_triple":{"biological_object":{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_15432","source":"CHEBI"},"biological_process":{"name":"thyroid hormone levels","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.0}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"ELISA","description":"Enzyme-linked immunosorbent assay used to measure total or free T3 and T4 concentrations in serum or tissues.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum"],"species":["rodent","human"],"measured_endpoint":"T3 and T4 concentrations","endpoint_direction":"change","ontology_terms":[{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_24121","source":"CHEBI"},{"name":"Thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_24122","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["The majority of T3 and T4 measurements are made using either RIA or ELISA kits.","The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method."],"kec_triple":{"biological_object":{"name":"Triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_24121","source":"CHEBI"},"biological_process":{"name":"hormone concentration","iri":"GO_0006609","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.0390625}}},"assay_idx":1}]},{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"HPLC-MS","description":"High-performance liquid chromatography coupled with mass spectrometry used for analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates in serum or tissues.","method_type":"in_vitro","cell_types":[],"organ_tissue":["serum","tissues"],"species":[],"measured_endpoint":"iodothyronines and their conjugates concentrations","endpoint_direction":"decrease","ontology_terms":[{"name":"triiodothyronine measurement","iri":null,"source":null},{"name":"thyroxine measurement","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Recently, analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates through methods employing HPLC and mass spectrometry have become more common (DeVito et al., 1999; Miller et al., 2009; Hornung et al., 2015; Nelson et al., 2016; Stinckens et al., 2016)."],"kec_triple":{"biological_object":{"name":"triiodothyronine","iri":"http://purl.obolibrary.org/obo/CHEBI_18287","source":"CHEBI"},"biological_process":{"name":"thyroid hormone metabolic 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The fluorescent signals were read by fluorescence imaging plate reader Synergy HT (BioTek, Winooski, VT) (Rai and others 2010)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_18363","source":"CHEBI"},"biological_process":{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006807","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":19.0}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Fluo-3 AM flow cytometry","description":"Measures intracellular calcium concentration ([Ca2+]i) by loading cells with Fluo-3/AM dye, resuspending pellets, and analyzing fluorescence via flow cytometry (FL-1 channel) after metal treatment.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular calcium concentration ([Ca2+]i)","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006807","source":"GO"},{"name":"calcium ion binding","iri":"http://purl.obolibrary.org/obo/GO_0005509","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Free intracellular calcium ions were measured using the fluorescent calcium indicator FLUO-3/AM (Molecular probes, Eugene, OR, USA). Cells (4 × 10^4 cells/cm^2) were seeded in 24-well plates for 24 h to reach 60%–70%, and then treated for 24 h with As(III) (0.5 and 1 mg/l), or coexposed to As(III) (1 mg/l) and F (2.5, 5, and 10 mg/l). After treatment, supernatant was collected and combined with trypsinized cells. Pelleted samples were resuspended in 500 μl of FLUO-3/AM (4 μmol/l) and incubated at 37 °C for 30 min. After centrifugation, cells were washed with HBSS (Hank's Buffered Salt Solution, Sigma), made up to 400 μl with HBSS and analyzed by flow cytometry. The signal from FLUO-3/AM bound to Ca2+ was recorded using the Fl-1 channel (Rocha et al., 2011)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_18363","source":"CHEBI"},"biological_process":{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006807","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":18.25}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Fluo-4 AM flow cytometry","description":"Measures intracellular calcium concentration ([Ca2+]i) in Cd-exposed cerebral cortical neurons by loading cells with Fluo-4/AM dye and analyzing fluorescence intensity via flow cytometry (BD-FACS Aria) after excitation at 494 nm and emission at 516 nm.","method_type":"in_vitro","cell_types":["cerebral cortical neurons"],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular calcium concentration ([Ca2+]i)","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006807","source":"GO"},{"name":"calcium ion binding","iri":"http://purl.obolibrary.org/obo/GO_0005509","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Fluo-4/AM was used as an intracellular free Ca2+ fluorescent probe to analyze [Ca2+]i in Cd-exposed cerebral cortical neurons. 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The data were analyzed by Cell Quest program (Becton Dickinson), and the mean fluorescence intensity was obtained by histogram statistics (Yuan et al., 2013)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_18363","source":"CHEBI"},"biological_process":{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006807","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":18.25}}},"assay_idx":2},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Fluo3 AM fluorescence imaging","description":"Intracellular calcium increase measured using Fluo3 AM dye after metal addition to culture wells, read by a fluorescence imaging plate reader.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular calcium concentration","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},{"name":"fluorescence","iri":"http://purl.obolibrary.org/obo/CHMO_0000054","source":"CHMO"}],"guideline":null,"throughput":"medium","evidence":["An increase in [Ca2+]i was measured using Fluo3 AM as an indicator dye after the addition of metals (single or in mixture) to the culture wells following an optimized protocol (Arey et al., 2022).","The fluorescent signals were read by fluorescence imaging plate reader Synergy HT (BioTek, Winooski, VT) (Rai and others 2010)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},"biological_process":{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.750000101630576}}},"assay_idx":0},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Fluo-4 fluorescence microscopy","description":"Calcium levels in human astrocytes monitored by fluorescence microscopy using the Ca2+ indicator fluo-4, with SR101 staining to confirm astrocyte identity.","method_type":"ex_vivo","cell_types":["human astrocytes"],"organ_tissue":["brain","hippocampus"],"species":["human"],"measured_endpoint":"intracellular calcium concentration","endpoint_direction":"change","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},{"name":"astrocyte","iri":"http://purl.obolibrary.org/obo/CL_0000098","source":"CL"},{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},{"name":"fluorescence microscopy","iri":"http://purl.obolibrary.org/obo/CHMO_0000054","source":"CHMO"}],"guideline":null,"throughput":"low","evidence":["Ca2+ levels in human astrocytes were monitored by fluorescence microscopy using the Ca2+ indicator fluo-4.","Slices were incubated with fluo-4-AM (2–5 µL of 2 mM dye were dropped over the tissue, attaining a final concentration of 2–10 µM and 0.01% of pluronic) and Sulforhodamine 101 (100 µM) for 30–60 min at room temperature (Navarrete and others 2013).","In these conditions, most of the Fluo-4-loaded cells were astrocytes as indicated by their SR101 staining (Nimmerjahn et al., 2004; 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Pelleted samples were resuspended in 500 μl of FLUO-3/AM (4 μmol/l) and incubated at 37 °C for 30 min. After centrifugation, cells were washed with HBSS (Hank's Buffered Salt Solution, Sigma), made up to 400 μl with HBSS and analyzed by flow cytometry.","The signal from FLUO-3/AM bound to Ca2+ was recorded using the Fl-1 channel (Rocha et al., 2011)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},"biological_process":{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.2500000298023224}}},"assay_idx":2},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Fluo-4/AM flow cytometry","description":"Intracellular free Ca2+ measured using Fluo-4/AM fluorescent probe in Cd-exposed cerebral cortical neurons, analyzed by flow cytometry.","method_type":"in_vitro","cell_types":["cerebral cortical neurons"],"organ_tissue":["cerebral cortex","brain"],"species":[],"measured_endpoint":"intracellular calcium concentration","endpoint_direction":"change","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},{"name":"neuron","iri":"http://purl.obolibrary.org/obo/CL_0000099","source":"CL"},{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},{"name":"flow cytometry","iri":"http://purl.obolibrary.org/obo/OBI_0000085","source":"OBI"},{"name":"fluorescence","iri":"http://purl.obolibrary.org/obo/CHMO_0000054","source":"CHMO"}],"guideline":null,"throughput":"medium","evidence":["Fluo-4/AM was used as an intracellular free Ca2+ fluorescent probe to analyze [Ca2+]i in Cd-exposed cerebral cortical neurons.","In short, the harvested cells were incubated with Fluo-4/AM (5 µmol/L final concentration) for 30 min at 37°C in the dark, washed with PBS, and analyzed on a BD-FACS Aria flow cytometry.","Intracellular [Ca2+]i levels were represented by fluorescent intensity. Fluorescent intensity was recorded by excitation at 494 nm and emission at 516 nm. The data were analyzed by Cell Quest program (Becton Dickinson), and the mean fluorescence intensity was obtained by histogram statistics (Yuan et al., 2013)."],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_25173","source":"CHEBI"},"biological_process":{"name":"calcium signaling pathway","iri":"http://purl.obolibrary.org/obo/GO_0051550","source":"GO"},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.499999985098839}}},"assay_idx":3},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Fluo-3 AM fluorescence imaging plate reader assay","description":"Measures intracellular calcium concentration in culture wells using Fluo-3 AM indicator dye, with fluorescent signals detected by a fluorescence imaging plate reader.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular calcium 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After centrifugation, cells were washed with HBSS (Hank's Buffered Salt Solution, Sigma), made up to 400 μl with HBSS and analyzed by flow cytometry.","(Rocha et al., 2011)."],"kec_triple":{"biological_object":{"name":"intracellular calcium ion","iri":null,"source":null},"biological_process":{"name":"calcium signaling","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.875000014901161}}},"assay_idx":3},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Fluo-4/AM flow cytometry assay","description":"Analyzes intracellular free calcium levels in cadmium-exposed cerebral cortical neurons using Fluo-4/AM probe and flow cytometry.","method_type":"in_vitro","cell_types":["cerebral cortical neurons"],"organ_tissue":["cerebral cortex"],"species":[],"measured_endpoint":"intracellular free calcium 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Instead of adding an enzyme extract and chitin precursors to the reaction, one could simply add homogenized chitin containing material to the reaction to quantify its chitin content."],"kec_triple":{"biological_object":{"name":"chitin","iri":null,"source":null},"biological_process":{"name":"chitin biosynthetic process","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.375}}},"assay_idx":4},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Non-radioactive chitin synthase activity","description":"This assay measures chitin content by quantifying the activity of chitin synthase using a non-radioactive method, where homogenized chitin-containing material is added to the reaction.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"chitin content","endpoint_direction":"decrease","ontology_terms":[{"name":"chitin synthase activity","iri":"http://purl.obolibrary.org/obo/GO_0004396","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Another possibility is to use the non-radioactive assay developed to measure chitin synthase activity. Instead of adding an enzyme extract and chitin precursors to the reaction, one could simply add homogenized chitin containing material to the reaction to quantify its chitin content"],"kec_triple":{"biological_object":{"name":"cuticle","iri":"http://purl.obolibrary.org/obo/UBERON_0002097","source":"UBERON"},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006030","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.96875}}},"assay_idx":4},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"chitin synthase activity assay","description":"Non-radioactive assay measuring chitin content by adding homogenized material to a reaction designed to measure chitin synthase activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"chitin content","endpoint_direction":"decrease","ontology_terms":[{"name":"chitin","iri":"http://purl.obolibrary.org/obo/CHEBI_15354","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["use the non-radioactive assay developed to measure chitin synthase activity","add homogenized chitin containing material to the reaction to quantify its chitin content"],"kec_triple":{"biological_object":{"name":"chitin","iri":"http://purl.obolibrary.org/obo/CHEBI_15354","source":"CHEBI"},"biological_process":{"name":"cuticular chitin content","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.624999880790718}}},"assay_idx":4},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Chitin synthase activity assay","description":"Non-radioactive assay measuring chitin content by adding homogenized chitin-containing material to a reaction.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"chitin content","endpoint_direction":"decrease","ontology_terms":[{"name":"chitin","iri":"http://purl.obolibrary.org/obo/CHEBI_15455","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["use the non-radioactive assay developed to measure chitin synthase activity","add homogenized chitin containing material to the reaction to quantify its chitin content"],"kec_triple":{"biological_object":{"name":"chitin","iri":"http://purl.obolibrary.org/obo/CHEBI_15455","source":"CHEBI"},"biological_process":{"name":"cuticular chitin content","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.49999976158145}}},"assay_idx":4}]},{"support":8,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-3-27b-it","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"Morgan-Elson assay","description":"Measures N-Acetylglucosamine (GlcNAc) colorimetrically after digestion of chitin by bacterial chitinase.","method_type":"not_specified","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"N-Acetylglucosamine amount","endpoint_direction":"not_specified","ontology_terms":[{"name":"N-Acetylglucosamine","iri":"http://purl.obolibrary.org/obo/CHEBI_58265","source":"CHEBI"},{"name":"chitin digestion","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["the N-Acetylglucosamine (GlcNAc) amount can be determined colorimetrically by a modified Morgan-Elson assay (Reissig et al. 1955; 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To detect the leakage of LDH into cell culture medium, a tetrazolium salt is used in this assay. In the first step, LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate. In the second step, a tetrazolium salt is converted to a colored formazan product using newly synthesized NADH in the presence of an electron acceptor. The amount of formazan product can be colorimetrically quantified by standard spectroscopy. Because of the linearity of the assay, it can be used to enumerate the percentage of necrotic cells in a sample (Chan et al., 2013)."],"kec_triple":{"biological_object":{"name":"cell","iri":"http://purl.obolibrary.org/obo/CL_0000000","source":null},"biological_process":{"name":"cell necrosis","iri":"http://purl.obolibrary.org/obo/GO_0055130","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.2499998500570655}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"LDH","description":"Measures the leakage of lactate dehydrogenase into the extracellular space as an indicator of plasma membrane damage and necrosis.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"percentage of necrotic 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By using a spectrophotometer, its fluorescence intensities were measured with a wavelength of 580 nm ( 13 , 14 )."],"kec_triple":{"biological_object":{"name":"kidney tubule","iri":null,"source":null},"biological_process":{"name":"lysosomal enzyme release","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.7500000558793545}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"NAG Assay","description":"Measures urinary N-acetyl-β-D-glucosaminidase activity using a colorimetric kit.","method_type":"in_vivo","cell_types":[],"organ_tissue":["http://purl.obolibrary.org/obo/UBERON_0002113"],"species":[],"measured_endpoint":"N-acetyl-β-D-glucosaminidase activity","endpoint_direction":"increase","ontology_terms":[{"name":"N-acetyl-β-D-glucosaminidase","iri":"http://purl.obolibrary.org/obo/PR_000016566","source":"PR"}],"guideline":null,"throughput":"high","evidence":["Urinary NAG activity was measured by using NAG Quantitative Kit (Shionogi, Osaka, Japan). After storing a synthetic substrate solution (1 mL) at 37°C for five minutes, the solution was mixed with the supernatant of the urine samples (50 mL) received after centrifugation. After storing it at 37°C for 15 min, stopping solution (2 mL) was added to and mixed with it. By using a spectrophotometer, its fluorescence intensities were measured with a wavelength of 580 nm."],"kec_triple":{"biological_object":{"name":"N-acetyl-β-D-glucosaminidase","iri":"http://purl.obolibrary.org/obo/PR_000016566","source":"PR"},"biological_process":{"name":"renal tubular function","iri":"http://purl.obolibrary.org/obo/GO_0006829","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.3281250074505806}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"NAG Assay","description":"Colorimetric/fluorescence measurement of N-acetyl-β-D-glucosaminidase (NAG) activity in urine.","method_type":"in_vitro","cell_types":[],"organ_tissue":["kidney"],"species":[],"measured_endpoint":"Urinary NAG activity","endpoint_direction":"change","ontology_terms":[{"name":"N-acetyl-beta-D-glucosaminidase 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The control group (vehicle) received a single intraperitoneal (i.p.) injection of saline solution (1 ml per 100 g body weight). Uranyl acetate was dissolved in normal saline. Rats were treated with single intraperitoneal (i.p.) injections of UA in doses 0.5, 1 and 2 mg/kg body weight. These dosages was selected based on previous studies [28], which is sufficient to induce oxidative stress in kidney without causing death and none died within the duration of experiments. Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran)."],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0000105","source":null},"biological_process":{"name":"kidney function","iri":"http://purl.obolibrary.org/obo/GO_0003009","source":null},"biological_action":{"name":"increase","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.000000047264621}}},"assay_idx":2},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Kidney Dysfunction Assay","description":"Determines serum blood urea nitrogen (BUN) and creatinine levels, which rise when glomerular filtration rate declines, indicating reduced kidney function.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["rat"],"measured_endpoint":"Serum BUN and creatinine concentrations","endpoint_direction":"change","ontology_terms":[{"name":"blood urea nitrogen","iri":null,"source":null},{"name":"serum creatinine","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Kidney Dysfunction Assay Measuring BUN and creatinine serum blood levels (Shaki et al., 2012)","For studies in vivo rats were fasted overnight, then animals were divided into two groups, with six rats in each group. The control group (vehicle) received a single intraperitoneal (i.p.) injection of saline solution (1 ml per 100 g body weight). Uranyl acetate was dissolved in normal saline. Rats were treated with single intraperitoneal (i.p.) injections of UA in doses 0.5, 1 and 2 mg/kg body weight. These dosages was selected based on previous studies [28], which is sufficient to induce oxidative stress in kidney without causing death and none died within the duration of experiments. Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran). The rats were killed by decapitation 24 h after injection. The kidney were immediately removed and placed in ice-cold mitochondria isolation medium (0.225 M D-mannitol, 75 mM sucrose, and 0.2 mM EDTA, pH=7.4)"],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"glomerular filtration","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.25}}},"assay_idx":3},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Kidney Dysfunction Assay","description":"Measures serum blood urea nitrogen (BUN) and creatinine levels as markers of kidney dysfunction in rats following uranyl acetate exposure.","method_type":"in_vivo","cell_types":[],"organ_tissue":["serum","blood","kidney"],"species":["rat"],"measured_endpoint":"serum BUN and creatinine levels","endpoint_direction":"increase","ontology_terms":[{"name":"blood urea nitrogen","iri":"http://purl.obolibrary.org/obo/CHEBI_16940","source":"CHEBI"},{"name":"creatinine","iri":"http://purl.obolibrary.org/obo/CHEBI_27648","source":"CHEBI"},{"name":"blood","iri":"http://purl.obolibrary.org/obo/UBERON_0000922","source":"UBERON"},{"name":"serum","iri":"http://purl.obolibrary.org/obo/UBERON_0000922","source":"UBERON"},{"name":"enzyme activity assay","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Kidney Dysfunction Assay","Measuring BUN and creatinine serum blood levels","For studies in vivo rats were fasted overnight, then animals were divided into two groups, with six rats in each group.","Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran).","Rats were killed by decapitation 24 h after injection.","The kidney were immediately removed and placed in ice-cold mitochondria isolation medium (0.225 M D-mannitol, 75 mM sucrose, and 0.2 mM EDTA, pH=7.4)"],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"kidney development","iri":"http://purl.obolibrary.org/obo/GO_0001891","source":"GO"},"biological_action":{"name":"pathological","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.9999999701976776}}},"assay_idx":2},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Kidney Dysfunction Assay","description":"Determines serum blood urea nitrogen (BUN) and creatinine levels in rats using commercial reagents to assess kidney dysfunction.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["Rattus norvegicus"],"measured_endpoint":"serum BUN and creatinine levels","endpoint_direction":"change","ontology_terms":[{"name":"blood urea nitrogen","iri":null,"source":null},{"name":"creatinine","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Measuring BUN and creatinine serum blood levels","Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran). The rats were killed by decapitation 24 h after injection. The kidney were immediately removed and placed in ice-cold mitochondria isolation medium (0.225 M D-mannitol, 75 mM sucrose, and 0.2 mM EDTA, pH=7.4)"],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"renal filtration","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.375000029802322}}},"assay_idx":3},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Kidney Dysfunction Assay","description":"Measures blood urea nitrogen (BUN) and serum creatinine levels in rats to assess kidney dysfunction.","method_type":"in_vivo","cell_types":[],"organ_tissue":["http://purl.obolibrary.org/obo/UBERON_0002113"],"species":["http://purl.obolibrary.org/obo/NCBITaxon_10116"],"measured_endpoint":"BUN and creatinine","endpoint_direction":"increase","ontology_terms":[{"name":"blood urea nitrogen","iri":"http://purl.obolibrary.org/obo/CHEBI_37827","source":"CHEBI"},{"name":"creatinine","iri":"http://purl.obolibrary.org/obo/CHEBI_16709","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran)."],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"renal function","iri":"http://purl.obolibrary.org/obo/GO_0006829","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.656249962397851}}},"assay_idx":3},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Kidney Dysfunction Assay","description":"Measurement of Blood Urea Nitrogen (BUN) and serum creatinine levels in rats to identify kidney dysfunction.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":[],"measured_endpoint":"BUN and creatinine serum blood levels","endpoint_direction":"increase","ontology_terms":[{"name":"Creatinine","iri":"http://purl.obolibrary.org/obo/CHEBI_15453","source":"CHMO"}],"guideline":null,"throughput":"low","evidence":["Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents","For studies in vivo rats were fasted overnight"],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0001067","source":"UBERON"},"biological_process":{"name":"kidney function","iri":"http://purl.obolibrary.org/obo/GO_0008030","source":"GO"},"biological_action":{"name":"pathological","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.125000078231096}}},"assay_idx":2}]},{"support":4,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","poolside--Laguna-S-2.1-NVFP4"],"assay":{"assay_name":"Kidney Function Assay","description":"Measures total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, and serum and urinary creatinine.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["human"],"measured_endpoint":"urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine","endpoint_direction":"not_specified","ontology_terms":[{"name":"urinary protein","iri":null,"source":null},{"name":"albumin","iri":"http://purl.obolibrary.org/obo/PR_000001417","source":"PR"},{"name":"transferrin","iri":"http://purl.obolibrary.org/obo/PR_000000048","source":"PR"},{"name":"β2-microglobulin","iri":"http://purl.obolibrary.org/obo/PR_000001001","source":"PR"},{"name":"N-acetyl-β-D-glucosaminidase activity","iri":"http://purl.obolibrary.org/obo/GO_0004568","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine","Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983).","The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996)."],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"renal system process","iri":"http://purl.obolibrary.org/obo/GO_0003014","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.3749999701976776}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Kidney Function Assay","description":"Measures total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, and serum and urinary creatinine.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["human"],"measured_endpoint":"urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine","endpoint_direction":"not_specified","ontology_terms":[{"name":"urinary protein","iri":null,"source":null},{"name":"albumin","iri":"http://purl.obolibrary.org/obo/PR_000001417","source":"PR"},{"name":"transferrin","iri":"http://purl.obolibrary.org/obo/PR_000000048","source":"PR"},{"name":"β2-microglobulin","iri":"http://purl.obolibrary.org/obo/PR_000001001","source":"PR"},{"name":"N-acetyl-β-D-glucosaminidase activity","iri":"http://purl.obolibrary.org/obo/GO_0004568","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine","Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983).","The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996)."],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0002113","source":"UBERON"},"biological_process":{"name":"renal system process","iri":"http://purl.obolibrary.org/obo/GO_0003014","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.3749999701976776}}},"assay_idx":0},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Kidney Function Assay","description":"Measures total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine to assess kidney function.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["human"],"measured_endpoint":"total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine","endpoint_direction":"change","ontology_terms":[{"name":"protein","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},{"name":"albumin","iri":"http://purl.obolibrary.org/obo/CHMO_0000001","source":null},{"name":"transferrin","iri":"http://purl.obolibrary.org/obo/CHMO_0000001","source":null},{"name":"beta-2-microglobulin","iri":"http://purl.obolibrary.org/obo/CHMO_0000001","source":null},{"name":"retinol-binding protein","iri":"http://purl.obolibrary.org/obo/CHMO_0000001","source":null},{"name":"N-acetyl-beta-D-glucosaminidase","iri":"http://purl.obolibrary.org/obo/GO_0004568","source":null},{"name":"creatinine","iri":"http://purl.obolibrary.org/obo/CHMO_0000001","source":null}],"guideline":null,"throughput":"not_specified","evidence":["All analyses of a given parameter were performed under similar experimental conditions in the same laboratories within 6mo of collection. Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). Acceptable limits for precision and accuracy of measurements and external quality controls were the same as those described in the Cadmibel study (Lauwerys et al., 1990). The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996). Only total NAG (NAG-T) was used for the purpose of this study. Serum and urinary creatinine (Creat-U) were measured by the methods of Heinegard and Tiderström (1973), and Jaffé, respectively (Henry, 1965)."],"kec_triple":{"biological_object":{"name":"kidney","iri":"http://purl.obolibrary.org/obo/UBERON_0000105","source":null},"biological_process":{"name":"kidney function","iri":"http://purl.obolibrary.org/obo/GO_0003009","source":null},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.7499999552965164}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Kidney Function Assay","description":"Measures a panel of urinary biomarkers of kidney tubular damage, including total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, and serum/urinary creatinine.","method_type":"in_vivo","cell_types":[],"organ_tissue":["kidney"],"species":[],"measured_endpoint":"Urinary biomarkers of kidney tubular damage (protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, NAG activity, creatinine)","endpoint_direction":"change","ontology_terms":[{"name":"urinary protein","iri":null,"source":null},{"name":"albuminuria","iri":null,"source":null},{"name":"N-acetyl-β-D-glucosaminidase activity","iri":null,"source":null},{"name":"β2-microglobulin","iri":null,"source":null},{"name":"brush border tubular antigens","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Kidney Function Assay Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine (de Burbure et al., 2003)","Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). Acceptable limits for precision and accuracy of measurements and external quality controls were the same as those described in the Cadmibel study (Lauwerys et al., 1990). The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996). Only total NAG (NAG-T) was used for the purpose of this study. 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Bound cyclophilin is revealed using anti-cyclophilin antiserum and anti-rabbit IgG coupled to alkaline phosphatase.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"CsA-cyclophilin binding","endpoint_direction":"change","ontology_terms":[{"name":"protein binding","iri":"GO_0005536","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Immunophilin-CNI complexes directly inhibit phosphatase activity of CN, therefore, as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit.","Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin.","Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase"],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":null,"source":null},"biological_process":{"name":"protein complex assembly","iri":"GO_0005654","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.0000000968575478}}},"assay_idx":1},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"ELISA","description":"A surrogate measurement of CN activity that detects the binding of cyclosporin A (CsA) with cyclophilin using microtiter plates precoated with BSA-conjugated cyclosporin.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"binding of CsA with cyclophilin","endpoint_direction":"change","ontology_terms":[{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit.","Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin.","Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase"],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.2499999329447746}}},"assay_idx":1},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"ELISA","description":"Detects the binding of cyclosporin A (CsA) with cyclophilin using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin. Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"cyclosporin A-cyclophilin binding","endpoint_direction":"increase","ontology_terms":[{"name":"cyclosporin A binding","iri":"http://purl.obolibrary.org/obo/CHMO_0000000","source":null},{"name":"cyclophilin","iri":"http://purl.obolibrary.org/obo/CL_0000000","source":null}],"guideline":null,"throughput":"not_specified","evidence":["Immunophilin-CNI complexes directly inhibit phosphatase activity of CN, therefore, as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin. Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase."],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":"http://purl.obolibrary.org/obo/CL_0000000","source":null},"biological_process":{"name":"cyclosporin A binding","iri":"http://purl.obolibrary.org/obo/CHMO_0000000","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.5000000447034836}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"ELISA","description":"Detects binding of cyclosporin A (CsA) to cyclophilin using microtiter plates precoated with BSA and conjugated to cyclosporin; bound cyclophilin is revealed with anti-cyclophilin antiserum and an alkaline phosphatase‑conjugated secondary antibody.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"cyclophilin‑CsA binding","endpoint_direction":"increase","ontology_terms":[{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Immunophilin-CNI complexes directly inhibit phosphatase activity of CN, therefore, as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit.","Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin.","Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase (Quesniaux et al. 1987)."],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":null,"source":null},"biological_process":{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.5}}},"assay_idx":1},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"ELISA","description":"Detects the binding of cyclosporin A to cyclophilin using a microtiter plate-based ELISA with anti-cyclophilin antibodies and an alkaline phosphatase-conjugated secondary antibody as a surrogate for calcineurin inhibition.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"cyclophilin-cyclosporin A binding","endpoint_direction":"increase","ontology_terms":[{"name":"ELISA","iri":null,"source":"OBI"},{"name":"protein binding","iri":null,"source":"GO"}],"guideline":null,"throughput":"medium","evidence":["as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin. Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase"],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":null,"source":null},"biological_process":{"name":"protein binding","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.375000000101863}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"ELISA","description":"Detects the binding of cyclophilin to cyclosporin A (CsA) using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin, followed by detection with anti-cyclophilin rabbit antiserum and anti-rabbit globulin goat IgG coupled to alkaline phosphatase.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"binding of cyclophilin to cyclosporin A","endpoint_direction":"increase","ontology_terms":[{"name":"enzyme-linked immunosorbent assay","iri":"http://purl.obolibrary.org/obo/OBI_0000377","source":"OBI"},{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["the binding of CsA with cyclophilin can be detected using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin. Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase (Quesniaux et al. 1987)."],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":"http://purl.obolibrary.org/obo/PR_000006256","source":"PR"},"biological_process":{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.625000084750354}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"ELISA","description":"A surrogate measurement of calcineurin activity detecting the binding of cyclosporin A with cyclophilin using anti-cyclophilin antibodies and alkaline phosphatase conjugation.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"binding of CsA with cyclophilin","endpoint_direction":"change","ontology_terms":[{"name":"enzyme-linked immunoadsorbent assay","iri":"http://purl.obolibrary.org/obo/OBI_0000010","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit.","Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase"],"kec_triple":{"biological_object":{"name":"cyclophilin","iri":null,"source":null},"biological_process":{"name":"binding","iri":null,"source":null},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.625000178115442}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"ELISA","description":"Detection of the binding of cyclosporin A with cyclophilin as a surrogate measurement of calcineurin activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"binding of CsA with cyclophilin","endpoint_direction":"change","ontology_terms":[{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0008040","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["as a surrogate measurement of the CN activity, the binding of CsA with cyclophilin can be detected using an ELISA kit.","Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum"],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000011331","source":"PR"},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0008163","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.500000046158675}}},"assay_idx":1}]},{"support":7,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"phosphatase assay","description":"Measures phosphatase activity of calcineurin (CN) in the presence of various inhibitors such as FK506, cyclosporin A, gossypol, or dibefurin.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0016791","source":"GO"},{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000001236","source":"PR"}],"guideline":null,"throughput":"medium","evidence":["Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Phosphatase activity of CN in the presence of cyclosporin A (CsA), gossypol or dibefurin can also be determined in a similar manner (Sieber et al. 2009)."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000001236","source":"PR"},"biological_process":{"name":"dephosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0016311","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.249999866820872}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"phosphatase assay","description":"Measures phosphatase activity of calcineurin (CN) in the presence of various inhibitors such as FK506, cyclosporin A, gossypol, or dibefurin.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0016791","source":"GO"},{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000001236","source":"PR"}],"guideline":null,"throughput":"medium","evidence":["Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Phosphatase activity of CN in the presence of cyclosporin A (CsA), gossypol or dibefurin can also be determined in a similar manner (Sieber et al. 2009)."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000001236","source":"PR"},"biological_process":{"name":"dephosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0016311","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.249999866820872}}},"assay_idx":0},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"phosphatase assay","description":"This assay measures phosphatase activity by incubating CN, calmodulin, FK506, and FKBP together and measuring the activity at various concentrations of FKBP. Kinetic analysis is then conducted to calculate the CN inhibition constant.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0004708","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Phosphatase activity can be measured using a phosphatase assay.","CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":null,"source":null},"biological_process":{"name":"protein phosphorylation","iri":"GO_0006468","source":"GO"},"biological_action":{"name":"inhibited","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.499999523643055}}},"assay_idx":0},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"phosphatase assay","description":"Measures the phosphatase activity of Calcineurin (CN) in the presence of calmodulin and inhibitors like FK506 or cyclosporin A through kinetic analysis.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0004581","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Phosphatase activity can be measured using a phosphatase assay.","CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0004581","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.4375000149011612}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"phosphatase assay","description":"Measures calcineurin phosphatase activity by incubating CN with calmodulin, FK506 and FKBP and quantifying activity at varying FKBP concentrations; kinetic analysis yields the inhibition constant Ki of the FKBP12-FK506 complex.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"change","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Phosphatase activity can be measured using a phosphatase assay.","CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted. (Bram et al. 1993)."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":null,"source":null},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.0}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"phosphatase assay","description":"Measures phosphatase activity of calcineurin (CN) in the presence of various inhibitors (FKBP, cyclosporin A, gossypol, dibefurin) by incubating CN, calmodulin, and the inhibitor, and quantifying the phosphatase activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0016791","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP.","Phosphatase activity of CN in the presence of cyclosporin A (CsA) , gossypol or dibefurin  can also be determined in a similar manner (Sieber et al. 2009)."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000006255","source":"PR"},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0016791","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.640624779451173}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Phosphatase Assay","description":"Measurement of calcineurin phosphatase activity through incubation with calmodulin and FKBP/FK506 complexes to determine inhibition constants.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0008463","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Phosphatase activity can be measured using a phosphatase assay.","CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/GO_0008463","source":"GO"},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0008463","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.37500002841989}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Phosphatase Assay","description":"Measurement of calcineurin phosphatase activity through kinetic analysis of FKBP12 concentration-dependent activity and inhibition constants.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0008163","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Phosphatase activity can be measured using a phosphatase assay.","Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted."],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000011331","source":"PR"},"biological_process":{"name":"phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0008163","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.624999992549419}}},"assay_idx":0}]},{"support":2,"models":["Qwen--Qwen3.6-27B","ibm-granite--granite-4.0-h-small-FP8"],"assay":{"assay_name":"Phosphatase assay","description":"Measures the phosphatase activity of calcineurin (CN) using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"calcineurin phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"calcineurin phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0034061","source":null}],"guideline":null,"throughput":"not_specified","evidence":["Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted.","Phosphatase activity of CN in the presence of cyclosporin A (CsA) , gossypol or dibefurin  can also be determined in a similar manner"],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"calcineurin activity","iri":"http://purl.obolibrary.org/obo/GO_0034061","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.000000253436156}}},"members":[{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Phosphatase assay","description":"Measures the phosphatase activity of calcineurin (CN) using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"calcineurin phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"calcineurin phosphatase activity","iri":"http://purl.obolibrary.org/obo/GO_0034061","source":null}],"guideline":null,"throughput":"not_specified","evidence":["Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted.","Phosphatase activity of CN in the presence of cyclosporin A (CsA) , gossypol or dibefurin  can also be determined in a similar manner"],"kec_triple":{"biological_object":{"name":"calcineurin","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"calcineurin activity","iri":"http://purl.obolibrary.org/obo/GO_0034061","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.000000253436156}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Phosphatase assay","description":"Measures calcineurin (CN) phosphatase activity by incubating the enzyme with calmodulin, FKBP, and various inhibitors, followed by kinetic analysis to determine inhibition constants.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"calcineurin phosphatase activity","endpoint_direction":"decrease","ontology_terms":[{"name":"phosphatase activity","iri":null,"source":"GO"},{"name":"calcineurin activity","iri":null,"source":"GO"}],"guideline":null,"throughput":"low","evidence":["Phosphatase activity can be measured using a phosphatase assay. 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Considered less sensitive than comet assay, but detected damage from 0.25 Gy ionizing radiation (Gradzka and Iwanenko 2005). 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failures."],"kec_triple":{"biological_object":{"name":"chromosome","iri":"http://purl.obolibrary.org/obo/GO_0005694","source":"GO"},"biological_process":{"name":"mitosis","iri":"http://purl.obolibrary.org/obo/GO_0007088","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.624999761582103}}},"assay_idx":9},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"chromosomal aberrations and micronuclei","description":"Chromosomal aberrations and micronuclei assays detect major DNA damage resulting from large breaks and rearrangements, or mitotic failures. 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Damage does not appear until DNA undergoes mitosis, so slower and limited to damage in replicating cells. Insensitive to small deletions and substitutions."],"kec_triple":{"biological_object":{"name":"chromosome","iri":"http://purl.obolibrary.org/obo/GO_0005694","source":"GO"},"biological_process":{"name":"chromosome organization","iri":"http://purl.obolibrary.org/obo/GO_0051251","source":"GO"},"biological_action":{"name":"morphological change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.499999870546162}}},"assay_idx":9}]},{"support":3,"models":["Qwen--Qwen3.6-27B","poolside--Laguna-S-2.1-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"labeled probes for oxidative damage and base excision repair","description":"Uses labeled probes including Biotrin OxyDNA and anti-8-oxoguanine-DNA glycosylase (OGG1) and AP endonuclease (APE1) to detect oxidative damage and base excision repair via microscopy or FACS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"nucleotide damage (oxidative damage and base excision repair)","endpoint_direction":"increase","ontology_terms":[{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006974","source":"GO"},{"name":"oxidative DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},{"name":"base-excision repair","iri":"http://purl.obolibrary.org/obo/GO_0006974","source":"GO"},{"name":"fluorescence microscopy","iri":"http://purl.obolibrary.org/obo/CHMO_0000027","source":"CHMO"},{"name":"flow cytometry","iri":"http://purl.obolibrary.org/obo/CHMO_0000000","source":"CHMO"}],"guideline":null,"throughput":"medium","evidence":["Labeled probes including Biotrin OxyDNA and anti- 8-oxoguanine-DNA glycosylase (OGG1) for oxidative damage and AP endonuclease (APE1) for Base Excision Repair of less bulky lesions such as oxidative damage.","Microscopy, FACS","Most useful with FACS or other measures of average or relative intensity, as locations and numbers of damaged nucleotides can be difficult to distinguish using fluorescence microscopy. (Ogawa, Kobayashi et al. 2003; Nikitaki, Nikolov et al. 2016)."],"kec_triple":{"biological_object":{"name":"DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_16991","source":"CHEBI"},"biological_process":{"name":"oxidative DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.2500001192092896}}},"members":[{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"labeled probes for oxidative damage and base excision repair","description":"Uses labeled probes including Biotrin OxyDNA and anti-8-oxoguanine-DNA glycosylase (OGG1) and AP endonuclease (APE1) to detect oxidative damage and base excision repair via microscopy or FACS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"nucleotide damage (oxidative damage and base excision repair)","endpoint_direction":"increase","ontology_terms":[{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006974","source":"GO"},{"name":"oxidative DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},{"name":"base-excision repair","iri":"http://purl.obolibrary.org/obo/GO_0006974","source":"GO"},{"name":"fluorescence microscopy","iri":"http://purl.obolibrary.org/obo/CHMO_0000027","source":"CHMO"},{"name":"flow cytometry","iri":"http://purl.obolibrary.org/obo/CHMO_0000000","source":"CHMO"}],"guideline":null,"throughput":"medium","evidence":["Labeled probes including Biotrin OxyDNA and anti- 8-oxoguanine-DNA glycosylase (OGG1) for oxidative damage and AP endonuclease (APE1) for Base Excision Repair of less bulky lesions such as oxidative damage.","Microscopy, FACS","Most useful with FACS or other measures of average or relative intensity, as locations and numbers of damaged nucleotides can be difficult to distinguish using fluorescence microscopy. (Ogawa, Kobayashi et al. 2003; Nikitaki, Nikolov et al. 2016)."],"kec_triple":{"biological_object":{"name":"DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_16991","source":"CHEBI"},"biological_process":{"name":"oxidative DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.2500001192092896}}},"assay_idx":1},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Labeled probes for oxidative DNA damage","description":"Uses labeled probes including Biotrin OxyDNA and anti-8-oxoguanine-DNA glycosylase (OGG1) for oxidative damage and AP endonuclease (APE1) for Base Excision Repair, detected by microscopy or FACS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxidative damage and base excision repair activity","endpoint_direction":"increase","ontology_terms":[{"name":"base 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2016)."],"kec_triple":{"biological_object":{"name":"DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_16991","source":"CHEBI"},"biological_process":{"name":"nucleotide-excision repair","iri":"http://purl.obolibrary.org/obo/GO_0006289","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.249999762279913}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"OECD TG 486 (Unscheduled DNA Synthesis)","description":"Measures DNA damage repaired via Nucleotide Excision Repair, primarily bulky adducts, using autoradiography.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"unscheduled DNA synthesis","endpoint_direction":"increase","ontology_terms":[{"name":"DNA repair","iri":"http://purl.obolibrary.org/obo/GO_0006281","source":"GO"},{"name":"nucleotide-excision 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The mitochondrial fractions (0.5 mg protein/ml) were incubated with various concentrations of uranyl acetate for 1 h at 30 °C and then 0.1 ml of mitochondrial fractions was added into 0.1 mol/l of phosphate buffers and 0.04% DTNB in a total volume of 3.0 ml (pH 7.4). The developed yellow color was read at 412 nm on a spectrophotometer (UV-1601 PC, Shimadzu, Japan). GSH content was expressed as µg/mg protein."],"kec_triple":{"biological_object":{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_17478","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.9999999701976776}}},"assay_idx":10},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"DTNB Spectrophotometry","description":"Measurement of mitochondrial GSH content using DTNB as an indicator and spectrophotometry.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"GSH content","endpoint_direction":"decrease","ontology_terms":[{"name":"Glutathione","iri":"null","source":"null"}],"guideline":null,"throughput":"not_specified","evidence":["GSH content was determined using DTNB as the indicator and spectrophotometer method for the isolated mitochondria."],"kec_triple":{"biological_object":{"name":"Glutathione","iri":"null","source":"null"},"biological_process":{"name":"antioxidant capacity","iri":"null","source":"null"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.374999864026904}}},"assay_idx":8}]},{"support":3,"models":["google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"flow cytometry (Dih123)","description":"Detects ROS by the cleavage of nonfluorescent Dih123 into fluorescent R123, combined with propidium iodide for cell viability.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ROS and cell viability","endpoint_direction":"change","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_40342","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["For determination of ROS, samples taken at the indicated time points were directly transferred to FACScan tubes. 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At t 5 9, propidium iodide (10 mM, final concentration) was added, and cells were analyzed by flow cytometry"],"kec_triple":{"biological_object":{"name":"cell","iri":"http://purl.obolibrary.org/obo/CL_0000000","source":"CL"},"biological_process":{"name":"oxidative stress","iri":null,"source":null},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.625000182539225}}},"members":[{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"flow cytometry (Dih123)","description":"Detects ROS by the cleavage of nonfluorescent Dih123 into fluorescent R123, combined with propidium iodide for cell viability.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ROS and cell viability","endpoint_direction":"change","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_40342","source":"CHEBI"}],"guideline":null,"throughput":"medium","evidence":["For determination of ROS, samples taken at the indicated time points were directly transferred to FACScan tubes. 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Nonfluorescent Dih123 is cleaved by ROS to fluorescent R123 and detected by the FL1 detector as described above for Dc (Van de Water 1995)"],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26519","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.250000052154064}}},"assay_idx":12},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Dih123 Flow Cytometry","description":"Detection of ROS by measuring the cleavage of nonfluorescent Dih123 to fluorescent R123.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ROS levels","endpoint_direction":"increase","ontology_terms":[{"name":"Reactive Oxygen Species","iri":"null","source":"null"}],"guideline":null,"throughput":"medium","evidence":["Nonfluorescent Dih123 is cleaved by ROS to fluorescent R123 and detected by the FL1 detector"],"kec_triple":{"biological_object":{"name":"cell","iri":"null","source":"null"},"biological_process":{"name":"oxidative stress","iri":"null","source":"null"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.624999830266461}}},"assay_idx":10}]},{"support":3,"models":["google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"DCFH-DA assay","description":"An indirect fluorescence assay where H2O2 oxidizes DCFH to the fluorescent product DCF.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular ROS production","endpoint_direction":"increase","ontology_terms":[{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16058","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF."],"kec_triple":{"biological_object":{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16058","source":"CHEBI"},"biological_process":{"name":"oxidation","iri":"http://purl.obolibrary.org/obo/GO_0016761","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.875000357654244}}},"members":[{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"DCFH-DA assay","description":"An indirect fluorescence assay where H2O2 oxidizes DCFH to the fluorescent product DCF.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular ROS production","endpoint_direction":"increase","ontology_terms":[{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16058","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF."],"kec_triple":{"biological_object":{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16058","source":"CHEBI"},"biological_process":{"name":"oxidation","iri":"http://purl.obolibrary.org/obo/GO_0016761","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.875000357654244}}},"assay_idx":13},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"H2-DCF-DA assay","description":"Measures intracellular superoxide or hydroxyl radical production via fluorescence of DCF.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"superoxide/hydroxyl production","endpoint_direction":"increase","ontology_terms":[{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_40342","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Assay Detection of superoxide production (Thiebault etal., 2007) This dye is a stable nonpolar compound which diffuses readily into the cells and yields H2-DCF. Intracellular OH or ONOO- react with H2-DCF"],"kec_triple":{"biological_object":{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_40342","source":"CHEBI"},"biological_process":{"name":"oxidation","iri":"http://purl.obolibrary.org/obo/GO_0016761","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.125000009691576}}},"assay_idx":14},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"DCFH-DA Flow Cytometry (Mitochondrial ROS)","description":"Measures mitochondrial ROS generation in isolated kidney mitochondria using DCFH-DA probe and flow cytometry at 488 nm laser with 530 nm bandpass filter.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["kidney"],"species":["rat"],"measured_endpoint":"Mitochondrial reactive oxygen species","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26519","source":"CHEBI"},{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"}],"guideline":null,"throughput":"low","evidence":["The mitochondrial ROS measurement was performed flow cytometry using DCFH-DA. Briefly, isolated kidney mitochondria were incubated with UA (0, 50, 100 and 200 µM) in respiration buffer containing (0.32 mM sucrose, 10mM Tris, 20 mM Mops, 50 µM EGTA, 0.5 mM MgCl2, 0.1 mM KH2PO4 and 5 mM sodium succinate) [32]. In the interval times of 5, 30 and 60 min following the UA addition, a sample was taken and DCFH-DA was added (final concentration, 10 µM) to mitochondria and was then incubated for 10 min. Uranyl acetate-induced ROS generation in isolated kidney mitochondria were determined through the flow cytometry (Partec, Deutschland) equipped with a 488-nm argon ion laser and supplied with the Flomax software and the signals were obtained using a 530-nm bandpass filter (FL-1 channel). Each determination is based on the mean fluorescence intensity of 15,000 counts."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.9999998454004526}}},"assay_idx":9},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"CM-H2DCFDA Flow Cytometry","description":"Detects intracellular reactive oxygen species using CM-H2DCFDA dye which is cleaved by esterases and reacts with intracellular glutathione, detected via flow cytometry.","method_type":"in_vitro","cell_types":["cells"],"organ_tissue":[],"species":["human"],"measured_endpoint":"Reactive oxygen species","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26519","source":"CHEBI"},{"name":"flow cytometry","iri":"http://purl.obolibrary.org/obo/OBI_0000085","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["The dye (CM-H2DCFDA) diffuses into the cell and is leaved by esterases, the thiol reactive chlormethyl group reacts with intracellular glutathione which can be detected using flow cytometry."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26519","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.7500000298023224}}},"assay_idx":15},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"DCFH-DA","description":"Measurement of intracellular ROS using DCFH-DA, which is oxidized to fluorescent DCF by ROS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular ROS","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"}],"guideline":null,"throughput":"high","evidence":["Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF. The probe is hydrolyzed intracellularly to DCFH carboxylate anion. No direct reaction with H2O2 to form fluorescent production."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.687499880894393}}},"assay_idx":4},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"H2-DCF-DA","description":"Measurement of superoxide production using H2-DCF-DA, which is oxidized to fluorescent DCF by superoxide.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"superoxide production","endpoint_direction":"increase","ontology_terms":[{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_17956","source":"CHEBI"}],"guideline":null,"throughput":"high","evidence":["This dye is a stable nonpolar compound which diffuses readily into the cells and yields H2-DCF. 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In the presence of horseradish peroxidase and H2O2, Amplex Red is oxidized to resorufin, a fluorescent molecule measurable by plate reader."],"kec_triple":{"biological_object":{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16145","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.0000000298023224}}},"assay_idx":16},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Amplex Red Assay","description":"Fluorescence analysis to measure extramitochondrial or extracellular H2O2 levels.","method_type":"not_specified","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"extracellular H2O2 levels","endpoint_direction":"increase","ontology_terms":[{"name":"Hydrogen Peroxide","iri":"null","source":"null"}],"guideline":null,"throughput":"not_specified","evidence":["Fluorescence analysis to measure extramitochond mitochondrial or extracellular H2O2 levels. In the presence of horseradish peroxidase and H2O2, Amplex Red is oxidized to resorufin"],"kec_triple":{"biological_object":{"name":"Hydrogen Peroxide","iri":"null","source":"null"},"biological_process":{"name":"oxidative stress","iri":"null","source":"null"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.125000411615474}}},"assay_idx":12}]},{"support":2,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","google--gemma-3-27b-it"],"assay":{"assay_name":"Chemiluminescence","description":"Measures ROS indirectly by detecting chemiluminescence emitted when ROS induce electron transitions in molecules, often amplified using reagents like luminol or lucigenin.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"chemiluminescence intensity","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},{"name":"chemiluminescence","iri":"http://purl.obolibrary.org/obo/OBI_0001938","source":"OBI"}],"guideline":"OECD TG 495","throughput":"not_specified","evidence":["Detection of ROS by chemiluminescence (https://www.sciencedirect.com/science/article/abs/pii/S0165993606001683)","Detection of ROS by chemiluminescence is also described in OECD TG 495 to assess phototoxic potential."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.250000196509063}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Chemiluminescence","description":"Measures ROS indirectly by detecting chemiluminescence emitted when ROS induce electron transitions in molecules, often amplified using reagents like luminol or lucigenin.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"chemiluminescence intensity","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},{"name":"chemiluminescence","iri":"http://purl.obolibrary.org/obo/OBI_0001938","source":"OBI"}],"guideline":"OECD TG 495","throughput":"not_specified","evidence":["Detection of ROS by chemiluminescence (https://www.sciencedirect.com/science/article/abs/pii/S0165993606001683)","Detection of ROS by chemiluminescence is also described in OECD TG 495 to assess phototoxic potential."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.250000196509063}}},"assay_idx":0},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"chemiluminescence","description":"ROS can induce electron transitions in molecules, leading to electronically excited products. 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DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.500000000001819}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Flow Cytometry with DCFH-DA","description":"Measures intracellular ROS production using DCFH-DA, which is oxidized to fluorescent DCF by ROS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DCF fluorescence intensity","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},{"name":"flow cytometry","iri":"http://purl.obolibrary.org/obo/OBI_0000268","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.500000000001819}}},"assay_idx":7},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"H2-DCF-DA Assay","description":"Measures superoxide production using H2-DCF-DA, which is oxidized to fluorescent DCF by intracellular ROS.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DCF fluorescence intensity","endpoint_direction":"increase","ontology_terms":[{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_26930","source":"CHEBI"},{"name":"fluorescence spectroscopy","iri":"http://purl.obolibrary.org/obo/OBI_0001937","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["H2-DCF-DA Assay Detection of superoxide production (Thiebault et al., 2007)","Intracellular OH or ONOO- react with H2-DCF when cells contain peroxides, to form the highly fluorescent compound DCF, which effluxes the cell."],"kec_triple":{"biological_object":{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_26930","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.375000000001819}}},"assay_idx":8},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Mitochondrial ROS Measurement with DCFH-DA","description":"Measures mitochondrial ROS production in isolated mitochondria using DCFH-DA and flow cytometry.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["kidney"],"species":[],"measured_endpoint":"DCF fluorescence intensity","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_26523","source":"CHEBI"},{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"}],"guideline":null,"throughput":"low","evidence":["The mitochondrial ROS measurement was performed flow cytometry using DCFH-DA. Briefly, isolated kidney mitochondria were incubated with UA (0, 50, 100 and 200 µM) in respiration buffer containing (0.32 mM sucrose, 10mM Tris, 20 mM Mops, 50 µM EGTA, 0.5 mM MgCl2, 0.1 mM KH2PO4 and 5 mM sodium succinate) [32]. In the interval times of 5, 30 and 60 min following the UA addition, a sample was taken and DCFH-DA was added (final concentration, 10 µM) to mitochondria and was then incubated for 10 min.Uranyl acetate-induced ROS generation in isolated kidney mitochondria were determined through the flow cytometry (Partec, Deutschland) equipped with a 488-nm argon ion laser and supplied with the Flomax software and the signals were obtained using a 530-nm bandpass filter (FL-1 channel). 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O2.− is reduced to O2 as DHE is oxidized to 2-hydroxyethidium, and this reaction can be measured by fluorescence."],"kec_triple":{"biological_object":{"name":"superoxide","iri":"http://purl.obolibrary.org/obo/CHEBI_33165","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0002919","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.249999810010195}}},"assay_idx":17}]},{"support":1,"models":["poolside--Laguna-S-2.1-NVFP4"],"assay":{"assay_name":"Protein Carbonylation Assay","description":"Detects protein oxidation by measuring carbonylation using ELISA or commercial assay kits as an indicator of oxidative stress levels.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"Protein oxidation (carbonylation)","endpoint_direction":"increase","ontology_terms":[{"name":"protein oxidation","iri":"http://purl.obolibrary.org/obo/GO_0034609","source":"GO"},{"name":"carbonyl group","iri":"http://purl.obolibrary.org/obo/CHEBI_23026","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Can be determined with ELISA or a commercial assay kit. Protein oxidation can indicate the level of oxidative stress."],"kec_triple":{"biological_object":{"name":"protein","iri":"http://purl.obolibrary.org/obo/CHEBI_33333","source":"CHEBI"},"biological_process":{"name":"protein oxidation","iri":"http://purl.obolibrary.org/obo/GO_0034609","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.5000000623986125}}},"members":[{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Protein Carbonylation Assay","description":"Detects protein oxidation by measuring carbonylation using ELISA or commercial assay kits as an indicator of oxidative stress levels.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"Protein oxidation (carbonylation)","endpoint_direction":"increase","ontology_terms":[{"name":"protein oxidation","iri":"http://purl.obolibrary.org/obo/GO_0034609","source":"GO"},{"name":"carbonyl group","iri":"http://purl.obolibrary.org/obo/CHEBI_23026","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Can be determined with ELISA or a commercial assay kit. 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Dih123 (10 mM, final concentration) was added and cells were incubated at 37°C in a humidified atmosphere (95% air/5% CO2) for 10 min. At t 5 9, propidium iodide (10 mM, final concentration) was added, and cells were analyzed by flow cytometry at 60 ml/min. Nonfluorescent Dih123 is cleaved by ROS to fluorescent R123 and detected by the FL1 detector as described above for Dc (Van de Water 1995)"],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.234375}}},"assay_idx":7}]},{"support":1,"models":["radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"mitochondrial ROS measurement","description":"Measurement of mitochondrial ROS using flow cytometry with DCFH-DA.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial ROS","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"}],"guideline":null,"throughput":"high","evidence":["The mitochondrial ROS measurement was performed flow cytometry using DCFH-DA. 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In the interval times of 5, 30 and 60 min following the UA addition, a sample was taken and DCFH-DA was added (final concentration, 10 µM) to mitochondria and was then incubated for 10 min."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.15625011921611}}},"members":[{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"mitochondrial ROS measurement","description":"Measurement of mitochondrial ROS using flow cytometry with DCFH-DA.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial ROS","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"}],"guideline":null,"throughput":"high","evidence":["The mitochondrial ROS measurement was performed flow cytometry using DCFH-DA. 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In the interval times of 5, 30 and 60 min following the UA addition, a sample was taken and DCFH-DA was added (final concentration, 10 µM) to mitochondria and was then incubated for 10 min."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_50801","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0006979","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.15625011921611}}},"assay_idx":9}]},{"support":1,"models":["radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"mitochondrial GSH content assay","description":"Measurement of mitochondrial GSH content using DTNB and spectrophotometry.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial GSH content","endpoint_direction":"decrease","ontology_terms":[{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_16565","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["GSH content was determined using DTNB as the indicator and spectrophotometer method for the isolated mitochondria. 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GSH content was expressed as µg/mg protein."],"kec_triple":{"biological_object":{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_16565","source":"CHEBI"},"biological_process":{"name":"antioxidant activity","iri":"http://purl.obolibrary.org/obo/GO_0016209","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.640624523162955}}},"members":[{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"mitochondrial GSH content assay","description":"Measurement of mitochondrial GSH content using DTNB and spectrophotometry.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial GSH content","endpoint_direction":"decrease","ontology_terms":[{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_16565","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["GSH content was determined using DTNB as the indicator and spectrophotometer method for the isolated mitochondria. The mitochondrial fractions (0.5 mg protein/ml) were incubated with various concentrations of uranyl acetate for 1 h at 30 °C and then 0.1 ml of mitochondrial fractions was added into 0.1 mol/l of phosphate buffers and 0.04% DTNB in a total volume of 3.0 ml (pH 7.4). The developed yellow color was read at 412 nm on a spectrophotometer (UV-1601 PC, Shimadzu, Japan). GSH content was expressed as µg/mg protein."],"kec_triple":{"biological_object":{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_16565","source":"CHEBI"},"biological_process":{"name":"antioxidant activity","iri":"http://purl.obolibrary.org/obo/GO_0016209","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.640624523162955}}},"assay_idx":10}]},{"support":1,"models":["rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Nrf2 qPCR","description":"Quantitative PCR of Nrf2 target genes (e.g., Nqo1, Hmox-1) to measure transcriptional activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mRNA levels of target genes","endpoint_direction":"increase","ontology_terms":[{"name":"gene expression","iri":"GO:0010465","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["qPCR of 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As excess GSSG is rapidly exported from most cells to maintain a constant GSH/GSSG ratio, a reduction of total glutathione (GSH/GSSG) is often a good surrogate measure for oxidative stress."],"kec_triple":{"biological_object":{"name":"glutathione","iri":null,"source":null},"biological_process":{"name":"cellular redox homeostasis","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.250000022351742}}},"assay_idx":8},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"GSH / GSSG determination assay","description":"Determines cellular glutathione (GSH) status and the GSH/GSSG ratio using DTNB (Ellman’s reagent). 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The developed yellow color was read at 412 nm on a spectrophotometer."],"kec_triple":{"biological_object":{"name":"glutathione","iri":null,"source":null},"biological_process":{"name":"cellular redox homeostasis","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.000000225380063}}},"assay_idx":14},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"GSH/GSSG determination assay","description":"Measures cellular glutathione status by determining GSH and GSSG levels biochemically using DTNB (Ellman’s reagent) and reading absorbance at 412 nm.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"GSH/GSSG ratio","endpoint_direction":"decrease","ontology_terms":[{"name":"glutathione metabolic process","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["GSH and GSSG levels are determinted biochemically with DTNB (Ellman’s reagent). 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The developed yellow color was read at 412 nm on a spectrophotometer."],"kec_triple":{"biological_object":{"name":"glutathione","iri":"http://purl.obolibrary.org/obo/CHEBI_15455","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.249999837833457}}},"assay_idx":7},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"GSH / GSSG Determination Assay","description":"Biochemical determination of GSH and GSSG levels using DTNB (Ellman's reagent) to assess cellular redox status.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"GSH/GSSG 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various commercially-available ATP assay kits are offered based on luciferin and luciferase activity."],"kec_triple":{"biological_object":{"name":"mitochondrial ATP synthesis","iri":"http://purl.obolibrary.org/obo/GO_0042773","source":"GO"},"biological_process":{"name":"ATP synthesis","iri":"http://purl.obolibrary.org/obo/GO_0015989","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.203124882777047}}},"assay_idx":3}]},{"support":6,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"mtDNA damage assay (QPCR)","description":"Detects changes in DNA structure and sequence in the mitochondrial genome using quantitative polymerase chain reaction (QPCR)-based 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These data support the idea that mtDNA damage in peripheral tissues in the rotenone model may provide a biomarker of past or ongoing mitochondrial toxin exposure (Sanders et al., 2014a and 2014b)."],"kec_triple":{"biological_object":{"name":"mitochondrial DNA","iri":null,"source":null},"biological_process":{"name":"DNA repair","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.249999802559614}}},"assay_idx":6},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"mtDNA damage assay (QPCR)","description":"Uses quantitative polymerase chain reaction to detect changes in DNA structure and sequence in the mitochondrial genome as a biomarker of dysfunction.","method_type":"in_vivo","cell_types":[],"organ_tissue":["blood","skeletal muscle"],"species":[],"measured_endpoint":"mtDNA damage","endpoint_direction":"increase","ontology_terms":[{"name":"mitochondrial DNA damage","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Various quantitative polymerase chain reaction (QPCR)-based assays have been developed to detect changes of DNA structure and sequence in the mitochondrial genome.","mtDNA damage can be detected in blood after low-level rotenone exposure, and the damage persists even after CI activity has returned to normal."],"kec_triple":{"biological_object":{"name":"mitochondrial DNA","iri":null,"source":null},"biological_process":{"name":"DNA damage response","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.750000000261934}}},"assay_idx":6},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"mtDNA damage","description":"Detection of changes in the mitochondrial genome using quantitative PCR (QPCR)-based assays.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mtDNA damage","endpoint_direction":"increase","ontology_terms":[{"name":"mitochondrial DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_33689","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Various quantitative polymerase chain reaction (QPCR)-based assays have been developed to detect changes of DNA structure and sequence in the mitochondrial genome."],"kec_triple":{"biological_object":{"name":"mitochondrial DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_33689","source":"CHEBI"},"biological_process":{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006302","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.093749880894393}}},"assay_idx":6},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"qPCR mtDNA Damage Assay","description":"Quantitative PCR-based assays to detect changes in the structure and sequence of the mitochondrial genome.","method_type":"in_vitro","cell_types":[],"organ_tissue":["blood","skeletal muscle"],"species":[],"measured_endpoint":"mtDNA damage","endpoint_direction":"increase","ontology_terms":[{"name":"mitochondrial DNA","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Various quantitative polymerase chain reaction (QPCR)-based assays have been developed to detect changes of DNA structure and sequence in the mitochondrial genome."],"kec_triple":{"biological_object":{"name":"mitochondrial DNA","iri":null,"source":null},"biological_process":{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0045893","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.25000000008913}}},"assay_idx":6}]},{"support":6,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"Aequorin-based bioluminescence assay","description":"Measures mitochondrial calcium influx using aequorin as a calcium sensor in conjunction with GFP for bioluminescence resonance energy transfer (BRET).","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial calcium influx","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_29108","source":"CHEBI"},{"name":"mitochondrial calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0070063","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Together with GFP, the aequorin moiety acts as Ca2+ sensor in vivo, which delivers emission energy to the GFP acceptor molecule in a BRET (Bioluminescence Resonance Energy Transfer) process; the Ca2+ can then be visualized with fluorescence microscopy."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0070063","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.375000238418806}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Aequorin-based bioluminescence assay","description":"Measures mitochondrial calcium influx using aequorin as a calcium sensor in conjunction with GFP for bioluminescence resonance energy transfer (BRET).","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial calcium influx","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_29108","source":"CHEBI"},{"name":"mitochondrial calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0070063","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Together with GFP, the aequorin moiety acts as Ca2+ sensor in vivo, which delivers emission energy to the GFP acceptor molecule in a BRET (Bioluminescence Resonance Energy Transfer) process; the Ca2+ can then be visualized with fluorescence microscopy."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0070063","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.375000238418806}}},"assay_idx":21},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"aequorin assay","description":"Increase in mitochondrial Ca2+ influx is measured using aequorin-based bioluminescence assay.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial calcium influx","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_2882","source":"CHEBI"}],"guideline":null,"throughput":"low","evidence":["Increase in mitochondrial Ca2+ influx."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/CL_0000082","source":"CL"},"biological_process":{"name":"calcium signaling","iri":"http://purl.obolibrary.org/obo/GO_0007025","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.000000000101863}}},"assay_idx":9},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Aequorin-based bioluminescence assay","description":"Uses the aequorin moiety and GFP as a Ca2+ sensor to visualize mitochondrial calcium influx via BRET.","method_type":"in_vivo","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial Ca2+ influx","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion influx","iri":"http://purl.obolibrary.org/obo/GO_0055076","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Together with GFP, the aequorin moiety acts as Ca2+ sensor in vivo , which delivers emission energy to the GFP acceptor molecule in a BRET (Bioluminescence Resonance Energy Transfer) process; the Ca2+ can then be visualized with fluorescence microscopy."],"kec_triple":{"biological_object":{"name":"calcium","iri":"http://purl.obolibrary.org/obo/CHEBI_28520","source":"CHEBI"},"biological_process":{"name":"calcium ion transport","iri":"http://purl.obolibrary.org/obo/GO_0006811","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.28125035762804}}},"assay_idx":9},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Aequorin-based bioluminescence assay","description":"Detects increases in mitochondrial Ca2+ influx using aequorin as a Ca2+ sensor in vivo, which delivers emission energy to a GFP acceptor molecule in a BRET (Bioluminescence Resonance Energy Transfer) process. 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the Ca2+ can then be visualized with fluorescence microscopy."],"kec_triple":{"biological_object":{"name":"mitochondria","iri":null,"source":null},"biological_process":{"name":"calcium ion transport","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.125000119230663}}},"assay_idx":9},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Aequorin-based bioluminescence assay","description":"Use of aequorin and GFP as a BRET-based sensor to visualize and measure mitochondrial Ca2+ influx in vivo.","method_type":"in_vivo","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial Ca2+ influx","endpoint_direction":"increase","ontology_terms":[{"name":"calcium ion concentration","iri":"http://purl.obolibrary.org/obo/GO_0008000","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Together with GFP, the aequorin moiety acts as Ca2+ sensor in vivo"],"kec_triple":{"biological_object":{"name":"calcium ion","iri":"http://purl.obolibrary.org/obo/CHEBI_26323","source":"CHEBI"},"biological_process":{"name":"calcium homeostasis","iri":"http://purl.obolibrary.org/obo/GO_0007050","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.609374880790718}}},"assay_idx":4}]},{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","google--gemma-3-27b-it","ibm-granite--granite-4.0-h-small-FP8","poolside--Laguna-S-2.1-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Cellular oxygen consumption","description":"Measures the oxygen consumption rate in cells or isolated mitochondria, often combined with other endpoints to derive specific information on mitochondrial function.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0009060","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/OBI_0000293","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Cellular oxygen consumption.","The oxygen consumption parameter can be combined with other endpoints to derive more specific information on the efficacy of mitochondrial function."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0009060","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.124999985098839}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Cellular oxygen consumption","description":"Measures the oxygen consumption rate in cells or isolated mitochondria, often combined with other endpoints to derive specific information on mitochondrial function.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0009060","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/OBI_0000293","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Cellular oxygen consumption.","The oxygen consumption parameter can be combined with other endpoints to derive more specific information on the efficacy of mitochondrial function."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0009060","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.124999985098839}}},"assay_idx":0},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"oxygen consumption","description":"Measures the oxygen consumption parameter to derive information on the efficacy of mitochondrial function. 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The oxygen consumption parameter can be combined with other endpoints to derive more specific information on the efficacy of mitochondrial function."],"kec_triple":{"biological_object":{"name":"mitochondria","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":null},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0009060","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.874999925494194}}},"assay_idx":0},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Cellular oxygen consumption","description":"Measures cellular oxygen consumption rate (OCR) to assess mitochondrial respiratory function. The ADP-to-O or P/O ratio can be derived to evaluate coupling efficiency of oxidative phosphorylation.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"Oxygen consumption rate (OCR) and ADP/O or P/O ratio","endpoint_direction":"change","ontology_terms":[{"name":"oxygen consumption rate","iri":null,"source":null},{"name":"ADP-to-O ratio","iri":null,"source":null},{"name":"P/O ratio","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["1. Cellular oxygen consumption. See KE1 for details of oxygen consumption assays. The oxygen consumption parameter can be combined with other endpoints to derive more specific information on the efficacy of mitochondrial function. One approach measures the ADP-to-O ratio (the number of ADP molecules phosphorylated per oxygen atom reduced (Hinkle, 1995 and Hafner et al., 1990). The related P/O ratio is calculated from the amount of ADP added, divided by the amount of O2 consumed while phosphorylating the added ADP (Ciapaite et al., 2005; Diepart et al., 2010; Hynes et al., 2006; James et al., 1995; von Heimburg, 2005)."],"kec_triple":{"biological_object":{"name":"mitochondrial respiratory chain","iri":null,"source":null},"biological_process":{"name":"oxidative phosphorylation","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.0}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Oxygen Consumption Assay","description":"Measurement of cellular oxygen consumption, often combined with ADP-to-O or P/O ratios to assess mitochondrial respiratory chain function.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption 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After 100 μl of the stop solution was added to each well; the optical density of each well was determined by the aforementioned microplate spectrophotometer set to 450 nm."],"kec_triple":{"biological_object":{"name":"cytochrome c","iri":null,"source":null},"biological_process":{"name":"apoptosis","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.624999524188752}}},"assay_idx":18},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Quantikine Cytochrome c Immunoassay","description":"Measures cytochrome c release using a rat/mouse-specific monoclonal antibody precoated on a microplate, with HRP-conjugated detection and colorimetric readout at 450 nm.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["rat","mouse"],"measured_endpoint":"Cytochrome c release","endpoint_direction":"increase","ontology_terms":[{"name":"cytochrome-c","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Cytochrome C release was measured a monoclonal antibody specific for rat/mouse cytochrome c was precoated onto the microplate.","After 100 μl of the stop solution was added to each well; the optical density of each well was determined by the aforementioned microplate spectrophotometer set to 450 nm."],"kec_triple":{"biological_object":{"name":"cytochrome c","iri":null,"source":null},"biological_process":{"name":"apoptosis","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.87500035763378}}},"assay_idx":11},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Quantikine Cytochrome c Immunoassay","description":"ELISA-based quantification of cytochrome c release using monoclonal antibodies and HRP-conjugate.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["rat","mouse"],"measured_endpoint":"cytochrome c release","endpoint_direction":"increase","ontology_terms":[{"name":"cytochrome c","iri":"http://purl.obolibrary.org/obo/PR_000001234","source":"PR"}],"guideline":null,"throughput":"not_specified","evidence":["Cytochrome C release was measured a monoclonal antibody specific for rat/mouse cytochrome c was precoated onto the microplate."],"kec_triple":{"biological_object":{"name":"cytochrome c","iri":"http://purl.obolibrary.org/obo/PR_000001234","source":"PR"},"biological_process":{"name":"cytochrome c release","iri":"http://purl.obolibrary.org/obo/GO_0005759","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.156249642372188}}},"assay_idx":6}]},{"support":5,"models":["Qwen--Qwen3.6-27B","google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"TBARS Assay","description":"Quantifies lipid peroxidation by measuring malondialdehyde (MDA) content through its reaction with thiobarbituric acid.","method_type":"in_vitro","cell_types":["kidney cells"],"organ_tissue":["kidney"],"species":[],"measured_endpoint":"MDA content","endpoint_direction":"increase","ontology_terms":[{"name":"lipid peroxidation","iri":"http://purl.obolibrary.org/obo/GO_0006644","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["MDA content, a product of lipid peroxidation, was measured using a thiobarbituric acid reactive substances (TBARS) assay. 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Briefly, the kidney cells were collected in 1 ml PBS buffer solution (pH 7.4) and sonicated."],"kec_triple":{"biological_object":{"name":"membrane lipid","iri":"http://purl.obolibrary.org/obo/CHEBI_16251","source":"CHEBI"},"biological_process":{"name":"lipid peroxidation","iri":"http://purl.obolibrary.org/obo/GO_0006644","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.2578125}}},"assay_idx":8},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"TBARS assay","description":"Quantifies lipid peroxidation by measuring malondialdehyde (MDA) content using a thiobarbituric acid reactive substances (TBARS) assay. 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A number of commercial assay kits are available for this assay using absorbance or fluorescence detection technologies."],"kec_triple":{"biological_object":{"name":"lipid peroxidation products","iri":null,"source":null},"biological_process":{"name":"lipid peroxidation","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.499999881521944}}},"assay_idx":9},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"TBARS assay","description":"Quantifies lipid peroxidation by measuring MDA content using a thiobarbituric acid reactive substances (TBARS) assay. 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MDA reacts with thiobarbituric acid forming a colored product which can be measured at an absorbance of 532 nm."],"kec_triple":{"biological_object":{"name":"lipid peroxidation products","iri":null,"source":null},"biological_process":{"name":"lipid peroxidation","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.124999880923497}}},"assay_idx":15},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"TBARS assay","description":"Quantifies lipid peroxidation by measuring malondialdehyde (MDA) content, which reacts with thiobarbituric acid to form a colored product measured at 532 nm.","method_type":"in_vitro","cell_types":["kidney cells"],"organ_tissue":[],"species":[],"measured_endpoint":"Malondialdehyde (MDA) content","endpoint_direction":"increase","ontology_terms":[{"name":"lipid 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PER is preferred over raw ECAR since it corrects for CO2-derived acidification (Desousa et al., 2023; Espinosa et al., 2022). Application of inhibitors of individual complexes of the respiratory chain allows the detection of ATP-linked OCR: portion of oxygen consumption directly driving ATP synthesis (lost after ATP synthase inhibition) (Yoo et al., 2024). The proton leak & non-mitochondrial OCR represents remaining oxygen consumption after ATP synthase and electron transport chain inhibitor addition. The difference yields the ATP-coupled respiration component."],"kec_triple":{"biological_object":{"name":"ATP synthesis","iri":null,"source":null},"biological_process":{"name":"mitochondrial ATP synthesis","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.500000014901161}}},"assay_idx":4},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Extracellular flux analysis (OCR/ECAR)","description":"Detects mitochondrial respiration via Oxygen Consumption Rate (OCR) and glycolysis via Extracellular Acidification Rate (ECAR) or Proton Efflux Rate (PER) to calculate ATP-coupled respiration.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"OCR, ECAR, PER, ATP production rate","endpoint_direction":"decrease","ontology_terms":[{"name":"cellular respiration","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate) / proton efflux rate (PER)","Application of inhibitors of individual complexes of the respiratory chain allows the detection of ATP-linked OCR"],"kec_triple":{"biological_object":{"name":"mitochondria","iri":null,"source":null},"biological_process":{"name":"oxidative phosphorylation","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.12499976158145}}},"assay_idx":4},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Extracellular Flux Analysis","description":"Detection of oxygen consumption rate (OCR) and proton efflux rate (PER) to assess ATP-linked OCR and mitochondrial ATP production.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial ATP production","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0015982","source":"GO"},{"name":"proton efflux","iri":"http://purl.obolibrary.org/obo/GO_0071943","source":"GO"}],"guideline":null,"throughput":"high","evidence":["The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate) / proton efflux rate (PER): reflects extracellular acidification, a proxy for glycolysis (lactate release) plus contributions from CO₂/HCO₃⁻. PER is preferred over raw ECAR since it corrects for CO₂-derived acidification (Desousa et al., 2023; Espinosa et al., 2022)."],"kec_triple":{"biological_object":{"name":"mitochondrial ATP synthesis","iri":"http://purl.obolibrary.org/obo/GO_0042773","source":"GO"},"biological_process":{"name":"ATP synthesis","iri":"http://purl.obolibrary.org/obo/GO_0015989","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.390625163709046}}},"assay_idx":4}]},{"support":4,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Western blot for cytochrome c release","description":"Measures the redistribution of cytochrome c in cytosolic and mitochondrial cellular fractions using immunoblotting.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"cytochrome c release","endpoint_direction":"increase","ontology_terms":[{"name":"cytochrome c","iri":"http://purl.obolibrary.org/obo/PR_000000034","source":"PR"},{"name":"release of cytochrome c from mitochondria","iri":"http://purl.obolibrary.org/obo/GO_0001836","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Examining the redistribution of Cyto c in cytosolic and mitochondrial cellular fractions. 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This type of side reaction can be strongly enhanced upon mitochondrial damage.","As superoxide may form hydrogen peroxide, hydroxyl radicals or other reactive oxygen species, a large number of direct ROS assays and assays assessing the effects of ROS (indirect ROS assays) are available (Adam-Vizi, 2005; Fan and Li 2014)."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"reactive oxygen species metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0072593","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.124999523162955}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"ROS production assay","description":"Measures the generation of reactive oxygen species (ROS) such as superoxide anions and hydroxyl radicals using direct or indirect assays.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ROS production","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/GO_0000002","source":"GO"},{"name":"superoxide anion","iri":"http://purl.obolibrary.org/obo/CHEBI_26622","source":"CHEBI"}],"guideline":null,"throughput":"high","evidence":["Electrons from the mitochondrial ETS may be transferred ‘erroneously’ to molecular oxygen to form superoxide anions. 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The most widely used chemiluminescent substrate is lucigenin."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"superoxide metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006801","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.749999523162955}}},"assay_idx":15},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Hydrogen peroxide production assay","description":"Measures hydrogen peroxide production using fluorogenic substrates such as diacetyldichloro-fluorescein or Amplex® Red in conjunction with horseradish peroxidase.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"hydrogen peroxide production","endpoint_direction":"increase","ontology_terms":[{"name":"hydrogen peroxide","iri":"http://purl.obolibrary.org/obo/CHEBI_16240","source":"CHEBI"},{"name":"hydrogen peroxide metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0042743","source":"GO"}],"guideline":null,"throughput":"high","evidence":["There are a number of fluorogenic substrates, which serve as hydrogen donors that have been used in conjunction with horseradish peroxidase (HRP) enzyme to produce intensely fluorescent products in the presence of hydrogen peroxide (Zhou et al., 1997: Ruch et al., 1983)."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"hydrogen peroxide metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0042743","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.99999976158145}}},"assay_idx":16},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"ROS assay","description":"Detects the generation of ROS and resultant oxidative stress using direct assays based on chemical modification of fluorescent/luminescent reporters or indirect assays assessing cellular metabolites.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"reactive oxygen species production","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_3823","source":"CHEBI"}],"guideline":null,"throughput":"not_specified","evidence":["Electrons from the mitochondrial ETS may be transferred ‘erroneously’ to molecular oxygen to form superoxide anions."],"kec_triple":{"biological_object":{"name":"reactive oxygen species","iri":"http://purl.obolibrary.org/obo/CHEBI_3823","source":"CHEBI"},"biological_process":{"name":"oxidative stress","iri":"http://purl.obolibrary.org/obo/GO_0009405","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.750000119469405}}},"assay_idx":6},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"ROS detection assay","description":"Measures reactive oxygen species (ROS) production, including superoxide anions, hydrogen peroxide, and hydroxyl radicals, using direct fluorescent/luminescent reporters or indirect assays assessing cellular metabolites like glutathione, malondialdehyde, and isoprostanes.","method_type":"in_vitro","cell_types":["cells"],"organ_tissue":[],"species":[],"measured_endpoint":"Reactive oxygen species (ROS) production","endpoint_direction":"increase","ontology_terms":[{"name":"reactive oxygen species production","iri":null,"source":null},{"name":"superoxide production","iri":null,"source":null},{"name":"hydrogen peroxide production","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["3. 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The best characterized of these probes are Hydro-Cy3 and Hydro-Cy5. generation of superoxide in mitochondria can be visualized using fluorescence microscopy with MitoSOX™ Red reagent (Life Technologies). 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The fluorescence was monitored using Schimadzou RF-5000U fluorescence spectrophotometer at the excitation and emission wavelength of 490 nm and 535 nm, respectively."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial membrane potential maintenance","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.750000000076398}}},"assay_idx":17},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"Rhodamine 123 assay","description":"Measures mitochondrial membrane potential (MMP) and its collapse using mitochondrial uptake of the cationic fluorescent dye rhodamine 123. 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The fluorescence was monitored using Schimadzou RF-5000U fluorescence spectrophotometer at the excitation and emission wavelength of 490 nm and 535 nm, respectively."],"kec_triple":{"biological_object":{"name":"mitochondrial inner membrane","iri":null,"source":null},"biological_process":{"name":"maintenance of mitochondrial membrane potential","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.374999973457307}}},"assay_idx":12},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Rhodamine 123 Assay","description":"Estimation of mitochondrial membrane potential by monitoring the uptake of the cationic fluorescent dye rhodamine 123.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"mitochondrial membrane potential","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0005759","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Mitochondrial uptake of cationic fluorescent dye, rhodamine 123, is used for estimation of mitochondrial membrane potential."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0044294","source":"GO"},"biological_process":{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0005759","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.375000014901161}}},"assay_idx":0}]},{"support":2,"models":["google--gemma-4-26B-A4B-it","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Extracellular flux analysis (OCR/ECAR)","description":"Uses Oxygen Consumption Rate (OCR) and Extracellular Acidification Rate (ECAR) to determine mitochondrial respiration and ATP-linked OCR.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"OCR and ECAR","endpoint_direction":"change","ontology_terms":[{"name":"oxygen consumption rate","iri":"http://purl.obolibrary.org/obo/OBI_0001234","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["Determination of mitochondrial ATP production based on extracellular flux analysis. 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The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate)"],"kec_triple":{"biological_object":{"name":"mitochondria","iri":"http://purl.obolibrary.org/obo/CL_0000001","source":"CL"},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006116","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.124999962281436}}},"assay_idx":4},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Extracellular Flux Analysis (OCR/PER)","description":"Detection of Oxygen Consumption Rate (OCR) and proton efflux rate (PER) to determine ATP-linked respiration and glycolytic activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ATP-linked OCR","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption rate","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate) / proton efflux rate (PER)"],"kec_triple":{"biological_object":{"name":"mitochondria","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"ATP production","iri":"http://purl.obolibrary.org/obo/GO_0006033","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.375000209081918}}},"assay_idx":4}]},{"support":2,"models":["google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4"],"assay":{"assay_name":"Mitochondrial permeability transition pore (PTP) opening assay","description":"Detects PTP opening through the translocation of cytochrome c, adenylate kinase, or AIF, or via calcein fluorescence quenching in permeabilized cells.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"cytochrome c translocation / calcein quenching","endpoint_direction":"increase","ontology_terms":[{"name":"mitochondrial permeability transition pore","iri":"http://purl.obolibrary.org/obo/GO_0031645","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["The opening of the PTP is associated with a permeabilization of mitochondrial membranes, so that different compounds and cellular constituents can change intracellular localization. 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Such assays are used extensively in drug discovery due to their high throughput efficiency, and may serve just as useful for risk assessment purposes."],"kec_triple":{"biological_object":{"name":"aryl hydrocarbon receptor","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"transcription, DNA-templated","iri":"http://purl.obolibrary.org/obo/GO_0006351","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.25000040064333}}},"assay_idx":2},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"stable cell line transactivation","description":"Stable cell lines containing both the nuclear receptor and appropriate reporter vector are used to eliminate variability associated with transfection.","method_type":"in_vitro","cell_types":["human cell line"],"organ_tissue":[],"species":["Homo sapiens"],"measured_endpoint":"reporter gene 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The occupied protein adsorbs onto the filter and the radioactivity is measured to determine saturation binging and/or competitive binding."],"kec_triple":{"biological_object":{"name":"aryl hydrocarbon receptor","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"ligand binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.875000358206307}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Whole cell filtration binding assay","description":"This assay measures the binding of radiolabeled ligands to the AHR in whole cells by incubating cells with the ligand, filtering them, and measuring the retained radioactivity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"ligand binding","endpoint_direction":"increase","ontology_terms":[{"name":"ligand binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},{"name":"aryl hydrocarbon receptor","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},{"name":"whole cell filtration binding assay","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Dold and Greenlee developed a method to detect specific binding of TCDD to whole mammalian cells in culture and was later modified by Farmahin et al. for avian species. 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Formation of NADH from NAD+ can be determined photometrically."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":null,"source":null},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006116","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":-1.2500000298023224}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Forward Electron Transfer","description":"Measures electron flow from NADH through complex I to an electron acceptor (e.g., CoQ10 analogs, ferricyanide, DCIP) by monitoring NADH consumption or acceptor reduction photometrically or fluorometrically in submitochondrial particles or isolated mitochondria, with parallel rotenone treatment to assess rotenone‑inhibitable activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH oxidation rate","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["1. Forward Electron Transfer. Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor. As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically (Lenaz et al. 2004; Spinazzi et al. 2012; Long et al. 2009; Kirby et al. 2007).","To identify the portion of rotenone-inhibitable CI activity, all samples investigated are assayed in parallel following treatment with rotenone."],"kec_triple":{"biological_object":{"name":"NADH","iri":"http://purl.obolibrary.org/obo/CHEBI_14753","source":"CHEBI"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.999999642372188}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Reverse Electron Transfer","description":"Measures NAD+ reduction to NADH via succinate-driven reverse electron flow through complex I, monitored photometrically in submitochondrial particles or intact mitochondria, with ATP present and KCN added to block forward electron transport to complex IV.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH formation rate","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["2. Reverse Electron Transfer. An alternative setup for the direct measurement of CI activity with minimal interference by the activities of complex III and complex IV make use of the observation of a general reversibility of oxidative phosphorylation and electron flow across the mitochondrial respiratory chain (Ernster et al. 1967). With this method, electrons enter the respiratory chain via complex II. Based on the reverse flux, this method allows the complete circumvention of complexes III and IV. As electron donor, succinate is applied, together with NAD+ as electron acceptor. Formation of NADH from NAD+ can be determined photometrically. The succinate-linked NAD+ reduction can be performed either with intact isolated mitochondria or with submitochondrial particles. For the direct assessment of CI activity, submitochondrial particles are used. For assays with intact mitochondria, the succinate-linked reduction of NAD+ is performed in the presence of ATP as energy source. Potassium cyanide (KCN) is added for inhibition of forward electron transport towards complex IV."],"kec_triple":{"biological_object":{"name":"NAD+","iri":"http://purl.obolibrary.org/obo/CHEBI_15854","source":"CHEBI"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.49999976158145}}},"assay_idx":1},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Forward Electron Transfer assay","description":"Measures Complex I enzymatic activity by incubating isolated mitochondria or submitochondrial particles with NADH and an electron acceptor, monitoring NADH consumption or acceptor reduction photometrically or fluorometrically.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH consumption or electron acceptor reduction","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase activity","iri":null,"source":null},{"name":"spectrophotometry","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor. As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically"],"kec_triple":{"biological_object":{"name":"Complex I","iri":null,"source":null},"biological_process":{"name":"electron transport","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.37499976158145}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Reverse Electron Transfer assay","description":"Measures Complex I activity by monitoring the photometric reduction of NAD+ to NADH when electrons are supplied via Complex II using succinate, thereby circumventing Complexes III and IV.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NAD+ reduction to NADH","endpoint_direction":"decrease","ontology_terms":[{"name":"reverse electron transport","iri":null,"source":null},{"name":"photometry","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["With this method, electrons enter the respiratory chain via complex II. Based on the reverse flux, this method allows the complete circumvention of complexes III and IV. As electron donor, succinate is applied, together with NAD+ as electron acceptor. Formation of NADH from NAD+ can be determined photometrically."],"kec_triple":{"biological_object":{"name":"Complex I","iri":null,"source":null},"biological_process":{"name":"electron transport","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.874999761582103}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Forward Electron Transfer","description":"Measures the flow of electrons from NADH through complex I to an electron acceptor, using photometric or fluorometric detection.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"electron flow from NADH to electron acceptor","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase activity","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},{"name":"electron transport","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor.","As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005743","source":"GO"},"biological_process":{"name":"electron transport","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.343749973922968}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Reverse Electron Transfer","description":"Measures the reduction of NAD+ to NADH by succinate, using photometric detection, to assess complex I activity.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NAD+ reduction to NADH","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase activity","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},{"name":"electron transport","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["With this method, electrons enter the respiratory chain via complex II. Based on the reverse flux, this method allows the complete circumvention of complexes III and IV.","As electron donor, succinate is applied, together with NAD+ as electron acceptor. Formation of NADH from NAD+ can be determined photometrically."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005743","source":"GO"},"biological_process":{"name":"electron transport","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.687500089406967}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Forward Electron Transfer Assay","description":"Measures Complex I activity by monitoring the consumption of NADH or the reduction of electron acceptors (e.g., CoQ1, DCIP) photometrically or fluorometrically.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH consumption or electron acceptor reduction","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH-ubiquinone oxidoreductase activity","iri":"http://purl.obolibrary.org/obo/GO_0005506","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor.","As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically"],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":"http://purl.obolibrary.org/obo/GO_0005506","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0016022","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.3750001463340595}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Forward Electron Transfer","description":"Measures Complex I activity by monitoring the flow of electrons from NADH to an acceptor (e.g., CoQ1, DB, ferricyanide, or DCIP) photometrically or fluorometrically.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH consumption or electron acceptor reduction","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH-ubiquinone oxidoreductase activity","iri":"http://purl.obolibrary.org/obo/GO_0005525","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor.","As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically"],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":"http://purl.obolibrary.org/obo/GO_0005525","source":"GO"},"biological_process":{"name":"electron transport chain","iri":"http://purl.obolibrary.org/obo/GO_0009986","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.874999927356839}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"Reverse Electron Transfer","description":"Measures Complex I activity by monitoring the reverse flux of electrons from Complex II to NAD+, resulting in the formation of NADH.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"NADH formation from NAD+","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH-ubiquinone oxidoreductase activity","iri":"http://purl.obolibrary.org/obo/GO_0005525","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["electrons enter the respiratory chain via complex II. Based on the reverse flux, this method allows the complete circumvention of complexes III and IV.","Formation of NADH from NAD+ can be determined photometrically."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":"http://purl.obolibrary.org/obo/GO_0005525","source":"GO"},"biological_process":{"name":"electron transport chain","iri":"http://purl.obolibrary.org/obo/GO_0009986","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.874999913387001}}},"assay_idx":1}]},{"support":6,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-4-26B-A4B-it","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Oxygen consumption assay (Clark electrode)","description":"Measures oxygen consumption as a surrogate for mitochondrial respiratory activity using a Clark electrode.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0034440","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Measurements are traditionally done with a Clark electrode, or with more sophisticated optical methods. At the cathode of a Clark electrode, oxygen is electrolytically reduced, which initiates a current in the electrode, causing a potential difference that is ultimately recorded."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.499999761732397}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Oxygen consumption assay (Clark electrode)","description":"Measures oxygen consumption as a surrogate for mitochondrial respiratory activity using a Clark electrode.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0034440","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Measurements are traditionally done with a Clark electrode, or with more sophisticated optical methods. At the cathode of a Clark electrode, oxygen is electrolytically reduced, which initiates a current in the electrode, causing a potential difference that is ultimately recorded."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.499999761732397}}},"assay_idx":3},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Oxygen consumption assay (optical sensor)","description":"Measures oxygen consumption using optical sensors based on dynamic fluorescence quenching.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0034440","source":"GO"}],"guideline":null,"throughput":"high","evidence":["Optical oxygen sensors work according to the principle of dynamic fluorescence quenching. The response of the respective fluorescence dye is proportional to the amount of oxygen in the sample investigated (Wang and Wolfbeis, 2014).","Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.374999524188752}}},"assay_idx":4},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Oxygen consumption (Clark electrode/Optical sensors)","description":"Measures the rate of oxygen depletion in a closed system using either electrochemical Clark electrodes or optical fluorescence quenching sensors.","method_type":"in_vitro","cell_types":["permeabilized cells","isolated mitochondria"],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen concentration/consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption rate","iri":null,"source":null},{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006116","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["In a closed system, this consumption of oxygen leads to a drop of the overall O2 concentration, and this can serve as parameter for mitochondrial respiratory activity.","Optical oxygen sensors work according to the principle of dynamic fluorescence quenching. The response of the respective fluorescence dye is proportional to the amount of oxygen in the sample investigated"],"kec_triple":{"biological_object":{"name":"mitochondria","iri":"http://purl.obolibrary.org/obo/UBERON_0000199","source":"UBERON"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006116","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":11.90624976162053}}},"assay_idx":3},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Oxygen consumption assay","description":"Measures the oxygen consumption rate (OCR) of cells or isolated mitochondria as an indirect readout of complex I activity, using optical oxygen sensors or extracellular flux analyzers.","method_type":"in_vitro","cell_types":["intact cells","permeabilized cells"],"organ_tissue":["mitochondria"],"species":["not_specified"],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"Oxygen","iri":"http://purl.obolibrary.org/obo/CHMO_0000045","source":null},{"name":"Mitochondrial respiratory chain","iri":"http://purl.obolibrary.org/obo/GO_0070469","source":null},{"name":"Oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0001511","source":null}],"guideline":"not_specified","throughput":"medium","evidence":["In a model of isolated mitochondria in the absence of complex II substrates, oxygen consumption can serve as surrogate readout for the assessment of the degree of CI inhibition.","A modern convenient method to measure oxygen consumption is provided by the Seahorse technology of extracellular flux (XF) analysis, in which cells are kept in a very small volume, so that changes of oxygen levels can be detected very sensitively by an oxygen sensor.","Optical oxygen sensors work according to the principle of dynamic fluorescence quenching. The response of the respective fluorescence dye is proportional to the amount of oxygen in the sample investigated."],"kec_triple":{"biological_object":{"name":"Mitochondria","iri":"http://purl.obolibrary.org/obo/CL_0000155","source":null},"biological_process":{"name":"Oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0001511","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.000000361702405}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Oxygen consumption measurement","description":"Measures mitochondrial oxygen consumption rate (OCR) as a readout of oxidative phosphorylation using Clark electrodes, optical oxygen sensors, or Seahorse XF extracellular flux analysis; OCR declines when complex I is inhibited.","method_type":"not_specified","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate (OCR)","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["Measurements are traditionally done with a Clark electrode, or with more sophisticated optical methods.","A modern convenient method to measure oxygen consumption is provided by the Seahorse technology of extracellular flux (XF) analysis, in which cells are kept in a very small volume, so that changes of oxygen levels can be detected very sensitively by an oxygen sensor.","Optical oxygen sensors operate on the principle of dynamic quenching of luminescence by molecular oxygen. These sensors typically utilize oxygen-sensitive fluorophores or phosphorescent dyes immobilized within an oxygen-permeable matrix. In the absence of oxygen, the fluorophores exhibit a characteristic luminescence—either fluorescence or phosphorescence—with defined intensity and lifetime upon excitation by a specific wavelength of light. When molecular oxygen is present, it acts as a dynamic quencher, reducing the luminescence intensity and/or shortening the emission lifetime through a collisional quenching mechanism governed by the Stern–Volmer relationship. The degree of quenching is quantitatively related to the local oxygen concentration, enabling precise and non-invasive measurements. Unlike electrochemical sensors, optical oxygen sensors do not consume oxygen during detection, making them particularly suitable for applications requiring high spatial and temporal resolution under physiologically relevant conditions. Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.49999976158145}}},"assay_idx":3},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Oxygen consumption assay","description":"Measures mitochondrial respiratory activity by monitoring the drop in O2 concentration using Clark electrodes, optical sensors, or Seahorse extracellular flux analyzers, serving as an indirect surrogate for Complex I inhibition.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"Oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption","iri":null,"source":null},{"name":"Clark electrode","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["In a closed system, this consumption of oxygen leads to a drop of the overall O2 concentration, and this can serve as parameter for mitochondrial respiratory activity. Measurements are traditionally done with a Clark electrode, or with more sophisticated optical methods.","A modern convenient method to measure oxygen consumption is provided by the Seahorse technology of extracellular flux (XF) analysis, in which cells are kept in a very small volume, so that changes of oxygen levels can be detected very sensitively by an oxygen sensor."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":null,"source":null},"biological_process":{"name":"oxidative phosphorylation","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.374999880790718}}},"assay_idx":3},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"Oxygen Consumption Rate (OCR) Assay","description":"Indirectly measures Complex I activity by detecting the decrease in oxygen concentration using Clark electrodes, optical sensors, or Seahorse XF analysis in live cells or isolated mitochondria.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate (OCR)","endpoint_direction":"decrease","ontology_terms":[{"name":"mitochondrial respiratory activity","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["In a closed system, this consumption of oxygen leads to a drop of the overall O2 concentration, and this can serve as parameter for mitochondrial respiratory activity.","Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection."],"kec_triple":{"biological_object":{"name":"mitochondria","iri":"http://purl.obolibrary.org/obo/GO_0009463","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0016022","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":14.06250011920963}}},"assay_idx":3}]},{"support":6,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","google--gemma-3-27b-it","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"Intracellular ATP levels assay","description":"Measures intracellular ATP levels as an indirect readout for mitochondrial function using a luminometric luciferase/luciferin assay.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular ATP levels","endpoint_direction":"decrease","ontology_terms":[{"name":"ATP metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0046034","source":"GO"},{"name":"cellular ATP levels","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["ATP levels can be easily measured from lysates of in vitro cell cultures or from tissues by a luminometric luciferase/luciferin assay. The amount of light emitted is proportional to the amount of ATP in the sample (Nguyen et al. 1988, Leist et al., 1997)."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"ATP synthesis coupled electron transport","iri":"http://purl.obolibrary.org/obo/GO_0042775","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.999999880802534}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Intracellular ATP levels assay","description":"Measures intracellular ATP levels as an indirect readout for mitochondrial function using a luminometric luciferase/luciferin assay.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"intracellular ATP levels","endpoint_direction":"decrease","ontology_terms":[{"name":"ATP metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0046034","source":"GO"},{"name":"cellular ATP levels","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["ATP levels can be easily measured from lysates of in vitro cell cultures or from tissues by a luminometric luciferase/luciferin assay. 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Once the membranes were dry, slots were analyzed and quantified in Odyssey CLx using ImageStudio Odyssey CLx Software."],"kec_triple":{"biological_object":{"name":"topoisomerase-DNA complex","iri":null,"source":null},"biological_process":{"name":"protein-DNA complex assembly","iri":"http://purl.obolibrary.org/obo/GO_0064677","source":"GO"},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.5000000298023224}}},"assay_idx":5},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"In vivo complex enzyme (ICE) assay","description":"A biochemical assay performed on cell lysates to quantify covalent topoisomerase-DNA complexes using CsCl gradient centrifugation followed by slot blotting or western blotting.","method_type":"in_vitro","cell_types":["human embryonic stem cells"],"organ_tissue":[],"species":["Homo sapiens"],"measured_endpoint":"levels of topoisomerase covalently bound to DNA","endpoint_direction":"increase","ontology_terms":[{"name":"protein-DNA complex","iri":null,"source":null},{"name":"topoisomerase-DNA cleavage complex","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["In vivo complex enzyme assay (Rodriguez et al. 2020): hESCs were either immediately lysed in 1 % (w/v) sarkosyl (Sigma L7414). 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Lysates were processed according to the in vivo complex of enzyme (ICE) assay (Nitiss, Soans, Rogojina, Seth, & Mishina, 2012; Schellenberg et al., 2017).","Briefly, sheared samples were centrifuged with a CsCl (Applichem-Panreac, A1098) gradient at 57,000 r.p.m. for 20 h at 25 °C using 3.3 ml 13 x 33 mm polyallomer Optiseal tubes (Beckman Coulter) in a TLN100 rotor (Beckman Coulter)."],"kec_triple":{"biological_object":{"name":"topoisomerase II-DNA complex","iri":null,"source":null},"biological_process":{"name":"DNA topological change","iri":"http://purl.obolibrary.org/obo/GO_0006261","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.484374574327376}}},"assay_idx":4}]},{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","radm--Athene-V2-Chat-AWQ","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm"],"assay":{"assay_name":"Comet assay","description":"This assay measures DNA damage by detecting DNA strand breaks in individual cells.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DNA strand breaks","endpoint_direction":"increase","ontology_terms":[{"name":"DNA strand break","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Comet assay (Li et al 2014, Schroeter et al., 2015, Castano et al 2016)"],"kec_triple":{"biological_object":{"name":"DNA","iri":null,"source":null},"biological_process":{"name":"DNA damage","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.750000226747943}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Comet assay","description":"This assay measures DNA damage by detecting DNA strand breaks in individual cells.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DNA strand breaks","endpoint_direction":"increase","ontology_terms":[{"name":"DNA strand break","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Comet assay (Li et al 2014, Schroeter et al., 2015, Castano et al 2016)"],"kec_triple":{"biological_object":{"name":"DNA","iri":null,"source":null},"biological_process":{"name":"DNA damage","iri":null,"source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.750000226747943}}},"assay_idx":2},{"model":"google--gemma-3-27b-it","assay":{"assay_name":"Comet assay","description":"The Comet assay indirectly detects DNA damage by measuring indicators of DNA damage response.","method_type":"not_specified","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DNA damage","endpoint_direction":"increase","ontology_terms":[{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006260","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["A cleavage can also be indirectly detected by measuring various indicators of DNA damage response, such as ATM activity, p53 expression, γH2AX or Comet assay (Li et al 2014, Schroeter et al., 2015, Castano et al 2016)."],"kec_triple":{"biological_object":{"name":"DNA","iri":"http://purl.obolibrary.org/obo/CHEBI_0001347","source":"CHEBI"},"biological_process":{"name":"DNA damage","iri":"http://purl.obolibrary.org/obo/GO_0006260","source":"GO"},"biological_action":{"name":"pathological","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.50000025978079}}},"assay_idx":2},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Comet assay","description":"An assay used to detect DNA damage by measuring DNA migration in an electric field.","method_type":"not_specified","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"DNA damage","endpoint_direction":"change","ontology_terms":[{"name":"DNA damage","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["A cleavage can also be indirectly detected by measuring various indicators of DNA damage response, such as ... 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Samples were run in 10% SDS-PAGE and transferred to Immobilon-FL Transfer Membranes (Millipore)."],"kec_triple":{"biological_object":{"name":"topoisomerase","iri":null,"source":null},"biological_process":{"name":"protein-DNA interaction","iri":null,"source":null},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.000000466126949}}},"assay_idx":3},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"western blot","description":"An immunoblotting technique used to detect specific topoisomerase proteins covalently associated with DNA in ICE samples.","method_type":"ex_vivo","cell_types":["hESCs"],"organ_tissue":[],"species":["human"],"measured_endpoint":"protein levels","endpoint_direction":"not_specified","ontology_terms":[{"name":"western blot","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["For western blot of ICE, samples were resuspended in 12,000 units of Micrococcal Nuclease (MNase, NEB 0247S), 1 x MNase buffer (NEB, B0247S) and 100 µg / mL BSA (NEB, B9000S), then incubated at 37 °C for 6 h. Samples were run in 10% SDS-PAGE and transferred to Immobilon-FL Transfer Membranes (Millipore)."],"kec_triple":{"biological_object":{"name":"topoisomerase","iri":null,"source":null},"biological_process":{"name":"covalent binding to DNA","iri":null,"source":null},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.8749999664723873}}},"assay_idx":9}]},{"support":2,"models":["google--gemma-3-27b-it","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"slot blotting","description":"Slot blotting is used to transfer ICE samples containing DNA onto membranes for analysis.","method_type":"in_vitro","cell_types":["hESCs"],"organ_tissue":[],"species":["human"],"measured_endpoint":"DNA levels","endpoint_direction":"increase","ontology_terms":[{"name":"DNA quantification","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["For slot blotting, ICE samples containing 1, 2 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reduction","endpoint_direction":"increase","ontology_terms":[{"name":"mitochondrial complex III activity","iri":null,"source":null},{"name":"cytochrome c reduction","iri":"http://purl.obolibrary.org/obo/GO_0045237","source":"GO"},{"name":"spectrophotometric assay","iri":"http://purl.obolibrary.org/obo/OBI_0000217","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["The decylubiquinol/cytochrome c reductase assay is the standard spectrophotometric method to measure the enzymatic activity of mitochondrial complex III (ubiquinol–cytochrome c reductase) (Krähenbühl et. al, 1994).","The reduction of cytochrome c results in a characteristic increase in absorbance at approximately 550 nm, which can be continuously monitored using a spectrophotometer."],"kec_triple":{"biological_object":{"name":"mitochondrial complex III","iri":"http://purl.obolibrary.org/obo/GO_0005750","source":"GO"},"biological_process":{"name":"electron transport 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The principle of the assay is based on the physiological role of complex III, which catalyzes the transfer of electrons from ubiquinol (QH₂) to cytochrome c in the respiratory chain. In the assay, the artificial substrate decylubiquinol (DB), a soluble analog of ubiquinol with a shortened aliphatic side chain, serves as the electron donor (Xia et al., 2013). Decylubiquinol is oxidized by complex III at the Qo site of cytochrome b, and the released electrons are transferred sequentially through the Rieske iron–sulfur protein and cytochrome c₁ subunit to the terminal electron acceptor, cytochrome c. The reduction of cytochrome c results in a characteristic increase in absorbance at approximately 550 nm, which can be continuously monitored using a spectrophotometer. The rate of cytochrome c reduction is directly proportional to the activity of complex III in the sample (Krähenbühl et. al, 1994). To ensure specificity, the assay is performed in the presence and absence of antimycin A, a potent inhibitor of the Qi site of complex III (Bujan et al., 2022). The difference between the total rate and the antimycin-insensitive rate defines the antimycin-sensitive activity, which corresponds to the true activity of complex III. This control is essential, as cytochrome c can also be reduced by other mitochondrial enzymes or non-specific redox reactions."],"kec_triple":{"biological_object":{"name":"cytochrome c","iri":null,"source":null},"biological_process":{"name":"electron transport chain","iri":"http://purl.obolibrary.org/obo/GO_0006118","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.249999676598236}}},"assay_idx":2},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"decylubiquinol/cytochrome c reductase assay","description":"A spectrophotometric assay measuring the enzymatic activity of mitochondrial complex III by monitoring the reduction of cytochrome c using decylubiquinol as an electron donor.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"rate of cytochrome c 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results in a characteristic increase in absorbance at approximately 550 nm","The rate of cytochrome c reduction is directly proportional to the activity of complex III in the sample"],"kec_triple":{"biological_object":{"name":"mitochondrial complex III","iri":"http://purl.obolibrary.org/obo/GO_0005522","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006062","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.750000003259629}}},"assay_idx":0}]},{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","google--gemma-4-26B-A4B-it","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","poolside--Laguna-S-2.1-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"optical oxygen sensor assay","description":"Measures oxygen consumption in cells using fluorescent or phosphorescent dyes that are quenched by oxygen, enabling real-time detection of mitochondrial respiration.","method_type":"in_vitro","cell_types":[],"organ_tissue":["cells"],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"decrease","ontology_terms":[{"name":"oxygen consumption rate","iri":"http://purl.obolibrary.org/obo/GO_0033300","source":"GO"},{"name":"optical oxygen sensor","iri":"http://purl.obolibrary.org/obo/OBI_0000219","source":"OBI"}],"guideline":null,"throughput":"high","evidence":["Optical oxygen sensors operate on the principle of dynamic quenching of luminescence by molecular oxygen.","Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018)."],"kec_triple":{"biological_object":{"name":"mitochondrial respiratory chain","iri":"http://purl.obolibrary.org/obo/GO_0005746","source":"GO"},"biological_process":{"name":"mitochondrial 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operate on the principle of dynamic quenching of luminescence by molecular oxygen.","Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018)."],"kec_triple":{"biological_object":{"name":"mitochondrial respiratory chain","iri":"http://purl.obolibrary.org/obo/GO_0005746","source":"GO"},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.875000001804437}}},"assay_idx":2},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Optical oxygen sensor (fluorescence/phosphorescence quenching)","description":"A method measuring oxygen concentration based on the dynamic quenching of luminescence by molecular oxygen using oxygen-sensitive fluorophores.","method_type":"in_vitro","cell_types":["adherent cells"],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate (OCR)","endpoint_direction":"change","ontology_terms":[{"name":"luminescence quenching","iri":null,"source":null},{"name":"oxygen consumption rate","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["Optical oxygen sensors operate on the principle of dynamic quenching of luminescence by molecular oxygen.","The consumption of oxygen by the cells within this microenvironment results in a measurable decrease in oxygen concentration, which is detected by changes in the fluorescence signal of the sensor.","This real-time, label-free detection enables the calculation of the oxygen consumption rate (OCR), a key parameter reflecting mitochondrial respiratory activity."],"kec_triple":{"biological_object":{"name":"cell","iri":null,"source":null},"biological_process":{"name":"cellular 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These sensors typically utilize oxygen-sensitive fluorophores or phosphorescent dyes immobilized within an oxygen-permeable matrix (Melnikov et al. 2022; Dmitriev et al. 2012). In the absence of oxygen, the fluorophores exhibit a characteristic luminescence—either fluorescence or phosphorescence—with defined intensity and lifetime upon excitation by a specific wavelength of light. When molecular oxygen is present, it acts as a dynamic quencher, reducing the luminescence intensity and/or shortening the emission lifetime through a collisional quenching mechanism governed by the Stern–Volmer relationship. The degree of quenching is quantitatively related to the local oxygen concentration, enabling precise and non-invasive measurements. Unlike electrochemical sensors, optical oxygen sensors do not consume oxygen during detection, making them particularly suitable for applications requiring high spatial and temporal resolution under physiologically relevant conditions. Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018). Optical oxygen sensors are integrated into the bottom of specialized microplates used for real-time measurement of cellular respiration. Fluorescent or phosphorescent oxygen-sensitive dyes are embedded in solid-state sensor patches adhered to each well. During an assay, a transient microchamber is formed above the adherent cells by lowering a sensor cartridge, temporarily isolating a small volume of medium. The consumption of oxygen by the cells within this microenvironment results in a measurable decrease in oxygen concentration, which is detected by changes in the fluorescence signal of the sensor. This real-time, label-free detection enables the calculation of the oxygen consumption rate (OCR), a key parameter reflecting mitochondrial respiratory activity."],"kec_triple":{"biological_object":{"name":"mitochondrion","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.874999523162955}}},"assay_idx":1},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"optical oxygen sensor / extracellular flux analyzer","description":"Real-time measurement of oxygen consumption rate (OCR) using fluorophore-based optical oxygen sensors integrated into microplate bottoms, typically via extracellular flux analyzers such as the Seahorse system. Enables high-content detection of mitochondrial respiration in live cells.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"oxygen consumption rate","endpoint_direction":"change","ontology_terms":[{"name":"respiratory chain complex III","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"},{"name":"oxygen consumption","iri":"http://purl.obolibrary.org/obo/GO_0002095","source":"GO"}],"guideline":null,"throughput":"high","evidence":["Optical oxygen sensors operate on the principle of dynamic quenching of luminescence by molecular oxygen.","Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018).","This real-time, label-free detection enables the calculation of the oxygen consumption rate (OCR), a key parameter reflecting mitochondrial respiratory activity."],"kec_triple":{"biological_object":{"name":"mitochondrial complex 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flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018).","In the 96 well format, a cell density in the range of 30.000-80.000 cells per well (depending on the cell type) is added in a volume of 80 µl and centrifuged (200 g for 1 min) to ensure attachment on the bottom of the plate."],"kec_triple":{"biological_object":{"name":"mitochondrial respiratory chain","iri":"http://purl.obolibrary.org/obo/GO_0005746","source":"GO"},"biological_process":{"name":"mitochondrial respiration","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.875000113621354}}},"assay_idx":3},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"Seahorse XF Extracellular Flux Analysis","description":"A high-content platform using integrated optical oxygen 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In the assay, the artificial substrate decylubiquinol (DB), a soluble analog of ubiquinol with a shortened aliphatic side chain, serves as the electron donor (Xia et al., 2013).","The reduction of cytochrome c results in a characteristic increase in absorbance at approximately 550 nm, which can be continuously monitored using a spectrophotometer. The rate of cytochrome c reduction is directly proportional to the activity of complex III in the sample (Krähenbühl et. al, 1994)."],"kec_triple":{"biological_object":{"name":"mitochondrial complex III","iri":"http://purl.obolibrary.org/obo/GO_0005759","source":null},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006118","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.500000071479008}}},"members":[{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Spectrophotometric complex III activity assay","description":"Measures enzymatic activity of mitochondrial complex III (ubiquinol–cytochrome c reductase) by monitoring the reduction of cytochrome c at 550 nm. 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In the assay, the artificial substrate decylubiquinol (DB), a soluble analog of ubiquinol with a shortened aliphatic side chain, serves as the electron donor (Xia et al., 2013).","The reduction of cytochrome c results in a characteristic increase in absorbance at approximately 550 nm, which can be continuously monitored using a spectrophotometer. The rate of cytochrome c reduction is directly proportional to the activity of complex III in the sample (Krähenbühl et. al, 1994)."],"kec_triple":{"biological_object":{"name":"mitochondrial complex III","iri":"http://purl.obolibrary.org/obo/GO_0005759","source":null},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006118","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.500000071479008}}},"assay_idx":0}]},{"support":1,"models":["ibm-granite--granite-4.0-h-small-FP8"],"assay":{"assay_name":"Oxygen consumption rate (OCR) assay for complex III activity in isolated mitochondria or permeabilized cells","description":"Detects complex III activity by measuring oxygen consumption using a Clark electrode or optical oxygen sensor. 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A second layer of WGA which is conjugated to horseradish peroxidase (HRP) is then added and subsequently incubated with a HRP substrate."],"kec_triple":{"biological_object":{"name":"CHS-1","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0000744","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.5000000596046448}}},"members":[{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"CHS-1 activity assay","description":"Measures the activity of chitin synthase 1 (CHS-1) using crude enzyme preparations from whole organisms. 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A second layer of WGA which is conjugated to horseradish peroxidase (HRP) is then added and subsequently incubated with a HRP substrate."],"kec_triple":{"biological_object":{"name":"CHS-1","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0000744","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.5000000596046448}}},"assay_idx":0},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"CHS-1 activity assay (non-radioactive)","description":"Measures the activity of chitin synthase 1 (CHS-1) using crude enzyme preparations from whole organisms. 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A second layer of WGA which is conjugated to horseradish peroxidase (HRP) is then added and subsequently incubated with a HRP substrate."],"kec_triple":{"biological_object":{"name":"CHS-1","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0000744","source":null},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":10.62499988135096}}},"assay_idx":1}]},{"support":1,"models":["nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4"],"assay":{"assay_name":"14C-UDP-GlcNAc scintillation counting","description":"Measures chitin synthase activity by incorporation of radiolabeled UDP-GlcNAc into chitin polymers, quantified by scintillation counting.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["Anopheles gambiae"],"measured_endpoint":"radioactivity counts (cpm) reflecting chitin synthesis","endpoint_direction":"increase","ontology_terms":[{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006030","source":"GO"},{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"}],"guideline":null,"throughput":"low","evidence":["One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990).","Since the purification or even recombinant production of CHS-1 has not been achieved yet, the most common way is to use crude enzyme preparations for CHS-1 activity assays.","It is noteworthy that in crude enzyme preparations of whole organisms both CHS isoforms, CHS-1 and CHS-2, are present. However, the expression of CHS-1 was shown to be much higher than CHS-2 in Anopheles gambiae (Zhang et al. 2012), therefore the effect of CHS-2 may be regarded as negligible."],"kec_triple":{"biological_object":{"name":"chitin","iri":null,"source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006030","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.999999880790718}}},"members":[{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"14C-UDP-GlcNAc scintillation counting","description":"Measures chitin synthase activity by incorporation of radiolabeled UDP-GlcNAc into chitin polymers, quantified by scintillation counting.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["Anopheles gambiae"],"measured_endpoint":"radioactivity counts (cpm) reflecting chitin synthesis","endpoint_direction":"increase","ontology_terms":[{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006030","source":"GO"},{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"}],"guideline":null,"throughput":"low","evidence":["One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990).","Since the purification or even recombinant production of CHS-1 has not been achieved yet, the most common way is to use crude enzyme preparations for CHS-1 activity assays.","It is noteworthy that in crude enzyme preparations of whole organisms both CHS isoforms, CHS-1 and CHS-2, are present. However, the expression of CHS-1 was shown to be much higher than CHS-2 in Anopheles gambiae (Zhang et al. 2012), therefore the effect of CHS-2 may be regarded as negligible."],"kec_triple":{"biological_object":{"name":"chitin","iri":null,"source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006030","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.999999880790718}}},"assay_idx":0}]},{"support":1,"models":["radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"radioactive chitin synthesis assay","description":"This assay measures the activity of chitin synthase by incubating crude enzyme preparations with radioactively labelled chitin precursors (e.g., 14C-UDP-GlcNAc) and quantifying the radioactivity in the formed chitin chains using scintillation counting.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["http://purl.obolibrary.org/obo/NCBITaxon_7165"],"measured_endpoint":"chitin synthesis","endpoint_direction":"decrease","ontology_terms":[{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006084","source":"GO"}],"guideline":null,"throughput":"low","evidence":["One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990)."],"kec_triple":{"biological_object":{"name":"chitin synthase 1","iri":null,"source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006084","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.5624999403953552}}},"members":[{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"radioactive chitin synthesis assay","description":"This assay measures the activity of chitin synthase by incubating crude enzyme preparations with radioactively labelled chitin precursors (e.g., 14C-UDP-GlcNAc) and quantifying the radioactivity in the formed chitin chains using scintillation counting.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["http://purl.obolibrary.org/obo/NCBITaxon_7165"],"measured_endpoint":"chitin synthesis","endpoint_direction":"decrease","ontology_terms":[{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006084","source":"GO"}],"guideline":null,"throughput":"low","evidence":["One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990)."],"kec_triple":{"biological_object":{"name":"chitin synthase 1","iri":null,"source":null},"biological_process":{"name":"chitin biosynthetic process","iri":"http://purl.obolibrary.org/obo/GO_0006084","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.5624999403953552}}},"assay_idx":0}]}]},{"ke_id":"KE1543","clusters":[{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"Mitochondrial Membrane Potential Assay","description":"Measures mitochondrial membrane potential using fluorescent dyes such as Rhodamine123, TMRE, TMRM, or JC1, where dye accumulation is proportional to membrane potential.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial membrane potential","endpoint_direction":"change","ontology_terms":[{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0036350","source":"GO"},{"name":"mitochondrial membrane","iri":"http://purl.obolibrary.org/obo/GO_0031966","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Mitochondrial Membrane potential using fluorescent dyes. Positive charged molecules will accumulated in the mitochondria in an inverse proportion as the membrane potential. More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. An exception is the dye JC1, because this dye has green fluorescence when present in low concentrations (depolarisation) and red fluorescence when accumulated (hyperpolarized","Perry, 2011, mitochondrial membrane potential probes and proton gradient","Mitra, 2010, analysis of mitochondrial dynamics and functions using imaging approaches"],"kec_triple":{"biological_object":{"name":"mitochondrial membrane","iri":"http://purl.obolibrary.org/obo/GO_0031966","source":"GO"},"biological_process":{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0036350","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.000000153668225}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Mitochondrial Membrane Potential Assay","description":"Measures mitochondrial membrane potential using fluorescent dyes such as Rhodamine123, TMRE, TMRM, or JC1, where dye accumulation is proportional to membrane potential.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"mitochondrial membrane potential","endpoint_direction":"change","ontology_terms":[{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0036350","source":"GO"},{"name":"mitochondrial membrane","iri":"http://purl.obolibrary.org/obo/GO_0031966","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Mitochondrial Membrane potential using fluorescent dyes. Positive charged molecules will accumulated in the mitochondria in an inverse proportion as the membrane potential. More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. An exception is the dye JC1, because this dye has green fluorescence when present in low concentrations (depolarisation) and red fluorescence when accumulated (hyperpolarized","Perry, 2011, mitochondrial membrane potential probes and proton gradient","Mitra, 2010, analysis of mitochondrial dynamics and functions using imaging approaches"],"kec_triple":{"biological_object":{"name":"mitochondrial membrane","iri":"http://purl.obolibrary.org/obo/GO_0031966","source":"GO"},"biological_process":{"name":"mitochondrial membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0036350","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.000000153668225}}},"assay_idx":1},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Mitochondrial Membrane Potential Assay","description":"Assesses mitochondrial membrane potential using fluorescent dyes such as Rhodamine123, TMRE, TMRM, and JC1. 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An exception is the dye JC1, because this dye has green fluorescence when present in low concentrations (depolarisation) and red fluorescence when accumulated (hyperpolarized"],"kec_triple":{"biological_object":{"name":"mitochondrial membrane","iri":"http://purl.obolibrary.org/obo/UBERON_0001276","source":null},"biological_process":{"name":"membrane potential","iri":"http://purl.obolibrary.org/obo/GO_0015992","source":null},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.374999985098839}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Mitochondrial membrane potential assay","description":"Measures mitochondrial membrane potential via uptake of cationic fluorescent dyes (e.g., Rhodamine123, TMRE, TMRM, JC1); fluorescence intensity correlates with membrane polarization.","method_type":"in_vitro","cell_types":[],"organ_tissue":["bovine heart"],"species":["Bos taurus"],"measured_endpoint":"mitochondrial membrane potential (fluorescence intensity of cationic dyes)","endpoint_direction":"change","ontology_terms":[{"name":"membrane potential","iri":null,"source":null},{"name":"fluorescence intensity","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Mitochondrial Membrane potential using fluorescent dyes","Positive charged molecules will accumulated in the mitochondria in an inverse proportion as the membrane potential. 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This has been demonstrated in HEK-293 cells stably transfected with human 5α-reductase type 1, 2, and 3 (Yamana et al., 2010), in CHO cells stably transfected with human 5α-reductase type 1 and 2 (Thigpens et al., 1993), and COS cells transfected with human and rat 5α-reductase with unspecified isoforms (Andersson & Russell, 1990).","The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations.","The use of radiolabeled steroids has historic and continued use for 5α-reductase inhibition examination (Andersson & Russell, 1990; Peng et al., 2020; Thigpens et al., 1993; Yamana et al., 2010); however, alternative methods are available, such as conventional ELISA kits or advanced analytical methods such as liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)."],"kec_triple":{"biological_object":{"name":"5α-reductase","iri":"http://purl.obolibrary.org/obo/GO_0030258","source":null},"biological_process":{"name":"steroid hormone metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0042445","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":9.749999763953383}}},"members":[{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"5α-reductase inhibition assay","description":"Measures the ability of chemicals to inhibit the activity of 5α-reductase enzymes using transfected cell lines or isolated enzymes.","method_type":"in_vitro","cell_types":["HEK-293","CHO","COS"],"organ_tissue":["not specified"],"species":["human","rat"],"measured_endpoint":"dihydrotestosterone (DHT) production","endpoint_direction":"decrease","ontology_terms":[{"name":"5α-reductase","iri":"http://purl.obolibrary.org/obo/GO_0030258","source":null},{"name":"dihydrotestosterone","iri":"http://purl.obolibrary.org/obo/CHEBI_15377","source":null},{"name":"enzyme inhibition","iri":"http://purl.obolibrary.org/obo/GO_0017144","source":null}],"guideline":"not specified","throughput":"not specified","evidence":["Assessing the ability of chemicals to inhibit the activity of 5α-reductase is challenging, but has been assessed using transfected cell lines. 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This has been demonstrated in HEK-293 cells stably transfected with human 5α-reductase type 1, 2, and 3 (Yamana et al., 2010), in CHO cells stably transfected with human 5α-reductase type 1 and 2 (Thigpens et al., 1993), and COS cells transfected with human and rat 5α-reductase with unspecified isoforms (Andersson & Russell, 1990).","The transfected cells are typically used as intact cells or cell homogenates.","The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations."],"kec_triple":{"biological_object":{"name":"5-alpha-reductase","iri":"http://purl.obolibrary.org/obo/GO_0004549","source":"GO"},"biological_process":{"name":"steroid 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allowing for examination of enzyme inhibition","The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations."],"kec_triple":{"biological_object":{"name":"5α-reductase","iri":"http://www.uniprot.org/uniprot/P11254","source":"UniProt"},"biological_process":{"name":"5-alpha-reductase activity","iri":"http://purl.obolibrary.org/obo/GO_0008241","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":19.0625}}},"assay_idx":1}]},{"support":3,"models":["google--gemma-3-27b-it","google--gemma-4-26B-A4B-it","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4"],"assay":{"assay_name":"cell-based assay","description":"This assay assesses 5α-reductase inhibition using transfected cell lines, either as intact cells or cell homogenates. 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GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003].","A concentration of 2.5 μM of colchicine is needed to inhibit microtubule polymerization by 50% [Zavala et al., 1980] and the ability of new chemicals to induce this effect is benchmarked against this value (e.g., combretastatin A-4 IC50 is 1.2 μM [Pettit et al., 1998])."],"kec_triple":{"biological_object":{"name":"microtubule","iri":"http://purl.obolibrary.org/obo/GO_0005882","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0007020","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.0000001043081284}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","assay":{"assay_name":"tubulin polymerization assay","description":"An acellular assay measuring the inhibition of tubulin polymerization by monitoring turbidity development at 350 nm using a spectrophotometer.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"IC50 of tubulin polymerization inhibition","endpoint_direction":"decrease","ontology_terms":[{"name":"microtubule disassembly","iri":"http://purl.obolibrary.org/obo/GO_0042538","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay","turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer","the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50)"],"kec_triple":{"biological_object":{"name":"tubulin","iri":"http://purl.obolibrary.org/obo/GO_0005524","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0042538","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.437499523162955}}},"assay_idx":0},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"tubulin polymerization assay","description":"An acellular assay measuring the turbidity development of tubulin polymerization at 350 nm to determine the inhibitory concentration (IC50) of a test agent.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"IC50 of tubulin polymerization inhibition","endpoint_direction":"decrease","ontology_terms":[{"name":"tubulin polymerization","iri":"http://purl.obolibrary.org/obo/GO_0042551","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay","turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer","the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50)"],"kec_triple":{"biological_object":{"name":"tubulin","iri":"http://purl.obolibrary.org/obo/GO_0005829","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0042551","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.062499761605523}}},"assay_idx":0}]},{"support":4,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","ibm-granite--granite-4.0-h-small-FP8","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"acellular tubulin polymerization assay","description":"Measures microtubule depolymerization by assessing turbidity development at 350 nm in a reaction mixture containing tubulin and a test agent, with GTP added to initiate polymerization.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"tubulin polymerization inhibition","endpoint_direction":"decrease","ontology_terms":[{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0046785","source":"GO"},{"name":"tubulin binding","iri":"http://purl.obolibrary.org/obo/GO_0015631","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010].","A reaction mixture containing tubulin and a test agent, after preincubation, is chilled on ice. GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]."],"kec_triple":{"biological_object":{"name":"microtubule","iri":"http://purl.obolibrary.org/obo/GO_0005874","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0046785","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.000000144354999}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"acellular tubulin polymerization assay","description":"Measures microtubule depolymerization by assessing turbidity development at 350 nm in a reaction mixture containing tubulin and a test agent, with GTP added to initiate polymerization.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"tubulin polymerization inhibition","endpoint_direction":"decrease","ontology_terms":[{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0046785","source":"GO"},{"name":"tubulin binding","iri":"http://purl.obolibrary.org/obo/GO_0015631","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010].","A reaction mixture containing tubulin and a test agent, after preincubation, is chilled on ice. GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]."],"kec_triple":{"biological_object":{"name":"microtubule","iri":"http://purl.obolibrary.org/obo/GO_0005874","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0046785","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.000000144354999}}},"assay_idx":0},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Tubulin polymerization assay","description":"An acellular assay that measures the ability of a test agent to inhibit tubulin polymerization. A reaction mixture containing purified tubulin and the test agent is preincubated, then chilled on ice. GTP is added to initiate polymerization, and turbidity development is monitored at 350 nm in a temperature-controlled spectrophotometer. The area under the curve is used to calculate the IC50, the concentration that inhibits tubulin polymerization by 50%.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"tubulin polymerization","endpoint_direction":"decrease","ontology_terms":[{"name":"tubulin polymerization","iri":"http://purl.obolibrary.org/obo/GO_0015630","source":null}],"guideline":null,"throughput":"low","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010].","A reaction mixture containing tubulin and a test agent, after preincubation, is chilled on ice. GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]."],"kec_triple":{"biological_object":{"name":"tubulin","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0015630","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.749999941559508}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"acellular tubulin polymerization assay","description":"An acellular spectrophotometric assay that quantifies microtubule depolymerization by monitoring turbidity development at 350 nm after GTP addition to a tubulin-test agent mixture, with results expressed as the IC50 for polymerization inhibition.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"tubulin polymerization inhibition (IC50)","endpoint_direction":"decrease","ontology_terms":[{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0007018","source":"GO"},{"name":"turbidity measurement","iri":null,"source":null},{"name":"spectrophotometry","iri":null,"source":null}],"guideline":null,"throughput":"not_specified","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay","GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50)"],"kec_triple":{"biological_object":{"name":"microtubule","iri":"http://purl.obolibrary.org/obo/GO_0005874","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0007018","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":17.875}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"tubulin polymerization assay","description":"This acellular assay measures the extent of tubulin polymerization by monitoring turbidity development at 350 nm in a temperature-controlled recording spectrophotometer after the addition of GTP.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"tubulin polymerization","endpoint_direction":"decrease","ontology_terms":[{"name":"tubulin polymerization","iri":"http://purl.obolibrary.org/obo/GO_0007018","source":"GO"},{"name":"spectrophotometry","iri":"http://purl.obolibrary.org/obo/OBI_0000116","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010].","GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]."],"kec_triple":{"biological_object":{"name":"microtubule","iri":"http://purl.obolibrary.org/obo/GO_0005874","source":"GO"},"biological_process":{"name":"microtubule polymerization","iri":"http://purl.obolibrary.org/obo/GO_0007018","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.656249781299266}}},"assay_idx":0}]},{"support":1,"models":["google--gemma-3-27b-it"],"assay":{"assay_name":"tubulin polymerization assay","description":"This acellular assay measures microtubule depolymerization by monitoring turbidity development at 350 nm following GTP addition to a tubulin and test agent mixture. 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The IC50, representing the concentration inhibiting tubulin polymerization by 50%, is determined.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"turbidity","endpoint_direction":"decrease","ontology_terms":[{"name":"tubulin polymerization","iri":null,"source":null},{"name":"turbidity","iri":"FIX:0000723","source":"FIX"}],"guideline":null,"throughput":"medium","evidence":["Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010].","GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer.","the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]."],"kec_triple":{"biological_object":{"name":"tubulin","iri":"CHEBI:52823","source":"CHEBI"},"biological_process":{"name":"microtubule polymerization","iri":"GO:0001564","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.24999976158145}}},"assay_idx":0}]}]},{"ke_id":"KE845","clusters":[{"support":5,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","Qwen--Qwen3.6-27B","ibm-granite--granite-4.0-h-small-FP8","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"UROD enzyme assay with HPLC","description":"Measures UROD activity by co-incubating uroporphyrinogen with UROD, esterifying the products, and quantifying porphyrin esters using high performance liquid chromatography.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"UROD activity","endpoint_direction":"decrease","ontology_terms":[{"name":"uroporphyrinogen decarboxylase activity","iri":"http://purl.obolibrary.org/obo/GO_0004852","source":"GO"},{"name":"porphyrin ester","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Once uroporphyrinogen is synthesized it is co-incubated with UROD under standardized conditions. The reaction is then stopped, reaction products and un-metabolized substrate are esterified, and the porphyrin esters are separated and quantified using high performance liquid chromatography","This enzyme assay classically utilizes milliliter quantities but has been modified to a microassay, minimizing cost and enhancing sensitivity"],"kec_triple":{"biological_object":{"name":"uroporphyrinogen decarboxylase","iri":"http://purl.obolibrary.org/obo/GO_0004852","source":"GO"},"biological_process":{"name":"porphyrin-containing compound metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0042168","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":2.3749999329447746}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"UROD enzyme assay with HPLC","description":"Measures UROD activity by co-incubating uroporphyrinogen with UROD, esterifying the products, and quantifying porphyrin esters using high performance liquid chromatography.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"UROD activity","endpoint_direction":"decrease","ontology_terms":[{"name":"uroporphyrinogen decarboxylase activity","iri":"http://purl.obolibrary.org/obo/GO_0004852","source":"GO"},{"name":"porphyrin ester","iri":null,"source":null}],"guideline":null,"throughput":"medium","evidence":["Once uroporphyrinogen is synthesized it is co-incubated with UROD under standardized conditions. 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This assay system uses either uroporphyrinogen III or pentacarboxyporphyrinogen I as substrate and liver homogenate in sucrose treated with a suspension of cellulose phosphate as enzyme source."],"kec_triple":{"biological_object":{"name":"uroporphyrinogen decarboxylase","iri":"http://purl.obolibrary.org/obo/GO_0004852","source":"GO"},"biological_process":{"name":"porphyrin-containing compound metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0042168","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.125000024971087}}},"assay_idx":1},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"UROD enzyme assay","description":"An enzyme assay that measures the activity of uroporphyrinogen decarboxylase (UROD) by synthesizing uroporphyrinogen, incubating it with UROD under standardized conditions, stopping the reaction, esterifying reaction products and un-metabolized substrate, and separating and quantifying the porphyrin esters using high performance liquid chromatography (HPLC).","method_type":"in_vitro","cell_types":[],"organ_tissue":["liver"],"species":["not_specified"],"measured_endpoint":"UROD enzyme activity","endpoint_direction":"decrease","ontology_terms":[{"name":"uroporphyrinogen decarboxylase","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},{"name":"porphyrin metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006777","source":null},{"name":"decreased","iri":null,"source":null}],"guideline":"not_specified","throughput":"low","evidence":["The reaction is then stopped, reaction products and un-metabolized substrate are esterified, and the porphyrin esters are separated and quantified using high performance liquid chromatography [7].","This enzyme assay classically utilizes milliliter quantities but has been modified to a microassay, minimizing cost and enhancing sensitivity [9].","Another method based on reverse-phase HPLC was developed [15]. This assay system uses either uroporphyrinogen III or pentacarboxyporphyrinogen I as substrate and liver homogenate in sucrose treated with a suspension of cellulose phosphate as enzyme source."],"kec_triple":{"biological_object":{"name":"uroporphyrinogen decarboxylase","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"porphyrin metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006777","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":5.250000082887709}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"UROD enzyme assay (HPLC quantification)","description":"This assay measures Uroporphyrinogen decarboxylase (UROD) activity by incubating synthesized uroporphyrinogen with UROD, stopping the reaction, esterifying products and unmetabolized substrate, and quantifying porphyrin esters via high performance liquid chromatography.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"UROD enzyme activity (porphyrin ester formation)","endpoint_direction":"change","ontology_terms":[{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Once uroporphyrinogen is synthesized it is co-incubated with UROD under standardized conditions. The reaction is then stopped, reaction products and un-metabolized substrate are esterified, and the porphyrin esters are separated and quantified using high performance liquid chromatography [7]. This enzyme assay classically utilizes milliliter quantities but has been modified to a microassay, minimizing cost and enhancing sensitivity [9]"],"kec_triple":{"biological_object":{"name":"uroporphyrinogen decarboxylase","iri":null,"source":null},"biological_process":{"name":"porphyrin metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006779","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.00000035762804}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Reverse-phase HPLC UROD assay","description":"This assay measures UROD activity using liver homogenate as the enzyme source and either uroporphyrinogen III or pentacarboxyporphyrinogen I as substrate, with product separation and quantification by reverse-phase HPLC.","method_type":"in_vitro","cell_types":[],"organ_tissue":["liver"],"species":[],"measured_endpoint":"UROD enzyme activity (porphyrin ester formation)","endpoint_direction":"change","ontology_terms":[{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/GO_0003824","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Another method based on reverse-phase HPLC was developed [15]. 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(Colorimetric)","description":"A microplate assay measures the enzymatic activity of complex I by quantifying the oxidation of NADH to NAD+ and the reduction of a dye, which increases absorbance at 450 nm. The assay uses capture antibodies specific for complex I subunits and determines activity in isolated mitochondrial extracts.","method_type":"in_vitro","cell_types":[],"organ_tissue":["not_specified"],"species":["human","rat","mouse","bovine"],"measured_endpoint":"complex I enzymatic activity","endpoint_direction":"decrease","ontology_terms":[{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/OBI_0000070","source":null}],"guideline":null,"throughput":"medium","evidence":["The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts (abcam: http://www.abcam.com/complex-i-enzyme-activity-microplate-assay-kit-colorimetric-ab109721). Capture antibodies specific for CI subunits are pre-coated in the microplate wells. Samples are added to the microplate wells which have been pre-coated with a specific capture antibody. After the target has been immobilized in the well, CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm."],"kec_triple":{"biological_object":{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},"biological_process":{"name":"enzyme activity","iri":"http://purl.obolibrary.org/obo/OBI_0000070","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.250000051019015}}},"assay_idx":2},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"Complex I enzyme activity (colorimetric)","description":"Quantifies mitochondrial complex I enzyme activity by capturing CI subunits via antibodies, measuring NADH oxidation linked to dye reduction, and detecting absorbance at 450 nm.","method_type":"in_vitro","cell_types":["human cells","rat cells","mouse cells","bovine cells"],"organ_tissue":[],"species":["human","rat","mouse","bovine"],"measured_endpoint":"CI enzyme activity (NADH oxidation rate)","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},{"name":"mitochondrial NADH:ubiquinone oxidoreductase complex","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["Complex I Enzyme Activity (Colorimetric)","The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts (abcam: http://www.abcam.com/complex-i-enzyme-activity-microplate-assay-kit-colorimetric-ab109721 ).","Capture antibodies specific for CI subunits are pre-coated in the microplate wells. Samples are added to the microplate wells which have been pre-coated with a specific capture antibody. After the target has been immobilized in the well, CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.999999880790718}}},"assay_idx":2},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Complex I Enzyme Activity (Colorimetric)","description":"Quantifies mitochondrial Complex I enzyme activity by measuring the oxidation of NADH to NAD+ and the simultaneous reduction of a dye, which increases absorbance at 450 nm, using capture antibodies to immobilize CI subunits in microplate wells.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["human","rat","mouse","bovine"],"measured_endpoint":"Complex I enzyme activity (NADH oxidation/dye reduction absorbance)","endpoint_direction":"decrease","ontology_terms":[{"name":"enzyme activity assay","iri":null,"source":null},{"name":"colorimetric assay","iri":null,"source":null}],"guideline":null,"throughput":"high","evidence":["The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts","CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm.","By analyzing the enzyme's activity in an isolated context, outside of the cell and free from any other variables, an accurate measurement of the enzyme's functional state can be evaluated."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":null,"source":null},"biological_process":{"name":"electron transport","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.37499976158145}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"Complex I Enzyme Activity (Colorimetric)","description":"Measures the activity of complex I by following the oxidation of NADH to NAD+ and the reduction of a dye, leading to increased absorbance at OD=450 nm, using a microplate assay with capture antibodies specific for CI subunits.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":["human","rat","mouse","bovine"],"measured_endpoint":"complex I activity","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0004096","source":"GO"},{"name":"colorimetric assay","iri":"http://purl.obolibrary.org/obo/OBI_0000879","source":"OBI"}],"guideline":null,"throughput":"medium","evidence":["The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts.","CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"oxidation-reduction process","iri":"http://purl.obolibrary.org/obo/GO_0055114","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.046875011175871}}},"assay_idx":3}]},{"support":4,"models":["BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","poolside--Laguna-S-2.1-NVFP4","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"Quantitative autoradiography","description":"Measures binding of an inhibitor at the rotenone binding site of complex I in tissues using radioactively labeled dihydrorotenone (DHR) and autoradiography.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"binding of [3H]-DHR","endpoint_direction":"not_specified","ontology_terms":[{"name":"complex I binding","iri":null,"source":null},{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000697","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Binding of this rotenone-derivative is detected by autoradiography."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},"biological_process":{"name":"inhibitor binding","iri":"http://purl.obolibrary.org/obo/GO_0042277","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.24999994039535522}}},"members":[{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Quantitative autoradiography","description":"Measures binding of an inhibitor at the rotenone binding site of complex I in tissues using radioactively labeled dihydrorotenone (DHR) and autoradiography.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"binding of [3H]-DHR","endpoint_direction":"not_specified","ontology_terms":[{"name":"complex I binding","iri":null,"source":null},{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000697","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Binding of this rotenone-derivative is detected by autoradiography."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},"biological_process":{"name":"inhibitor binding","iri":"http://purl.obolibrary.org/obo/GO_0042277","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.24999994039535522}}},"assay_idx":0},{"model":"BrainForge--Devstral-2-123B-Instruct-2512-NVFP4","assay":{"assay_name":"Quantitative autoradiography (ex vivo)","description":"Measures binding of an inhibitor at the rotenone binding site of complex I in tissues of living animals using radioactively labeled dihydrorotenone (DHR) and autoradiography.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":[],"measured_endpoint":"binding of [3H]-DHR","endpoint_direction":"not_specified","ontology_terms":[{"name":"complex I binding","iri":null,"source":null},{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000697","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["the in vitro method was further extended for in vivo labeling of CI in the brains of living animals, and detection of binding after preparation of the tissue from such animals."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0008137","source":"GO"},"biological_process":{"name":"inhibitor binding","iri":"http://purl.obolibrary.org/obo/GO_0042277","source":"GO"},"biological_action":{"name":"increased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":12.124999761649633}}},"assay_idx":1},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"autoradiography","description":"Measures binding of inhibitor to the rotenone binding site of mitochondrial complex I by quantifying displacement of [3H]-dihydrorotenone in tissue slices via autoradiography.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"[3H]-DHR binding to complex I","endpoint_direction":"decrease","ontology_terms":[{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},{"name":"mitochondrial NADH:ubiquinone oxidoreductase complex","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Measurement of binding by quantitative autoradiography","To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Most commonly, binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.249999880790718}}},"assay_idx":0},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"autoradiography","description":"Measures binding of inhibitor to complex I in vivo after intraventricular application of [3H]-DHR and subsequent tissue processing, allowing spatial assessment of CI inhibition in brain regions.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"[3H]-DHR binding to complex I","endpoint_direction":"decrease","ontology_terms":[{"name":"protein binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},{"name":"mitochondrial NADH:ubiquinone oxidoreductase complex","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"}],"guideline":null,"throughput":"low","evidence":["b) Ex vivo measurements. As rotenone can pass the blood brain barrier, the in vitro method was further extended for in vivo labeling of CI in the brains of living animals, and detection of binding after preparation of the tissue from such animals.","Animals are exposed to test compounds and [3H]-DHR is applied intraventricularly for 2-6 h before the brain is dissected and arranged for the preparation of tissue slices (Talpade et al. 2000).","In untreated animals, this method allows a precise spatial resolution of the expression pattern of CI. In animals with impaired CI activity, either as a result of CI deficiencies, or upon treatment with CI inhibitors, the assay allows an assessment of the degree of CI inhibition."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005747","source":"GO"},"biological_process":{"name":"mitochondrial electron transport, NADH to ubiquinone","iri":"http://purl.obolibrary.org/obo/GO_0006120","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":16.499999880790718}}},"assay_idx":1},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"quantitative autoradiography","description":"Measures binding of inhibitors at the rotenone binding site of CI in living animals by applying [3H]-DHR intraventricularly after in vivo exposure to test compounds, followed by brain dissection and autoradiographic detection of binding in tissue slices.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":["rat","mouse"],"measured_endpoint":"in vivo binding of [3H]-DHR at the rotenone binding site of CI in brain tissue","endpoint_direction":"change","ontology_terms":[{"name":"autoradiography","iri":"http://www.bioassayontology.org/bao#BAO_0000143","source":"BAO"},{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["b) Ex vivo measurements. As rotenone can pass the blood brain barrier, the in vitro method was further extended for in vivo labeling of CI in the brains of living animals, and detection of binding after preparation of the tissue from such animals.","Animals are exposed to test compounds and [3H]-DHR is applied intraventricularly for 2-6 h before the brain is dissected and arranged for the preparation of tissue slices (Talpade et al. 2000).","In untreated animals, this method allows a precise spatial resolution of the expression pattern of CI.","In animals with impaired CI activity, either as a result of CI deficiencies, or upon treatment with CI inhibitors, the assay allows an assessment of the degree of CI inhibition."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005749","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":8.749999902429408}}},"assay_idx":1},{"model":"rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm","assay":{"assay_name":"quantitative autoradiography","description":"Quantification of the displacement of a radioactively labelled ligand ([3H]-DHR) at the rotenone binding site of Complex I in tissue slices.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["substantia nigra","striatum","brain"],"species":[],"measured_endpoint":"displacement of [3H]-labeled dihydrorotenone (DHR)","endpoint_direction":"change","ontology_terms":[{"name":"radioligand binding assay","iri":"http://purl.obolibrary.org/obo/OBI_0000123","source":"OBI"}],"guideline":null,"throughput":"low","evidence":["the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation","Binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue","Binding of this rotenone-derivative is detected by autoradiography"],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":"http://purl.obolibrary.org/obo/GO_0005524","source":"GO"},"biological_process":{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005634","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.375}}},"assay_idx":0}]},{"support":4,"models":["Qwen--Qwen3.6-27B","ibm-granite--granite-4.0-h-small-FP8","poolside--Laguna-S-2.1-NVFP4","radm--Athene-V2-Chat-AWQ"],"assay":{"assay_name":"Autoradiography","description":"Quantitative autoradiography measures binding of a radioactively labeled ligand ([3H]-dihydrorotenone) to the rotenone binding site of complex I in tissue sections. The assay detects competitive inhibitors that bind to the rotenone site by displacement of the labeled ligand.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":["not_specified"],"measured_endpoint":"binding of inhibitor to complex I rotenone site","endpoint_direction":"decrease","ontology_terms":[{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},{"name":"inhibitor binding","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Binding of this rotenone-derivative is detected by autoradiography. Unselective binding is determined by measurement of [3H]-DHR binding in the presence of an excess of unlabeled rotenone.","The method can be used for (a) in vitro measurements and for (b) ex vivo measurements: a) In vitro measurements. Tissues are embedded in a matrix for cutting by a cryostat. The tissue slices are then mounted onto slides. For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR. Then the tissue slices are washed and prepared for autoradiographic detection (Greenamyre et al. 1992; Higgins and Greenamyre, 1996)."],"kec_triple":{"biological_object":{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},"biological_process":{"name":"inhibitor binding","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.25}}},"members":[{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Autoradiography","description":"Quantitative autoradiography measures binding of a radioactively labeled ligand ([3H]-dihydrorotenone) to the rotenone binding site of complex I in tissue sections. The assay detects competitive inhibitors that bind to the rotenone site by displacement of the labeled ligand.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":["not_specified"],"measured_endpoint":"binding of inhibitor to complex I rotenone site","endpoint_direction":"decrease","ontology_terms":[{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},{"name":"inhibitor binding","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Binding of this rotenone-derivative is detected by autoradiography. Unselective binding is determined by measurement of [3H]-DHR binding in the presence of an excess of unlabeled rotenone.","The method can be used for (a) in vitro measurements and for (b) ex vivo measurements: a) In vitro measurements. Tissues are embedded in a matrix for cutting by a cryostat. The tissue slices are then mounted onto slides. For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR. Then the tissue slices are washed and prepared for autoradiographic detection (Greenamyre et al. 1992; Higgins and Greenamyre, 1996)."],"kec_triple":{"biological_object":{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},"biological_process":{"name":"inhibitor binding","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.25}}},"assay_idx":0},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"Autoradiography (ex vivo)","description":"Ex vivo autoradiography assesses complex I inhibition in vivo by intraventricular application of [3H]-dihydrorotenone after exposure of animals to test compounds. The brains are dissected, tissue slices prepared and binding detected by autoradiography.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":["not_specified"],"measured_endpoint":"binding of inhibitor to complex I rotenone site","endpoint_direction":"decrease","ontology_terms":[{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},{"name":"inhibitor binding","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["As rotenone can pass the blood brain barrier, the in vitro method was further extended for in vivo labeling of CI in the brains of living animals, and detection of binding after preparation of the tissue from such animals. Animals are exposed to test compounds and [3H]-DHR is applied intraventricularly for 2-6 h before the brain is dissected and arranged for the preparation of tissue slices (Talpade et al. 2000)."],"kec_triple":{"biological_object":{"name":"complex I","iri":"http://purl.obolibrary.org/obo/GO_0005751","source":null},"biological_process":{"name":"inhibitor binding","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":7.500000079162419}}},"assay_idx":1},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"quantitative autoradiography","description":"Measures binding of inhibitors at the rotenone binding site of complex I (CI) by quantifying displacement of radioactively labelled [3H]-dihydrorotenone (DHR) using autoradiography, allowing spatial resolution of CI expression and competitive inhibitor binding.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum","brain"],"species":["rat","mouse","human","bovine"],"measured_endpoint":"displacement of [3H]-DHR binding at the rotenone binding site of CI","endpoint_direction":"change","ontology_terms":[{"name":"autoradiography","iri":"http://www.bioassayontology.org/bao#BAO_0000143","source":"BAO"},{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0006091","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Most commonly, binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue.","Binding of this rotenone-derivative is detected by autoradiography.","Unselective binding is determined by measurement of [3H]-DHR binding in the presence of an excess of unlabeled rotenone.","This method allows a spatial resolution of CI expression and the mapping of the binding of a competitive inhibitor on CI.","The method can be used for (a) in vitro measurements and for (b) ex vivo measurements:","a) In vitro measurements. Tissues are embedded in a matrix for cutting by a cryostat. The tissue slices are then mounted onto slides. For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR. Then the tissue slices are washed and prepared for autoradiographic detection (Greenamyre et al. 1992; Higgins and Greenamyre, 1996)."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005749","source":"GO"},"biological_process":{"name":"oxidative phosphorylation","iri":"http://purl.obolibrary.org/obo/GO_0006119","source":"GO"},"biological_action":{"name":"functional change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.7500000298023224}}},"assay_idx":0},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Quantitative autoradiography","description":"Measures the binding of an inhibitor at the rotenone binding site of Complex I by quantifying the displacement of a radioactively labeled ligand ([3H]-DHR) in tissue slices, detected via autoradiography.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["substantia nigra","striatum","brain"],"species":[],"measured_endpoint":"displacement of [3H]-DHR binding at Complex I rotenone site","endpoint_direction":"decrease","ontology_terms":[{"name":"binding assay","iri":null,"source":null},{"name":"autoradiography","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Most commonly, binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue. Binding of this rotenone-derivative is detected by autoradiography.","The method can be used for (a) in vitro measurements and for (b) ex vivo measurements"],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":null,"source":null},"biological_process":{"name":"ligand binding","iri":null,"source":null},"biological_action":{"name":"occurrence","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.00000035763378}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"quantitative autoradiography","description":"Measures the displacement of [3H]-labeled dihydrorotenone (DHR) by the test compound to assess binding at the rotenone binding site of complex I in tissues.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"binding of CI inhibitor","endpoint_direction":"decrease","ontology_terms":[{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000622","source":"OBI"},{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0004096","source":"GO"},{"name":"rotenone binding site","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","This method allows a spatial resolution of CI expression and the mapping of the binding of a competitive inhibitor on CI."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.187500212341547}}},"assay_idx":0},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"quantitative autoradiography (in vitro)","description":"Measures the displacement of [3H]-labeled dihydrorotenone (DHR) by the test compound in tissue slices mounted on slides to assess binding at the rotenone binding site of complex I.","method_type":"in_vitro","cell_types":[],"organ_tissue":["substantia nigra","striatum"],"species":[],"measured_endpoint":"binding of CI inhibitor","endpoint_direction":"decrease","ontology_terms":[{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000622","source":"OBI"},{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0004096","source":"GO"},{"name":"rotenone binding site","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["Tissues are embedded in a matrix for cutting by a cryostat. The tissue slices are then mounted onto slides. For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.546874880790718}}},"assay_idx":1},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"quantitative autoradiography (ex vivo)","description":"Measures the displacement of [3H]-labeled dihydrorotenone (DHR) by the test compound in brain tissue slices from animals exposed to the test compound and [3H]-DHR intraventricularly to assess binding at the rotenone binding site of complex I.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["brain"],"species":[],"measured_endpoint":"binding of CI inhibitor","endpoint_direction":"decrease","ontology_terms":[{"name":"autoradiography","iri":"http://purl.obolibrary.org/obo/OBI_0000622","source":"OBI"},{"name":"NADH dehydrogenase (ubiquinone) activity","iri":"http://purl.obolibrary.org/obo/GO_0004096","source":"GO"},{"name":"rotenone binding site","iri":null,"source":null}],"guideline":null,"throughput":"low","evidence":["As rotenone can pass the blood brain barrier, the in vitro method was further extended for in vivo labeling of CI in the brains of living animals, and detection of binding after preparation of the tissue from such animals."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase (complex I)","iri":"http://purl.obolibrary.org/obo/GO_0005739","source":"GO"},"biological_process":{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.593749880790718}}},"assay_idx":2}]},{"support":3,"models":["google--gemma-3-27b-it","rdtand--Gemma4-31B-IT-PrismaQuant-5.5bit-vllm","rdtand--Gemma4-31B-IT-PrismaQuant-6bit-vllm"],"assay":{"assay_name":"Complex I Enzyme Activity (Colorimetric)","description":"This assay measures Complex I enzyme activity using a microplate assay kit. It quantifies the oxidation of NADH to NAD+ and the simultaneous reduction of a dye, resulting in increased absorbance at OD=450 nm.","method_type":"in_vitro","cell_types":["human","rat","mouse","bovine"],"organ_tissue":["tissue","cell"],"species":[],"measured_endpoint":"enzyme activity (oxidation of NADH)","endpoint_direction":"decrease","ontology_terms":[{"name":"NADH dehydrogenase activity","iri":"GO:0004545","source":"GO"},{"name":"enzyme activity","iri":"GO:0004395","source":"GO"}],"guideline":null,"throughput":"medium","evidence":["The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts (abcam: http://www.abcam.com/complex-i-enzyme-activity-microplate-assay-kit-colorimetric-ab109721 ).","After the target has been immobilized in the well, CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":null,"source":null},"biological_process":{"name":"electron transport chain","iri":"GO:0006757","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":13.999999523163865}}},"members":[{"model":"google--gemma-3-27b-it","assay":{"assay_name":"Complex I Enzyme Activity (Colorimetric)","description":"This assay measures Complex I enzyme activity using a microplate assay kit. 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For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR.","Then the tissue slices are washed and prepared for autoradiographic detection (Greenamyre et al. 1992; Higgins and Greenamyre, 1996)."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":null,"source":null},"biological_process":{"name":"ligand binding","iri":"GO:0005102","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.4999999701976776}}},"assay_idx":1},{"model":"google--gemma-4-26B-A4B-it","assay":{"assay_name":"quantitative autoradiography","description":"Measures the displacement of a radioactively labeled ligand ([3H]-DHR) from the rotenone binding site of Complex I in tissue slices to assess inhibitor binding.","method_type":"ex_vivo","cell_types":[],"organ_tissue":["substantia nigra","striatum","brain"],"species":[],"measured_endpoint":"displacement of a radioactively labelled ligand","endpoint_direction":"decrease","ontology_terms":[{"name":"binding","iri":"http://purl.obolibrary.org/obo/OBI_0000076","source":"OBI"},{"name":"ligand binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation.","Most commonly, binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue. Binding of this rotenone-derivative is detected by autoradiography."],"kec_triple":{"biological_object":{"name":"NADH-ubiquinone oxidoreductase","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":"PR"},"biological_process":{"name":"ligand binding","iri":"http://purl.obolibrary.org/obo/GO_0005515","source":"GO"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":4.843749764375389}}},"assay_idx":0}]},{"support":2,"models":["google--gemma-4-26B-A4B-it","poolside--Laguna-S-2.1-NVFP4"],"assay":{"assay_name":"colorimetric Complex I Enzyme Activity Assay","description":"Quantifies Complex I activity by measuring the oxidation of NADH to NAD+ coupled with the reduction of a dye, resulting in increased absorbance at OD=450 nm using capture antibodies.","method_type":"in_vitro","cell_types":["human 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They inlude, for example, sphingomyelin (SM) and glycosphingolipids such as gangliosides (GM), and are essential constituents or eukaryotic membranes (Kolter and Sandhoff, 2006).","Considering their biologically relevant role as components of the cell membrane and thus basal functioning of cells, a decrease in sphingolipids may result in a variety of adverse effecfts.","sphingolipids have been assigned a role in the pathogenesis of various metabolic diseases (sphingolipidoses), myocardial infarction, hypertension and diabetis mellitus (Borodzicz et al., 2015; Kolter and Sandhoff, 2006)."],"kec_triple":{"biological_object":{"name":"sphingolipid","iri":"http://purl.obolibrary.org/obo/CHEBI_60956","source":null},"biological_process":{"name":"sphingolipid metabolic process","iri":"http://purl.obolibrary.org/obo/GO_0006665","source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"description","logprobs":{"endpoint_direction":{"margin":13.250000119210881}}},"assay_idx":0},{"model":"poolside--Laguna-S-2.1-NVFP4","assay":{"assay_name":"sphingolipid quantification","description":"A biochemical assay measuring the levels of complex sphingolipids, such as sphingomyelin and glycosphingolipids, in biological samples to assess changes in their abundance.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"complex sphingolipid levels","endpoint_direction":"decrease","ontology_terms":[{"name":"sphingomyelin","iri":"http://purl.obolibrary.org/obo/CHEBI_17336","source":"CHEBI"},{"name":"glycosphingolipid","iri":"http://purl.obolibrary.org/obo/CHEBI_17087","source":"CHEBI"},{"name":"ceramide","iri":"http://purl.obolibrary.org/obo/CHEBI_16336","source":"CHEBI"},{"name":"membrane","iri":"http://purl.obolibrary.org/obo/GO_0016020","source":"GO"}],"guideline":null,"throughput":"not_specified","evidence":["Complex sphingolipids are derived from ceramide and have a rather large structural diversity. 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For example, sphinoglipids have been assigned a role in the pathogenesis of various metabolic diseases (sphingolipidoses), myocardial infarction, hypertension and diabetis mellitus"],"kec_triple":{"biological_object":{"name":"sphingolipid","iri":"http://purl.obolibrary.org/obo/CHEBI_18058","source":"CHEBI"},"biological_process":{"name":"cell membrane organization","iri":"http://purl.obolibrary.org/obo/GO_0006896","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"description","logprobs":{"endpoint_direction":{"margin":12.484374761589606}}},"assay_idx":0}]},{"support":1,"models":["google--gemma-3-27b-it"],"assay":{"assay_name":"lipidomics","description":"This assay measures complex sphingolipids, including sphingomyelin (SM) and gangliosides (GM), which are essential constituents of eukaryotic membranes. 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It can be measured by use of the water-soluble dye 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) in the presence of the intermediate electron carrier phenazine methosulfate (PMS), to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction."],"kec_triple":{"biological_object":{"name":"succinate dehydrogenase","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"succinate dehydrogenase activity","iri":null,"source":null},"biological_action":{"name":"inhibited","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.25}}},"assay_idx":0},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"SDH inhibition assay","description":"Determines the inhibitory strength of a putative SDH inhibitor by measuring the alteration in the rate of colour change of an electron acceptor in the presence of succinate as substrate.","method_type":"in_vitro","cell_types":[],"organ_tissue":["isolated mitochondria"],"species":[],"measured_endpoint":"SDH inhibition","endpoint_direction":"decrease","ontology_terms":[{"name":"succinate dehydrogenase inhibition","iri":null,"source":null},{"name":"oxidation-reduction process","iri":"http://purl.obolibrary.org/obo/GO_0055114","source":null}],"guideline":null,"throughput":"not_specified","evidence":["Alteration in rate of colour change in the presence of a putative inhibitor determining the strength of that inhibition."],"kec_triple":{"biological_object":{"name":"succinate dehydrogenase","iri":"http://purl.obolibrary.org/obo/PR_000000001","source":null},"biological_process":{"name":"succinate dehydrogenase activity","iri":null,"source":null},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":3.999999962747097}}},"assay_idx":3},{"model":"nvidia--NVIDIA-Nemotron-3-Super-120B-A12B-NVFP4","assay":{"assay_name":"MTT-based SDH activity assay","description":"Measures succinate dehydrogenase (SDH) activity by monitoring the reduction of MTT to formazan, which produces a colorimetric change, using succinate as substrate and phenazine methosulfate as an intermediate electron carrier.","method_type":"in_vitro","cell_types":[],"organ_tissue":["mitochondria"],"species":[],"measured_endpoint":"SDH activity","endpoint_direction":"decrease","ontology_terms":[{"name":"succinate dehydrogenase activity","iri":"http://purl.obolibrary.org/obo/GO_0008038","source":"GO"}],"guideline":null,"throughput":"low","evidence":["Succinate dehydrogenase activity is generally measured by the spectrophotometric detection of colour change in the presence of an electron acceptor, with succinate (succinic acid) as substrate.","SDH activity Succinate dehydrogenase (SDH) activity corresponds to reaction (1), above. 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It can be measured by reduction of 2,6-dichlorophenolindophenol (DCPIP) in the presence of the 2,3-dimethoxy-6-methyl-1,4-benzoquinone (UQ2), which accepts electrons from the ubiquinone reduction site and transfers them to DCPIP, thus being a measure of the rate of the entire reaction catalysed by complex II."],"kec_triple":{"biological_object":{"name":"succinate dehydrogenase","iri":null,"source":null},"biological_process":{"name":"tricarboxylic acid cycle","iri":"http://purl.obolibrary.org/obo/GO_0006099","source":"GO"},"biological_action":{"name":"decreased","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":15.999999880790718}}},"assay_idx":1}]},{"support":2,"models":["google--gemma-3-27b-it","ibm-granite--granite-4.0-h-small-FP8"],"assay":{"assay_name":"MTT assay","description":"SDH activity can be measured by use of the water-soluble dye MTT in the presence of the intermediate electron carrier PMS, to intercept electrons 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When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced."],"kec_triple":{"biological_object":{"name":"transthyretin","iri":"http://purl.obolibrary.org/obo/PR_0000041010","source":"null"},"biological_process":{"name":"thyroid hormone binding","iri":"http://purl.obolibrary.org/obo/GO_0006636","source":"null"},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":6.937500034109689}}},"assay_idx":6},{"model":"ibm-granite--granite-4.0-h-small-FP8","assay":{"assay_name":"fluorescence displacement assay (FLU-TTR)","description":"The fluorescence displacement assay (FLU-TTR) uses a protein-binding fluorescent probe (ANSA) that becomes highly fluorescent after binding to T4. 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This allows generation of binding constant (K) data as opposed to past efforts that generated IC50 values."],"kec_triple":{"biological_object":{"name":"transthyretin","iri":"http://purl.obolibrary.org/obo/CL_0000163","source":null},"biological_process":{"name":"binding","iri":"http://purl.obolibrary.org/obo/GO_0005488","source":null},"biological_action":{"name":"change","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":1.7500000447034836}}},"assay_idx":2},{"model":"Qwen--Qwen3.6-27B","assay":{"assay_name":"Fluorescence displacement assay (FLU-TTR)","description":"Uses a fluorescent probe (ANSA) that fluoresces upon binding to T4; introduction of a displacing compound reduces fluorescence, enabling quantification of binding constants in a microtiter format.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"fluorescence intensity / binding constant","endpoint_direction":"decrease","ontology_terms":[{"name":"fluorescence assay","iri":"http://purl.obolibrary.org/obo/OBI_0000377","source":"OBI"}],"guideline":null,"throughput":"high","evidence":["Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced.","Cao et al 2011 developed a fluorescent microtiter method for pTTR and TBG tested with bisphenol A.","Montano et al 2012 developed a competitive T4-TTR fluorescence displacement assay in a 96-well format, modified from the original method (Nilsson and Petersen 1975) and using a new selective method to extract hydroxylated metabolites while reducing fatty acid interference (modified from Hovander et al 2000)."],"kec_triple":{"biological_object":{"name":"thyroxine","iri":null,"source":null},"biological_process":{"name":"thyroid hormone 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The high-throughput screening mode is capable of detecting T4 in water at the part-per-trillion level and in the part-per-billion level in urine."],"kec_triple":{"biological_object":{"name":"transthyretin","iri":null,"source":null},"biological_process":{"name":"thyroid hormone transport","iri":null,"source":null},"biological_action":{"name":"disrupted","iri":null,"source":null}},"source_field":"measurement_methodology","logprobs":{"endpoint_direction":{"margin":0.375}}},"assay_idx":6},{"model":"radm--Athene-V2-Chat-AWQ","assay":{"assay_name":"LC-MS/MS competitive binding","description":"Measures the displacement of T4 from TTR using a competitive binding assay with immunomagnetic beads, flow cytometry, and UPLC-MS, capable of high-throughput screening for T4 in water and urine.","method_type":"in_vitro","cell_types":[],"organ_tissue":[],"species":[],"measured_endpoint":"displacement of T4 from TTR","endpoint_direction":"increase","ontology_terms":[{"name":"thyroxine","iri":"http://purl.obolibrary.org/obo/CHEBI_16508","source":"CHEBI"},{"name":"transthyretin","iri":"http://purl.obolibrary.org/obo/PR_000006752","source":"PR"}],"guideline":null,"throughput":"high","evidence":["Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. 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