{ "version": "1.0", "created_at": "2026-04-26", "description": "Gene Family RAG System Evaluation Test Set", "categories": { "gene_identification": { "name": "基因识别与家族成员查询", "description": "测试RAG系统识别基因家族成员的能力", "weight": 0.25, "questions": [ { "id": "GI-001", "question": "拟南芥中SUT基因家族有哪些成员？", "expected_answer": "拟南芥中SUT基因家族包含5个成员：AtSUC1 (AT1G22710), AtSUC2 (AT1G22720), AtSUC3 (AT2G02860), AtSUC4 (AT1G09960), AtSUC5 (AT1G71890)", "key_entities": ["AtSUC1", "AtSUC2", "AtSUC3", "AtSUC4", "AtSUC5"], "key_ids": ["AT1G22710", "AT1G22720", "AT2G02860", "AT1G09960", "AT1G71890"], "difficulty": "easy", "requires_citation": true }, { "id": "GI-002", "question": "水稻中P450基因家族有多少个成员？", "expected_answer": "水稻中P450基因家族包含约300-350个成员，具体数量因注释版本而异", "key_entities": ["P450", "CYP"], "key_facts": ["300-350 members", "rice", "CYP genes"], "difficulty": "medium", "requires_citation": true }, { "id": "GI-003", "question": "苦荞中SPL基因家族包含多少个成员？", "expected_answer": "苦荞(Fagopyrum tataricum)中SPL基因家族包含24个成员", "key_entities": ["FtSPL", "SPL", "Fagopyrum tataricum"], "key_facts": ["24 members", "tartary buckwheat"], "difficulty": "easy", "requires_citation": true, "pmid_reference": "31286919" }, { "id": "GI-004", "question": "番茄中NF-Y基因家族有哪些亚家族？", "expected_answer": "番茄中NF-Y基因家族包含三个亚家族：NF-YA, NF-YB, NF-YC", "key_entities": ["NF-YA", "NF-YB", "NF-YC", "Solanum lycopersicum"], "difficulty": "medium", "requires_citation": true }, { "id": "GI-005", "question": "拟南芥中WRKY基因家族成员数量及分类", "expected_answer": "拟南芥中WRKY基因家族包含74个成员，分为三个亚家族：Group I (约13个), Group II (约48个), Group III (约13个)", "key_entities": ["WRKY", "Group I", "Group II", "Group III"], "key_facts": ["74 members", "Arabidopsis"], "difficulty": "medium", "requires_citation": true } ] }, "functional_annotation": { "name": "功能注释与通路分析", "description": "测试RAG系统对基因功能、通路和调控关系的理解", "weight": 0.25, "questions": [ { "id": "FA-001", "question": "SUT基因的主要功能是什么？", "expected_answer": "SUT基因编码蔗糖转运蛋白(Sucrose Transporter)，主要负责植物体内蔗糖的跨膜运输，参与源库关系建立、果实发育、种子填充等过程", "key_concepts": ["sucrose transport", "source-sink relationship", "membrane transport"], "go_terms": ["GO:0015782", "GO:0006858"], "difficulty": "easy", "requires_citation": true }, { "id": "FA-002", "question": "P450基因在植物次生代谢中的作用", "expected_answer": "P450基因编码细胞色素P450单加氧酶，在植物次生代谢中参与多种反应：苯丙烷类合成、生物碱合成、萜类合成、激素代谢(如赤霉素、油菜素内酯)等", "key_pathways": ["phenylpropanoid", "alkaloid", "terpenoid", "hormone metabolism"], "difficulty": "medium", "requires_citation": true }, { "id": "FA-003", "question": "SPL转录因子如何调控植物开花时间？", "expected_answer": "SPL转录因子通过调控miR156-SPL模块影响开花时间。SPL3/4/5直接激活FUL、SOC1等开花整合基因，SPL9/15通过调控miR172影响AP2-like基因", "key_genes": ["SPL3", "SPL4", "SPL5", "SPL9", "SPL15", "FUL", "SOC1", "AP2"], "key_mirnas": ["miR156", "miR172"], "difficulty": "hard", "requires_citation": true }, { "id": "FA-004", "question": "NF-Y转录因子复合体的组成及其DNA结合特异性", "expected_answer": "NF-Y是由NF-YA、NF-YB、NF-YC三个亚基组成的异源三聚体。NF-YA负责DNA结合(识别CCAAT盒)，NF-YB和NF-YC提供蛋白相互作用界面", "key_concepts": ["heterotrimer", "CCAAT box", "DNA binding", "subunit interaction"], "difficulty": "medium", "requires_citation": true }, { "id": "FA-005", "question": "WRKY转录因子在植物免疫应答中的调控网络", "expected_answer": "WRKY转录因子形成复杂的调控网络：WRKY18/40/60作为负调控因子形成反馈环路，WRKY70调控SA和JA信号交叉，WRKY33参与MAPK级联反应", "key_genes": ["WRKY18", "WRKY40", "WRKY60", "WRKY70", "WRKY33"], "key_pathways": ["SA signaling", "JA signaling", "MAPK cascade"], "difficulty": "hard", "requires_citation": true } ] }, "comparative_genomics": { "name": "比较基因组学与进化分析", "description": "测试RAG系统跨物种比较和进化分析能力", "weight": 0.25, "questions": [ { "id": "CG-001", "question": "比较拟南芥和水稻SUT基因家族的异同", "expected_answer": "拟南芥有5个SUT基因，水稻有5个OsSUT基因。两者都分为SUT1/2/4亚家族，但水稻特有的OsSUT5属于不同的进化分支。序列相似度在60-80%之间", "key_species": ["Arabidopsis", "Oryza sativa"], "key_facts": ["5 members each", "SUT1/2/4 clades", "60-80% similarity"], "difficulty": "medium", "requires_citation": true }, { "id": "CG-002", "question": "SPL基因家族在单子叶和双子叶植物中的扩张模式", "expected_answer": "SPL基因家族在双子叶(拟南芥17个)和单子叶(水稻19个)中数量相似。但SPL3/4/5亚家族在单子叶中发生扩张，与开花时间调控相关", "key_species": ["Arabidopsis", "Oryza sativa", "monocot", "dicot"], "key_subfamilies": ["SPL3", "SPL4", "SPL5"], "difficulty": "hard", "requires_citation": true }, { "id": "CG-003", "question": "P450基因家族在不同植物基因组中的拷贝数变异", "expected_answer": "P450基因家族拷贝数变异显著：拟南芥~246个，水稻~338个，大豆~360个，杨树~300个。扩张主要发生在CYP71和CYP72家族", "key_numbers": {"Arabidopsis": 246, "rice": 338, "soybean": 360, "poplar": 300}, "key_families": ["CYP71", "CYP72"], "difficulty": "hard", "requires_citation": true }, { "id": "CG-004", "question": "NF-Y基因家族在豆科植物中的特异性扩张", "expected_answer": "豆科植物中NF-YA亚家族发生特异性扩张，与根瘤共生相关。大豆中有21个NF-YA基因，显著多于拟南芥的10个", "key_species": ["Glycine max", "legume"], "key_subfamily": "NF-YA", "key_trait": "nodulation", "difficulty": "medium", "requires_citation": true }, { "id": "CG-005", "question": "WRKY基因家族的系统发育分布和古老起源", "expected_answer": "WRKY基因家族起源于绿色植物共同祖先，在苔藓(Physcomitrella)中有约40个成员。Group I是最古老的，包含两个WRKY结构域", "key_species": ["Physcomitrella patens", "green plants"], "key_evolutionary_notes": ["ancient origin", "Group I oldest", "two WRKY domains"], "difficulty": "hard", "requires_citation": true } ] }, "multi_hop_reasoning": { "name": "多跳推理与复杂查询", "description": "测试RAG系统的多步推理和复杂关系理解能力", "weight": 0.25, "questions": [ { "id": "MR-001", "question": "SUT基因的表达受哪些转录因子调控，这些转录因子又受什么信号通路控制？", "expected_answer": "SUT基因受多种转录因子调控：WRKY调控SUT1/2响应胁迫，NAC调控SUT4参与衰老，bZIP调控SUT响应糖信号。WRKY受MAPK级联通路调控，NAC受乙烯信号调控", "hops": 3, "key_relationships": ["WRKY-SUT", "NAC-SUT", "bZIP-SUT", "MAPK-WRKY", "ethylene-NAC"], "difficulty": "hard", "requires_citation": true }, { "id": "MR-002", "question": "SPL基因如何通过miR156影响植物发育阶段转换？", "expected_answer": "miR156在幼年期高表达，抑制SPL3/4/5/9/15等基因，维持幼年性状。随年龄增长miR156下降，SPL基因表达上升，促进开花和成熟。SPL进一步激活miR172，抑制AP2-like基因，加速发育阶段转换", "hops": 4, "key_relationships": ["miR156-SPL", "SPL-miR172", "miR172-AP2", "SPL-flowering"], "difficulty": "hard", "requires_citation": true }, { "id": "MR-003", "question": "P450基因在植物-微生物互作中的功能及其调控机制", "expected_answer": "P450基因参与植物防御化合物合成：CYP71家族合成生物碱，CYP72家族合成萜类。这些化合物受JA信号通路调控，WRKY和MYC转录因子直接激活P450基因表达", "hops": 3, "key_relationships": ["JA-P450", "WRKY-P450", "MYC-P450", "P450-defense compounds"], "difficulty": "hard", "requires_citation": true }, { "id": "MR-004", "question": "NF-Y复合体如何整合环境信号调控植物开花？", "expected_answer": "NF-Y复合体整合光周期和温度信号：NF-YB2/3与CO蛋白互作响应光周期，NF-YA1/4响应春化信号。复合体结合FT启动子CCAAT盒，激活开花整合基因", "hops": 3, "key_relationships": ["NF-Y-CO", "NF-Y-FT", "photoperiod-NF-Y", "vernalization-NF-Y"], "difficulty": "hard", "requires_citation": true }, { "id": "MR-005", "question": "WRKY转录因子网络如何协调植物生长与防御的平衡？", "expected_answer": "WRKY18/40/60形成负反馈环路防止过度免疫。WRKY70作为SA和JA信号交叉节点，调控生长-防御权衡。WRKY33激活防御同时抑制生长相关基因", "hops": 3, "key_relationships": ["WRKY18-WRKY40-WRKY60", "WRKY70-SA-JA", "WRKY33-growth-defense"], "difficulty": "hard", "requires_citation": true } ] } }, "metadata": { "total_questions": 20, "difficulty_distribution": { "easy": 4, "medium": 8, "hard": 8 }, "category_distribution": { "gene_identification": 5, "functional_annotation": 5, "comparative_genomics": 5, "multi_hop_reasoning": 5 }, "gene_families_covered": ["SUT", "P450", "SPL", "NF-Y", "WRKY"], "species_covered": ["Arabidopsis", "Oryza sativa", "Fagopyrum tataricum", "Solanum lycopersicum", "Glycine max", "Physcomitrella patens"] } }