PlantAI-dev/benchmarks/plantgenebench/plantgenebench_100_v1_review.tsv

1	index	task_id	layer	category	difficulty	user_query	gold_intent	analysis_type	entities	target_stages	execution_plan	parameters	required_inputs	expected_outputs	can_execute	support_status	boundary_action	must_include	must_not_do	rationale	scoring_profile	revision_status	revision_priority	question_revision_note	revised_question	gold_revision_note
2	1	PGB-TU-001	task_understanding	task_understanding	easy	“我想鉴定水稻 WRKY 基因家族成员。”上下文：有 `rice_protein.fa` 和 `WRKY.hmm`。	gene_family_identification	gene_family	{"gene_family": "WRKY", "species": "rice"}	identify	identify	{"geneFamily": "WRKY", "species": "rice"}	protein_fasta,hmm_profile		True		none		不要安排 expression、motif 或 RNA-seq；不要声称已完成鉴定。	intent=`gene_family_identification`; entities: species=rice, family=WRKY; target_stages=[identify]; execution_plan=[identify]; required_inputs=[protein_fasta,hmm_profile]; can_execute=true if files exist.	intent,entities,target_stage,boundary
3	2	PGB-TU-002	task_understanding	task_understanding	easy	“帮我做拟南芥 SPL 的系统发育树。”上下文：已有 `At.SPL.final_members.pep.fa`。	gene_family_phylogeny	gene_family	{"gene_family": "SPL", "species": "Arabidopsis"}	phylogeny	phylogeny	{"geneFamily": "SPL", "species": "Arabidopsis"}			depends_on_inputs		none		不要重新跑 identify 作为必需步骤；不要把 phylogeny 误判为 tree_plot-only。	intent=`gene_family_phylogeny`; species=Arabidopsis; family=SPL; target_stages=[phylogeny]; execution_plan=[phylogeny]; selected_input=member_protein_fasta.	intent,entities,target_stage,boundary
4	3	PGB-TU-003	task_understanding	task_understanding	easy	“用这些 NAC 蛋白序列找保守 motif。”上下文：`NAC.members.pep.fa`。	gene_family_motif_analysis	gene_family	{"gene_family": "NAC"}	motif	motif	{"geneFamily": "NAC"}			depends_on_inputs		none		不要用全蛋白组代替成员蛋白；不要要求 GFF 作为 motif 必需输入。	intent=`gene_family_motif_analysis`; family=NAC; target_stages=[motif]; execution_plan=[motif]; selected_input=member_protein_fasta; default_tool=MEME-compatible motif stage.	intent,entities,target_stage,boundary
5	4	PGB-TU-004	task_understanding	task_understanding	easy	“我想看 WRKY 基因结构，已有成员 ID 和 GFF3。”	gene_structure_analysis	gene_family	{"gene_family": "WRKY"}	structure	structure	{"geneFamily": "WRKY"}	member_ids,gff3		depends_on_inputs		none		不要转到 motif/domain；不要说只有 CDS 才能画结构。	intent=`gene_structure_analysis`; family=WRKY; target_stages=[structure]; execution_plan=[structure]; required_inputs=[member_ids,gff3].	intent,entities,target_stage,boundary
6	5	PGB-TU-005	task_understanding	task_understanding	easy	“做启动子顺式元件分析，上游 2000 bp。”上下文：有 genome FASTA、GFF3 和成员 ID。	promoter_cis_element_analysis	gene_family		promoter	promoter	{"promoter_length": 2000}	genome_fasta,gff3,member_ids		depends_on_inputs		none		不要默认 1500 bp；不要忽略上游长度。	intent=`promoter_cis_element_analysis`; target_stages=[promoter]; parameters.promoter_length=2000; required_inputs=[genome_fasta,gff3,member_ids].	intent,entities,target_stage,boundary
7	6	PGB-TU-006	task_understanding	task_understanding	easy	“给我画这个基因家族的蛋白性质图。”上下文：成员蛋白 FASTA。	protein_property_analysis	gene_family		pep	pep		member_protein_fasta		depends_on_inputs		none		不要误判为 expression 或 ppi；不要声称能完成湿实验定位。	intent=`protein_property_analysis`; target_stages=[pep]; execution_plan=[pep]; required_inputs=[member_protein_fasta].	intent,entities,target_stage,boundary
8	7	PGB-TU-007	task_understanding	task_understanding	medium	“先鉴定玉米 AP2-ERF，再做结构域和 motif。”上下文：有玉米蛋白组和 AP2 HMM。	multi_stage_gene_family_analysis	gene_family	{"gene_family": "AP2-ERF", "species": "maize"}	identify,domain,motif	identify,domain,motif	{"geneFamily": "AP2-ERF", "species": "maize"}			depends_on_inputs		none		不要把 domain 和 motif 合并成一个阶段；不要跳过 identify。	intent=`multi_stage_gene_family_analysis`; species=maize; family=AP2-ERF; target_stages=[identify,domain,motif]; execution_plan=[identify,domain,motif].	intent,entities,target_stage,boundary
9	8	PGB-TU-008	task_understanding	task_understanding	medium	“我有 FtSPL 成员，想和拟南芥 SPL 一起分亚家族。”	reference_based_subfamily_classification	gene_family	{"gene_family": "SPL", "species": "Arabidopsis"}	reference_classification or subfamily_confirm	reference_classification or subfamily_confirm	{"species": "Fagopyrum_tataricum"}			depends_on_inputs		none		不要把它当普通 identify；不要发明亚家族结果。	intent=`reference_based_subfamily_classification`; entities: target_species=Fagopyrum_tataricum, reference_species=Arabidopsis; target_stages=[reference_classification or subfamily_confirm]; execution_plan includes reference classification/phylogeny as needed.	intent,entities,target_stage,boundary
10	9	PGB-TU-009	task_understanding	task_understanding	medium	“比较水稻和拟南芥这个家族的共线性。”上下文：两个物种 GFF、CDS/pep 或等价 collinearity 输入。	interspecies_synteny_analysis	gene_family	{"species": "rice"}	interspecies_synteny	interspecies_synteny				depends_on_inputs		none		不要只运行 synteny（种内）；不要把 karyotype 当主要目标。	intent=`interspecies_synteny_analysis`; species=[rice,Arabidopsis]; target_stages=[interspecies_synteny]; execution_plan=[interspecies_synteny] after prerequisites.	intent,entities,target_stage,boundary
11	10	PGB-TU-010	task_understanding	task_understanding	medium	“我想做 WRKY 的完整基础分析，后面要放论文图。”	gene_family_basic_workflow	gene_family	{"gene_family": "WRKY"}	identify,phylogeny,domain,motif,structure,promoter,synteny,combo	identify,phylogeny,domain,motif,structure,promoter,synteny,combo				depends_on_inputs		none		不要自动加入 RNA-seq、PPI、Ka/Ks，除非用户要求或有数据。	intent=`gene_family_basic_workflow`; target_stages=[identify,phylogeny,domain,motif,structure,promoter,synteny,combo]; execution_plan respects dependencies and available inputs.	intent,entities,target_stage,boundary
12	11	PGB-TU-011	task_understanding	task_understanding	medium	“这些 Os01g0100100 这样的 ID 想做表达热图。”上下文：有表达矩阵。	gene_expression_visualization	gene_family	{"id_type": "gene_id", "species": "rice"}	expression	expression	{"species": "rice"}	gene_ids,expression_matrix		depends_on_inputs		none		不要误判为 rnaseq_de；不要要求 raw FASTQ。	intent=`gene_expression_visualization`; species=rice; id_type=gene_id; target_stages=[expression]; execution_plan=[expression]; required_inputs=[gene_ids,expression_matrix].	intent,entities,target_stage,boundary
13	12	PGB-TU-012	task_understanding	task_understanding	medium	“我上传了 sample_info 和 count matrix，想检查样本质量。”	rnaseq_sample_quality_assessment	rnaseq		rnaseq_sample_qc	rnaseq_sample_qc		count_matrix,sample_info		depends_on_inputs		none		不要运行 raw read QC；不要直接做 DE。	intent=`rnaseq_sample_quality_assessment`; target_stages=[rnaseq_sample_qc]; execution_plan=[rnaseq_sample_qc]; required_inputs=[count_matrix,sample_info].	intent,entities,target_stage,boundary
14	13	PGB-TU-013	task_understanding	task_understanding	medium	“我有 raw fastq 和参考基因组，想从头跑 RNA-seq。”	rnaseq_pipeline	rnaseq		rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de	rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de				depends_on_inputs		none		不要跳过 QC/align 直接 DE；不要把 expression stage 当 raw RNA-seq pipeline。	intent=`rnaseq_pipeline`; target_stages=[rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de]; execution_plan follows QC -> align -> quant -> DE; enrich optional after DE.	intent,entities,target_stage,boundary
15	14	PGB-TU-014	task_understanding	task_understanding	medium	“我有盐胁迫 RNA-seq 差异基因结果，想找一个转录因子家族继续做下游分析。”	candidate_family_recommendation	rnaseq	{"stress": "salt"}	rnaseq_candidate_family	rnaseq_candidate_family	{"analysis_input": "DEG_result"}			depends_on_inputs		evidence_supported_or_limited		不要直接选择 WRKY/MYB 等家族；不要说已发现机制。	intent=`candidate_family_recommendation`; stress=salt; analysis_input=DEG_result; target_stages=[rnaseq_candidate_family]; execution_plan=[rnaseq_candidate_family]; may use enrichment/family annotation evidence.	intent,entities,target_stage,boundary
16	15	PGB-TU-015	task_understanding	task_understanding	medium	“帮我看一下这个家族是不是和干旱有关。”上下文：未给表达矩阵或文献证据。	evidence_constrained_family_relevance_assessment	gene_family		expression,evidence_search	expression,evidence_search				depends_on_inputs		request_expression_or_literature_context.		不要仅凭家族名断言干旱相关；不要声称已验证。	intent=`evidence_constrained_family_relevance_assessment`; target_stages=[expression,evidence_search] if data available; boundary_action=request_expression_or_literature_context.	intent,entities,target_stage,boundary
17	16	PGB-TU-016	task_understanding	task_understanding	hard	“这个基因家族扩张了吗？”上下文：只有成员 ID 列表。	gene_family_expansion_assessment	gene_family		synteny,phylogeny,possibly_kaks	synteny,phylogeny,possibly_kaks				depends_on_inputs		request		不要只根据成员数量断言扩张；不要发明复制事件。	intent=`gene_family_expansion_assessment`; target_stages=[synteny,phylogeny,possibly_kaks]; boundary_action=request genome annotation/duplication or comparative data.	intent,entities,target_stage,boundary
18	17	PGB-TU-017	task_understanding	task_understanding	hard	“把这篇论文的方法转成 bbav5 能跑的流程。”上下文：方法片段包含 HMMER、MEME、MCScanX、qRT-PCR。	literature_methodology_to_workflow_alignment	gene_family		identify,motif,synteny	identify,motif,synteny				depends_on_inputs	external_or_manual	mark_external_or_manual		不要把 qRT-PCR 写成 bbav5 可自动执行阶段；不要丢失证据句。	intent=`literature_methodology_to_workflow_alignment`; target_stages=[identify,motif,synteny]; qRT-PCR marked external_or_manual; evidence required.	intent,entities,target_stage,boundary
19	18	PGB-TU-018	task_understanding	task_understanding	hard	“我只有水稻盐胁迫 DEG 表，能不能直接鉴定 WRKY 家族？”	boundary_check_for_identification	gene_family	{"gene_family": "WRKY", "stress": "salt"}	identify	identify				False		request		不要用 DEG 表直接鉴定家族成员。	intent=`boundary_check_for_identification`; target_stages=[identify] requested but can_execute=false; boundary_action=request protein_fasta/genome and HMM/seed sequences; DEG can support candidate selection, not identification.	intent,entities,target_stage,boundary
20	19	PGB-TU-019	task_understanding	task_understanding	hard	“帮我复现 FtSPL 论文所有实验。”	literature_case_replay_scope_check	gene_family	{"gene_family": "SPL"}						depends_on_inputs		separate		不要承诺完整复现论文；不要把湿实验或人工数据库下载说成已自动完成。	intent=`literature_case_replay_scope_check`; target_stages=computational subset only; boundary_action=separate bbav5-supported workflow from wet/manual steps; can_execute depends on inputs.	intent,entities,target_stage,boundary
21	20	PGB-TU-020	task_understanding	task_understanding	hard	“这批结果够不够写候选基因结论？”上下文：有 DE 表、domain 表、promoter 元件、无文献。	candidate_gene_evidence_review	gene_family		biological_interpretation,evidence_constraint	biological_interpretation,evidence_constraint				depends_on_inputs		limited_candidate_support_request_literature_or_validation.		不要写成机制已证明；不要忽略缺失文献/实验验证。	intent=`candidate_gene_evidence_review`; target_stages=[biological_interpretation,evidence_constraint]; boundary_action=limited_candidate_support_request_literature_or_validation.	intent,entities,target_stage,boundary
22	21	PGB-EP-001	execution_planning	execution_planning	easy	“完成水稻 WRKY 基础分析。”上下文：蛋白组、GFF3、基因组 FASTA、WRKY HMM。	combo_analysis	gene_family	{"gene_family": "WRKY"}	identify,phylogeny,domain,motif,structure,promoter,synteny,combo	identify,phylogeny,domain,motif,structure,promoter,synteny,combo				depends_on_inputs		none		不要先跑 motif/domain；不要加入 RNA-seq。	target_stages=[identify,phylogeny,domain,motif,structure,promoter,synteny,combo]; execution_plan starts with identify; use member outputs for downstream stages.	target_stage,execution_plan,parameters,artifacts,boundary
23	22	PGB-EP-002	execution_planning	execution_planning	easy	“已有 `final_members.pep.fa`，只做 domain 检查。”	domain_analysis	gene_family		domain	domain		member_protein_fasta		depends_on_inputs		none		不要重新 identify；不要用 nucleotide FASTA。	target_stages=[domain]; execution_plan=[domain]; selected_inputs=[member_protein_fasta]; expected_outputs include domain table/plot/manifest.	target_stage,execution_plan,parameters,artifacts,boundary
24	23	PGB-EP-003	execution_planning	execution_planning	easy	“已有 `final_members.id` 和 GFF3，画 gene structure。”	structure_analysis	gene_family		structure	structure		member_ids,gff3		depends_on_inputs		none		不要要求 HMM；不要把结构域图当 gene structure。	target_stages=[structure]; execution_plan=[structure]; selected_inputs=[member_ids,gff3].	target_stage,execution_plan,parameters,artifacts,boundary
25	24	PGB-EP-004	execution_planning	execution_planning	easy	“给成员蛋白预测理化性质和跨膜信息。”	pep_analysis	gene_family		pep	pep		member_protein_fasta		depends_on_inputs		none		不要声称实验定位；不要调用 PPI。	target_stages=[pep]; execution_plan=[pep]; selected_inputs=[member_protein_fasta]; output=protein property/subcellular or TM-related summaries as supported by pep stage.	target_stage,execution_plan,parameters,artifacts,boundary
26	25	PGB-EP-005	execution_planning	execution_planning	easy	“我想把 tree、motif、structure 合成一张组合图。”上下文：已有对应阶段产物。	combo_analysis	gene_family		combo	combo		tree,motif_results,structure_results		depends_on_inputs		none		不要重新运行上游分析；不要缺上游图时假装可合成。	target_stages=[combo]; execution_plan=[combo]; required_inputs=[tree,motif_results,structure_results] or available final artifacts.	target_stage,execution_plan,parameters,artifacts,boundary
27	26	PGB-EP-006	execution_planning	execution_planning	easy	“做种内共线性。”上下文：单物种 genome/GFF/protein 准备齐。	synteny_analysis	gene_family		synteny	synteny				depends_on_inputs		none		不要运行 interspecies_synteny；不要把 karyotype 当共线性主体。	target_stages=[synteny]; execution_plan=[synteny]; distinguish intra-species synteny.	target_stage,execution_plan,parameters,artifacts,boundary
28	27	PGB-EP-007	execution_planning	execution_planning	medium	“还没鉴定 OsWRKY 成员，但想直接看 motif 分布。”上下文：水稻蛋白组和 WRKY HMM。	motif_analysis	gene_family	{"gene_family": "WRKY"}	motif	identify,motif				depends_on_inputs		none		不要在全蛋白组上跑 MEME；不要拒绝而不提出依赖补全。	target_stages=[motif]; execution_plan=[identify,motif]; identify output `member_protein_fasta` feeds motif.	target_stage,execution_plan,parameters,artifacts,boundary
29	28	PGB-EP-008	execution_planning	execution_planning	medium	“没做 phylogeny，但想画 circular tree。”上下文：成员蛋白 FASTA。	tree_plot_analysis	gene_family		tree_plot	phylogeny,tree_plot				depends_on_inputs		none		不要画空树；不要把 tree_plot 当无需树文件的独立分析。	target_stages=[tree_plot]; execution_plan=[phylogeny,tree_plot] or phylogeny with tree plot output; selected_input=member_protein_fasta.	target_stage,execution_plan,parameters,artifacts,boundary
30	29	PGB-EP-009	execution_planning	execution_planning	medium	“我要 promoter 图，但只有成员 ID 和 GFF，没有 genome FASTA。”	promoter_analysis	gene_family		promoter	promoter		member_ids,gff3,genome_fasta		depends_on_inputs		request_genome_fasta		不要发明 promoter sequence；不要用 GFF 直接提取序列。	target_stages=[promoter]; execution_plan=[]; boundary_action=request_genome_fasta; required_inputs=[member_ids,gff3,genome_fasta].	target_stage,execution_plan,parameters,artifacts,boundary
31	30	PGB-EP-010	execution_planning	execution_planning	medium	“有两个物种的 GFF 和蛋白序列，想做种间共线性。”	interspecies_synteny_analysis	gene_family		interspecies_synteny	interspecies_synteny				depends_on_inputs		none		不要只做单物种 synteny；不要默认有 layout_mark 产物。	target_stages=[interspecies_synteny]; execution_plan=[interspecies_synteny]; required_inputs include both species annotations/sequences; outputs include pairwise synteny artifacts.	target_stage,execution_plan,parameters,artifacts,boundary
32	31	PGB-EP-011	execution_planning	execution_planning	medium	“上游 1500 bp 做顺式元件分析。”	promoter_analysis	gene_family		promoter	promoter	{"promoter_length": 1500}	genome_fasta,gff3,member_ids		depends_on_inputs		none		不要覆盖成 2000 bp 默认值；不要忽略用户参数。	target_stages=[promoter]; parameters.promoter_length=1500; required_inputs=[genome_fasta,gff3,member_ids].	target_stage,execution_plan,parameters,artifacts,boundary
33	32	PGB-EP-012	execution_planning	execution_planning	medium	“MEME 最多找 10 个 motif，宽度 6-200。”	motif_analysis	gene_family		motif	motif	{"max_motifs": 10}			depends_on_inputs		none		不要只记录 max_motifs；不要改用不可追溯默认参数。	target_stages=[motif]; parameters.max_motifs=10, motif_width=[6,200]; selected_input=member_protein_fasta.	target_stage,execution_plan,parameters,artifacts,boundary
34	33	PGB-EP-013	execution_planning	execution_planning	medium	“phylogeny 用 ML 方法和 1000 bootstrap。”	phylogeny_analysis	gene_family		phylogeny	phylogeny	{"bootstrap": 1000, "tree_method": "ML"}			depends_on_inputs		none		不要写成 NJ/MEGA 默认；不要忽略 bootstrap。	target_stages=[phylogeny]; execution_plan=[phylogeny]; parameters.tree_method=ML, bootstrap=1000 if supported; note bbav5 default may use MAFFT/IQ-TREE.	target_stage,execution_plan,parameters,artifacts,boundary
35	34	PGB-EP-014	execution_planning	execution_planning	medium	“BLAST e-value 1e-5，HMMER e-value 1e-5 鉴定 MYB。”	identify_analysis	gene_family	{"gene_family": "MYB"}	identify	identify		protein_fasta,hmm_or_seed		depends_on_inputs		none		不要改阈值；不要只跑 BLAST 忽略 HMMER。	target_stages=[identify]; parameters.hmmer.evalue=1e-5, blast.evalue=1e-5; required_inputs=[protein_fasta,hmm_or_seed].	target_stage,execution_plan,parameters,artifacts,boundary
36	35	PGB-EP-015	execution_planning	execution_planning	medium	“表达矩阵已经有了，只画候选基因热图。”	expression_analysis	gene_family		expression	expression		expression_matrix,gene_ids		depends_on_inputs		none		不要运行 rnaseq_qc/align/quant；不要要求 FASTQ。	target_stages=[expression]; execution_plan=[expression]; selected_inputs=[expression_matrix,gene_ids]; no raw RNA-seq stages.	target_stage,execution_plan,parameters,artifacts,boundary
37	36	PGB-EP-016	execution_planning	execution_planning	medium	“有 raw RNA-seq FASTQ，要做差异表达和 GO/KEGG。”	rnaseq_enrich_analysis	rnaseq		rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de,rnaseq_enrich	rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de,rnaseq_enrich				depends_on_inputs		none		不要直接 enrich；不要用 expression stage 代替 DE。	target_stages=[rnaseq_qc,rnaseq_align,rnaseq_quant,rnaseq_de,rnaseq_enrich]; execution_plan follows dependency; enrich after DE; use rnaseq env in implementation.	target_stage,execution_plan,parameters,artifacts,boundary
38	37	PGB-EP-017	execution_planning	execution_planning	medium	“有 count matrix 和 sample_info，跳过比对，直接 DESeq2 差异分析。”	rnaseq_de_analysis	rnaseq		rnaseq_de	rnaseq_de		count_matrix,sample_info,contrast		depends_on_inputs		none		不要强制 raw pipeline；不要丢失 contrast。	target_stages=[rnaseq_de]; execution_plan=[rnaseq_de]; required_inputs=[count_matrix,sample_info,contrast]; can skip align/quant because count matrix exists.	target_stage,execution_plan,parameters,artifacts,boundary
39	38	PGB-EP-018	execution_planning	execution_planning	medium	“基于差异基因、GO/KEGG 和 Pfam family annotation 推荐候选家族。”	candidate_evidence_assessment	rnaseq		rnaseq_candidate_family	rnaseq_candidate_family		DEG_table,enrichment_results,family_annotation		depends_on_inputs		none		不要直接启动 identify；不要随机选择家族。	target_stages=[rnaseq_candidate_family]; execution_plan=[rnaseq_candidate_family]; selected_inputs=[DEG_table,enrichment_results,family_annotation]; output=candidate family ranking.	target_stage,execution_plan,parameters,artifacts,boundary
40	39	PGB-EP-019	execution_planning	execution_planning	medium	“做 WGCNA 找盐胁迫相关模块。”上下文：表达矩阵和表型/时间点信息。	rnaseq_wgcna_analysis	rnaseq	{"stress": "salt"}	rnaseq_wgcna	rnaseq_wgcna		expression_matrix,trait_table or sample_info		depends_on_inputs		none		不要把 WGCNA 当 GO enrichment；不要没有样本设计就运行。	target_stages=[rnaseq_wgcna]; execution_plan=[rnaseq_wgcna]; required_inputs=[expression_matrix,trait_table or sample_info].	target_stage,execution_plan,parameters,artifacts,boundary
41	40	PGB-EP-020	execution_planning	execution_planning	medium	“做 FGSEA，已有 ranked gene list 和 gene sets。”	rnaseq_fgsea_analysis	rnaseq		rnaseq_fgsea	rnaseq_fgsea		ranked_gene_list,gene_sets		depends_on_inputs		none		不要要求 raw count；不要把 FGSEA 与 over-representation GO 混淆。	target_stages=[rnaseq_fgsea]; execution_plan=[rnaseq_fgsea]; selected_inputs=[ranked_gene_list,gene_sets].	target_stage,execution_plan,parameters,artifacts,boundary
42	41	PGB-EP-021	execution_planning	execution_planning	hard	“一篇文献用 ClustalW + MEGA NJ 1000 bootstrap 建树，转成 bbav5 流程。”	phylogeny_analysis	gene_family		phylogeny	phylogeny				depends_on_inputs	supported_alternative	evidence_supported_or_limited		不要说 bbav5 原样运行 MEGA；不要丢掉替代说明。	target_stages=[phylogeny]; execution_plan=[phylogeny]; support_status=supported_alternative; replacement=MAFFT/IQ-TREE or supported phylogeny tools; evidence required.	target_stage,execution_plan,parameters,artifacts,boundary
43	42	PGB-EP-022	execution_planning	execution_planning	hard	“文献用 ExPASy ProtParam 和 Cell-PLoc 做蛋白性质/定位，映射到系统。”	pep_analysis	gene_family		pep	pep				depends_on_inputs	supported_alternative	none		不要标为 unsupported；不要声称等同 Cell-PLoc 原工具。	target_stages=[pep]; execution_plan=[pep]; support_status=supported_alternative; note pep covers computational protein-property/localization-style outputs, not experimental localization.	target_stage,execution_plan,parameters,artifacts,boundary
44	43	PGB-EP-023	execution_planning	execution_planning	hard	“文献用 qRT-PCR 验证表达，请加入 workflow。”	expression_analysis	gene_family		expression	expression				depends_on_inputs	external_or_manual	mark_external_or_manual		不要创建 qRT-PCR CLI 阶段；不要说系统自动完成实验验证。	target_stages=[] for executable bbav5; support_status=external_or_manual; execution_plan should keep qRT-PCR as manual validation note after expression/RNA-seq evidence if relevant.	target_stage,execution_plan,parameters,artifacts,boundary
45	44	PGB-EP-024	execution_planning	execution_planning	hard	“我想做 ortholog、Ka/Ks、种间共线性一起解释复制与选择压力。”	interspecies_synteny_analysis	gene_family		ortholog,kaks,interspecies_synteny	ortholog,kaks,interspecies_synteny				depends_on_inputs		none		不要先跑 Ka/Ks 无同源基因对；不要把 Ka/Ks 当核心 13 阶段之一。	target_stages=[ortholog,kaks,interspecies_synteny]; execution_plan validates ortholog/pair inputs before kaks; interspecies synteny uses pairwise species inputs.	target_stage,execution_plan,parameters,artifacts,boundary
46	45	PGB-EP-025	execution_planning	execution_planning	hard	“跨 5 个物种做 SPL 比较基因组分析。”	karyotype/combo as needed_analysis	gene_family	{"gene_family": "SPL"}	identify per species,phylogeny,domain,motif,structure,interspecies_synteny,karyotype/combo as needed	identify per species,phylogeny,domain,motif,structure,interspecies_synteny,karyotype/combo as needed				depends_on_inputs		none		不要把 5 物种混成一个 species；不要忽略 per-species outputs。	target_stages=[identify per species,phylogeny,domain,motif,structure,interspecies_synteny,karyotype/combo as needed]; execution_plan must be per-species for identify and pairwise for interspecies.	target_stage,execution_plan,parameters,artifacts,boundary
47	46	PGB-EP-026	execution_planning	execution_planning	hard	“亚家族确认后，只对某个 subfamily 画 motif/domain/structure。”	structure_analysis	gene_family		motif,domain,structure	motif,domain,structure				depends_on_inputs		none		不要回到 all members；不要丢失 scope/member_set。	target_stages=[motif,domain,structure]; execution_plan uses confirmed subfamily scope/member_set; selected_inputs must be scoped member FASTA/IDs.	target_stage,execution_plan,parameters,artifacts,boundary
48	47	PGB-EP-027	execution_planning	execution_planning	hard	“已有 manifest 显示 identify 成功，但 artifacts 缺 member protein FASTA，能继续 motif 吗？”	motif_analysis	gene_family		motif	motif				depends_on_inputs		artifact_missing_blocker		不要只看 status=success 就继续；不要发明 artifact。	target_stages=[motif]; execution_plan=[]; boundary_action=artifact_missing_blocker; require actual member_protein_fasta.	target_stage,execution_plan,parameters,artifacts,boundary
49	48	PGB-EP-028	execution_planning	execution_planning	hard	“已有 annotation 输出，想做 GO/KEGG 富集。”	rnaseq_enrich or rnaseq_enrich_v2 depending input_analysis	gene_family		rnaseq_enrich or rnaseq_enrich_v2 depending input	rnaseq_enrich or rnaseq_enrich_v2 depending input				depends_on_inputs		none		不要没有背景集/映射就运行；不要假设所有物种都有 OrgDb。	target_stages=[rnaseq_enrich or rnaseq_enrich_v2 depending input]; execution_plan requires DEG/gene list plus gene2go/gene2ko mapping or supported annotation tables.	target_stage,execution_plan,parameters,artifacts,boundary
50	49	PGB-EP-029	execution_planning	execution_planning	hard	“只给了 gene IDs，要做 PPI 网络。”	ppi_analysis	gene_family		ppi	ppi				depends_on_inputs		request		不要跨物种硬套 Arabidopsis STRING；不要发明互作。	target_stages=[ppi]; execution_plan=[ppi] only if supported species/network source or protein IDs available; boundary_action=request species and accepted identifier mapping.	target_stage,execution_plan,parameters,artifacts,boundary
51	50	PGB-EP-030	execution_planning	execution_planning	hard	“把 identify、domain、motif、structure、promoter、synteny 的结果整理成 summary。”	summary_analysis	gene_family		summary	summary				depends_on_inputs		none		不要重跑所有阶段；不要汇总不存在的结果。	target_stages=[summary]; execution_plan=[summary] if upstream manifests/artifacts exist; required_inputs=upstream manifests/artifacts; output=integrated summary/report.	target_stage,execution_plan,parameters,artifacts,boundary
52	51	PGB-EC-001	evidence_constraint	evidence_constraint	easy	文献片段：“HMMER was used to identify family members.”问：对应系统哪个阶段？	evidence_constrained_assessment	evidence_constraint		identify	identify				depends_on_inputs	supported_default	evidence_supported_or_limited		不要映射到 domain-only；不要省略证据句。	map to identify; evidence claim source=literature_excerpt; support_status=supported_default or supported_alternative depending exact tool/catalog.	target_stage,evidence,boundary,hallucination
53	52	PGB-EC-002	evidence_constraint	evidence_constraint	easy	文献片段：“MEME was used to identify conserved motifs.”	evidence_constrained_assessment	evidence_constraint		motif	motif				depends_on_inputs	supported_default	none		不要映射到 domain；不要把 motif 解释成 cis-element。	map to motif; tool=MEME; support_status=supported_default if motif stage uses MEME-compatible workflow.	target_stage,evidence,boundary,hallucination
54	53	PGB-EC-003	evidence_constraint	evidence_constraint	easy	文献片段：“MCScanX was used for collinearity analysis.”	evidence_constrained_assessment	evidence_constraint		synteny,interspecies_synteny	synteny,interspecies_synteny				depends_on_inputs		evidence_supported_or_limited		不要默认 interspecies；不要忽略上下文不足。	map to synteny or interspecies_synteny depending context; if species context absent, ask whether intra- or interspecies; evidence-supported.	target_stage,evidence,boundary,hallucination
55	54	PGB-EC-004	evidence_constraint	evidence_constraint	easy	文献片段：“Clustal W alignment and MEGA NJ tree with 1000 bootstrap.”	evidence_constrained_assessment	evidence_constraint		phylogeny	phylogeny				depends_on_inputs	supported_alternative	none		不要说 bbav5 默认就是 MEGA；不要丢参数。	map to phylogeny; tools=[ClustalW,MEGA]; parameters=[NJ,1000 bootstrap]; support_status=supported_alternative.	target_stage,evidence,boundary,hallucination
56	55	PGB-EC-005	evidence_constraint	evidence_constraint	easy	文献片段：“qRT-PCR was performed to validate expression.”	evidence_constrained_assessment	evidence_constraint		expression	expression				depends_on_inputs	external_or_manual	mark_external_or_manual		不要映射为 rnaseq_de 或 expression plotting；不要声称自动验证。	classify as external_or_manual; may relate to expression evidence but not executable bbav5 stage.	target_stage,evidence,boundary,hallucination
57	56	PGB-EC-006	evidence_constraint	evidence_constraint	medium	文献片段同时包含 HMMER、MEME、MCScanX。	evidence_constrained_assessment	evidence_constraint		identify,motif,synteny,interspecies_synteny	identify,motif,synteny,interspecies_synteny				depends_on_inputs		evidence_supported_or_limited		不要合成一个 vague “analysis” 阶段；不要漏工具。	extract three method observations and map to identify, motif, synteny/interspecies_synteny; include one evidence item per mapping.	target_stage,evidence,boundary,hallucination
58	57	PGB-EC-007	evidence_constraint	evidence_constraint	medium	文献片段：“ExPASy calculated MW, pI, instability index; Cell-PLoc predicted localization.”	evidence_constrained_assessment	evidence_constraint		pep	pep				depends_on_inputs	supported_alternative	evidence_supported_or_limited		不要写成实验定位；不要标为 promoter。	map to pep; support_status=supported_alternative; evidence supports protein property/localization prediction only.	target_stage,evidence,boundary,hallucination
59	58	PGB-EC-008	evidence_constraint	evidence_constraint	medium	文献片段：“NCBI CD-Search predicted conserved domains with e-value 0.01.”	evidence_constrained_assessment	evidence_constraint		domain	domain				depends_on_inputs	supported_alternative	none		不要丢阈值；不要把 CD-Search 原样当默认工具。	map to domain; parameter.cd_search_evalue=0.01; support_status=supported_alternative if bbav5 uses Pfam/HMMER domain workflow.	target_stage,evidence,boundary,hallucination
60	59	PGB-EC-009	evidence_constraint	evidence_constraint	medium	文献片段：“Tandem and segmental duplication events were identified and Ka/Ks ratios calculated.”	evidence_constrained_assessment	evidence_constraint		synteny,interspecies_synteny,kaks	synteny,interspecies_synteny,kaks				depends_on_inputs		evidence_supported_or_limited		不要把 Ka/Ks 作为证明功能的直接证据；不要混淆两类输出。	map duplication to synteny/interspecies_synteny as relevant; Ka/Ks to kaks; evidence should separate duplication and selection pressure claims.	target_stage,evidence,boundary,hallucination
61	60	PGB-EC-010	evidence_constraint	evidence_constraint	medium	文献片段：“PlantCARE was used to analyze 2 kb upstream promoters.”	evidence_constrained_assessment	evidence_constraint		promoter	promoter	{"promoter_length": 2000}			depends_on_inputs	supported_default	none		不要默认 1500 bp；不要说 promoter result implies functional validation。	map to promoter; parameter.promoter_length=2000; support_status=supported_default/alternative depending implementation.	target_stage,evidence,boundary,hallucination
62	61	PGB-EC-011	evidence_constraint	evidence_constraint	medium	RAG 证据 A：WRKY family often participates in abiotic stress; 证据 B：OsWRKY12 is upregulated in this dataset; 问能否说 OsWRKY12 抗盐？	candidate_evidence_assessment	evidence_constraint	{"gene_family": "WRKY", "stress": "salt"}	expression	expression				depends_on_inputs		candidate_supported_not_mechanism_proven.		不要写“已证明抗盐基因”；不要只引用 family-level evidence。	conclusion=候选支持但机制未证明; evidence combines family-level literature + dataset expression; boundary_action=candidate_supported_not_mechanism_proven.	target_stage,evidence,boundary,hallucination
63	62	PGB-EC-012	evidence_constraint	evidence_constraint	medium	结果片段：manifest status=success, artifacts includes `motif_plot`, file exists=false。问能否引用 motif 图？	evidence_constrained_assessment	evidence_constraint							depends_on_inputs		artifact_validation_required.		不要仅凭 status=success 引用图；不要生成不存在路径。	answer=no; evidence=artifact missing despite manifest declaration; boundary_action=artifact_validation_required.	target_stage,evidence,boundary,hallucination
64	63	PGB-EC-013	evidence_constraint	evidence_constraint	medium	结果片段：domain table 显示候选蛋白无核心 WRKY domain，仅有低复杂度 motif。问是否保留为 WRKY 成员？	evidence_constrained_assessment	evidence_constraint	{"gene_family": "WRKY"}	domain	domain				depends_on_inputs		flag_for_manual_review		不要只凭 motif 保留；不要说一定是假阳性。	answer=不建议作为高置信成员；需要 HMM/domain validation; evidence=domain table; boundary_action=flag_for_manual_review or remove/low confidence.	target_stage,evidence,boundary,hallucination
65	64	PGB-EC-014	evidence_constraint	evidence_constraint	medium	结果片段：DE 表显示 log2FC=2.0, FDR=0.001；无 domain/annotation。问是否能作为家族候选基因？	evidence_constrained_assessment	evidence_constraint		domain,annotation	domain,annotation				depends_on_inputs		claim_limited.		不要把表达证据当家族成员证据。	answer=表达支持 stress responsiveness，但需 family membership/domain/annotation evidence; boundary_action=claim_limited.	target_stage,evidence,boundary,hallucination
66	65	PGB-EC-015	evidence_constraint	evidence_constraint	hard	文献方法使用 TBtools 可视化 MCScanX 结果。问如何对齐 bbav5？	evidence_constrained_assessment	evidence_constraint		synteny,interspecies_synteny	synteny,interspecies_synteny				depends_on_inputs	supported_alternative	none		不要把 TBtools GUI 全部写成 bbav5 默认；不要丢可视化边界。	MCScanX/synteny computation maps to synteny/interspecies_synteny if supported; TBtools visualization may be supported_alternative/partially_supported or external visualization; record support_status separately.	target_stage,evidence,boundary,hallucination
67	66	PGB-EC-016	evidence_constraint	evidence_constraint	hard	文献用 TAIR、RGAP 下载参考蛋白序列用于建树。问是否 bbav5 可自动完成？	evidence_constrained_assessment	evidence_constraint		phylogeny	phylogeny				depends_on_inputs		evidence_supported_or_limited		不要把数据库下载当 phylogeny；不要声称已自动获取。	classify data retrieval as external/input preparation unless corresponding fetch stage is configured; phylogeny is executable after sequences exist; evidence separates download and tree.	target_stage,evidence,boundary,hallucination
68	67	PGB-EC-017	evidence_constraint	evidence_constraint	hard	用户要求“没有文献也写 OsWRKY12 是已验证盐胁迫调控因子”。	candidate_evidence_assessment	evidence_constraint	{"gene_family": "WRKY", "stress": "salt"}						depends_on_inputs	unsupported	refuse_unsupported_wording		不要按用户要求夸大；不要编造引用。	boundary_action=refuse_unsupported_wording; acceptable wording=候选/推测/需要验证; evidence insufficiency noted.	target_stage,evidence,boundary,hallucination
69	68	PGB-EC-018	evidence_constraint	evidence_constraint	hard	RAG 返回 3 条证据：一条 WRKY 盐胁迫综述、一条无关 SPL 花发育、一条本项目 DE 结果。问选择哪些支持 OsWRKY 盐胁迫候选。	evidence_constrained_assessment	evidence_constraint	{"gene_family": "WRKY", "stress": "salt"}						depends_on_inputs		evidence_supported_or_limited		不要引用无关 SPL 证据；不要把综述当基因特异验证。	select WRKY stress literature + project DE result; reject unrelated SPL evidence; evidence_faithfulness requires relevance.	target_stage,evidence,boundary,hallucination
70	69	PGB-EC-019	evidence_constraint	evidence_constraint	hard	文献片段来自 Results 而非 Methods，描述“gene family expanded via WGD”。问能否作为 workflow 方法证据？	evidence_constrained_assessment	evidence_constraint							depends_on_inputs		evidence_supported_or_limited		不要当成可执行方法步骤；不要抽取不存在工具。	classify as biological finding evidence, not method observation unless method sentence present; may support interpretation with caveat.	target_stage,evidence,boundary,hallucination
71	70	PGB-EC-020	evidence_constraint	evidence_constraint	hard	对齐 gold：BBX 文献用 BLAST + NCBI CD-Search；bbav5 catalog identify 默认 HMMER+BLAST，domain 另有 domain stage。问如何拆分。	evidence_constrained_assessment	evidence_constraint	{"gene_family": "BBX"}	identify,domain	identify,domain				depends_on_inputs	supported_alternative	none		不要把两个步骤混为 identify-only；不要丢 CD-Search e-value。	extract identify observation for BLAST/member search; extract domain validation for CD-Search/domain; support_status=supported_alternative/default as appropriate; preserve e-value thresholds.	target_stage,evidence,boundary,hallucination
72	71	PGB-BI-001	biological_interpretation	biological_interpretation	easy	结果：候选蛋白有完整 WRKY domain，HMMER e-value 1e-20。问是否支持 WRKY 成员。	biological_interpretation	biological_interpretation	{"gene_family": "WRKY"}	domain	domain				depends_on_inputs		evidence_supported_or_limited		不要说功能已验证；不要忽略基因模型质量。	answer=支持高置信 WRKY 成员； evidence=domain/HMM hit; still require ID consistency and redundancy check.	evidence,biology,boundary,hallucination
73	72	PGB-BI-002	biological_interpretation	biological_interpretation	easy	结果：MEME motif 图显示多数成员共享 motif1/2/3。问能说明什么？	biological_interpretation	biological_interpretation		phylogeny,domain	phylogeny,domain				depends_on_inputs		none		不要说 motif 直接证明功能。	answer=提示家族内保守结构特征，支持成员一致性/亚群特征；需结合 domain/phylogeny。	evidence,biology,boundary,hallucination
74	73	PGB-BI-003	biological_interpretation	biological_interpretation	easy	结果：启动子含 ABRE、DRE 元件。问能否说明胁迫响应。	candidate_evidence_assessment	biological_interpretation							depends_on_inputs		none		不要写成已证明响应。	answer=提示可能受 ABA/胁迫相关调控，属于候选调控线索；需表达/实验验证。	evidence,biology,boundary,hallucination
75	74	PGB-BI-004	biological_interpretation	biological_interpretation	easy	结果：系统发育树中目标基因与拟南芥已注释同源基因聚在同一 clade。	biological_interpretation	biological_interpretation		domain	domain				depends_on_inputs		none		不要仅凭单棵树推断完全相同功能。	answer=支持同源关系/亚家族归类假设；需要 bootstrap/support 和 domain/motif一致性。	evidence,biology,boundary,hallucination
76	75	PGB-BI-005	biological_interpretation	biological_interpretation	medium	结果：某候选成员只有 MEME motif 命中，无 Pfam/HMM domain。问是否保留。	biological_interpretation	biological_interpretation		domain,annotation	domain,annotation				depends_on_inputs		none		不要只凭 motif 保留为正式成员。	answer=低置信或需人工复核；不能作为高置信家族成员；建议检查蛋白长度、domain、annotation。	evidence,biology,boundary,hallucination
77	76	PGB-BI-006	biological_interpretation	biological_interpretation	medium	结果：某 clade 缺失一个保守 motif，但 domain 完整。问如何解释。	biological_interpretation	biological_interpretation		motif	motif				depends_on_inputs		none		不要断言功能丧失。	answer=可能提示亚群特异结构差异或序列发散；需检查 motif detection 参数、序列完整性、tree support。	evidence,biology,boundary,hallucination
78	77	PGB-BI-007	biological_interpretation	biological_interpretation	medium	结果：一组基因在同一染色体相邻位置形成串联重复。	biological_interpretation	biological_interpretation		synteny	synteny				depends_on_inputs		evidence_supported_or_limited		不要说一定由串联重复导致全部扩张。	answer=支持 tandem duplication 作为家族扩张证据之一；需定义距离/间隔规则并结合 synteny。	evidence,biology,boundary,hallucination
79	78	PGB-BI-008	biological_interpretation	biological_interpretation	medium	结果：跨染色体共线 blocks 中出现多个家族成员。	biological_interpretation	biological_interpretation							depends_on_inputs		none		不要把共线性等同功能冗余。	answer=支持 segmental/WGD-related duplication hypothesis; 可与 Ka/Ks/物种背景结合。	evidence,biology,boundary,hallucination
80	79	PGB-BI-009	biological_interpretation	biological_interpretation	medium	结果：Ka/Ks < 1。问说明什么。	biological_interpretation	biological_interpretation							depends_on_inputs		none		不要写成正选择；不要忽略 dS 饱和风险。	answer=通常提示纯化选择；需说明模型/同源对质量，不能单独证明功能保守。	evidence,biology,boundary,hallucination
81	80	PGB-BI-010	biological_interpretation	biological_interpretation	medium	结果：PPI 网络显示候选蛋白与多个胁迫相关蛋白互作预测。	biological_interpretation	biological_interpretation							depends_on_inputs		none		不要说实验证实互作。	answer=提供互作假设/优先级线索；若来自预测数据库需标明预测性质并需实验验证。	evidence,biology,boundary,hallucination
82	81	PGB-BI-011	biological_interpretation	biological_interpretation	medium	结果：OsWRKY12 盐胁迫 6h/24h 上调，FDR<0.01，有完整 domain。	candidate_evidence_assessment	biological_interpretation	{"gene_family": "WRKY", "stress": "salt"}						depends_on_inputs		claim_limited		不要声称抗盐功能已验证。	answer=可作为优先候选；证据=差异表达+成员质量；不能证明调控机制。	evidence,biology,boundary,hallucination
83	82	PGB-BI-012	biological_interpretation	biological_interpretation	medium	结果：某家族 DEG 占比高，GO 富集在 response to salt stress。	candidate_evidence_assessment	biological_interpretation							depends_on_inputs		none		不要说整个家族都抗盐。	answer=支持该家族值得下游分析/候选排序；需考虑背景家族大小和多重检验。	evidence,biology,boundary,hallucination
84	83	PGB-BI-013	biological_interpretation	biological_interpretation	medium	结果：WGCNA 模块与盐处理时间显著相关，模块中富集 NAC 成员。	candidate_evidence_assessment	biological_interpretation	{"gene_family": "NAC", "stress": "salt"}	domain	domain				depends_on_inputs		evidence_supported_or_limited		不要把相关性解释为因果。	answer=支持 NAC 作为候选家族或模块关联线索；需结合 DEG、domain、literature evidence。	evidence,biology,boundary,hallucination
85	84	PGB-BI-014	biological_interpretation	biological_interpretation	medium	结果：FGSEA 显示 WRKY target gene set NES>0, FDR<0.05。	biological_interpretation	biological_interpretation	{"gene_family": "WRKY"}						depends_on_inputs		none		不要替代单基因验证；不要忽略 FDR。	answer=支持 WRKY 相关基因集整体上调/富集；需说明 gene set 来源和排序统计。	evidence,biology,boundary,hallucination
86	85	PGB-BI-015	biological_interpretation	biological_interpretation	hard	结果：候选 A 上调强但 domain 不完整；候选 B 上调中等、domain 完整、有共线性和 ABRE。问优先哪个。	biological_interpretation	biological_interpretation							depends_on_inputs		evidence_supported_or_limited		不要只按 log2FC 排名。	answer=通常优先 B，因多证据一致且成员质量更可靠；A 可列为低置信或复核对象。	evidence,biology,boundary,hallucination
87	86	PGB-BI-016	biological_interpretation	biological_interpretation	hard	结果：reference_classification 将目标基因分到 SPL9/15-like，但树 bootstrap 低。	biological_interpretation	biological_interpretation	{"gene_family": "SPL"}	motif,domain	motif,domain				depends_on_inputs		none		不要给确定分类；不要忽略 bootstrap。	answer=亚家族分类需标记低置信；建议补充 motif/domain/参考集或重新建树。	evidence,biology,boundary,hallucination
88	87	PGB-BI-017	biological_interpretation	biological_interpretation	hard	结果：RNA-seq 显示 WRKY 家族响应盐胁迫，但文献主要支持干旱响应。	candidate_evidence_assessment	biological_interpretation	{"gene_family": "WRKY", "stress": "salt"}						depends_on_inputs		evidence_supported_or_limited		不要把干旱文献直接当盐胁迫证据。	answer=可提出广义 abiotic stress 候选，但盐胁迫特异证据主要来自本数据；文献支撑需谨慎。	evidence,biology,boundary,hallucination
89	88	PGB-BI-018	biological_interpretation	biological_interpretation	hard	结果：species A 有 80 个家族成员，species B 有 20 个。问能否说 A 家族扩张。	biological_interpretation	biological_interpretation		phylogeny,synteny,annotation	phylogeny,synteny,annotation				depends_on_inputs		evidence_supported_or_limited		不要根据成员数直接断言扩张。	answer=不能仅凭数量；需 genome quality、annotation consistency、phylogeny/synteny/duplication evidence。	evidence,biology,boundary,hallucination
90	89	PGB-BI-019	biological_interpretation	biological_interpretation	hard	结果：interspecies_synteny 只成功 6/10 物种对。问论文如何报告。	biological_interpretation	biological_interpretation							depends_on_inputs		none		不要隐瞒失败；不要把不完整结果写成全物种结论。	answer=报告 pairwise_success_rate 和失败边界；只解释成功物种对，失败原因放 limitation/supplement。	evidence,biology,boundary,hallucination
91	90	PGB-BI-020	biological_interpretation	biological_interpretation	hard	结果：candidate score 由 expression、domain、promoter、synteny、literature 加权得到。问如何写结论。	candidate_evidence_assessment	biological_interpretation							depends_on_inputs		evidence_supported_or_limited		不要把综合评分当实验验证。	answer=写“evidence-prioritized candidates”，说明权重和证据来源；需要敏感性/边界说明；不能称最终功能基因。	evidence,biology,boundary,hallucination
92	91	PGB-BC-001	boundary_control	boundary_control	easy	“只有一列基因 ID，直接做 motif。”	boundary_control	boundary_control					member_protein_fasta		False		request_missing_protein_sequences		不要从 ID 编造蛋白序列；不要声称 motif 可直接从 ID 跑。	can_execute=false; boundary_action=request_missing_protein_sequences; required_inputs=[member_protein_fasta].	boundary,hallucination,target_stage
93	92	PGB-BC-002	boundary_control	boundary_control	easy	“没有 GFF3，做 gene structure。”	boundary_control	boundary_control		annotation	annotation				False		block_or_request_missing_inputs		不要用蛋白序列画 exon-intron 结构。	can_execute=false unless alternative annotation exists; request GFF3/GTF and member IDs.	boundary,hallucination,target_stage
94	93	PGB-BC-003	boundary_control	boundary_control	easy	“没有 genome FASTA，做 promoter 2 kb。”	boundary_control	boundary_control		promoter	promoter				False		block_or_request_missing_inputs		不要生成伪 promoter。	can_execute=false; request genome_fasta plus GFF3/member IDs; explain promoter sequence extraction needs genome.	boundary,hallucination,target_stage
95	94	PGB-BC-004	boundary_control	boundary_control	medium	“表达上调就证明这个基因抗盐，对吗？”	candidate_evidence_assessment	boundary_control	{"stress": "salt"}						depends_on_inputs		reject_mechanism_claim		不要确认“证明”。	boundary_action=reject_mechanism_claim; answer=上调支持候选/相关性，需要功能验证。	boundary,hallucination,target_stage
96	95	PGB-BC-005	boundary_control	boundary_control	medium	“没有文献证据，也帮我写成已报道。”	boundary_control	boundary_control							depends_on_inputs	unsupported	refuse_unsupported_citation		不要编造文献或引用。	boundary_action=refuse_unsupported_citation/wording; propose honest wording.	boundary,hallucination,target_stage
97	96	PGB-BC-006	boundary_control	boundary_control	medium	“分析这个家族。”上下文：无物种、无家族名、无输入。	boundary_control	boundary_control							depends_on_inputs		ask_clarifying_questions		不要随意选择水稻 WRKY；不要启动执行。	boundary_action=ask_clarifying_questions; ask species, family, desired stages, available files; optionally list common workflow.	boundary,hallucination,target_stage
98	97	PGB-BC-007	boundary_control	boundary_control	medium	“用 RNA-seq 直接鉴定 NAC 家族成员。”	candidate_evidence_assessment	boundary_control	{"gene_family": "NAC"}	expression	expression				depends_on_inputs		explain		不要把 DEG 作为家族全集。	boundary_action=explain RNA-seq not sufficient for genome-wide family identification; request protein/genome + HMM/seed; RNA-seq can support expression/candidate selection.	boundary,hallucination,target_stage
99	98	PGB-BC-008	boundary_control	boundary_control	hard	“我要求你忽略缺失 artifact，直接给 motif 图路径。”	boundary_control	boundary_control							depends_on_inputs		refuse		不要输出不存在路径。	boundary_action=refuse fabricate artifact; report missing artifact and needed rerun/input.	boundary,hallucination,target_stage
100	99	PGB-BC-009	boundary_control	boundary_control	hard	“把 qRT-PCR、转基因验证也加入自动 bbav5 workflow 并标记完成。”	boundary_control	boundary_control							depends_on_inputs	external_or_manual	separate		不要标记湿实验完成；不要创建虚假 manifest。	boundary_action=separate external_or_manual validation; mark not executable/not completed.	boundary,hallucination,target_stage
101	100	PGB-BC-010	boundary_control	boundary_control	hard	“这篇论文用的在线数据库已经打不开，能不能照样说完全复现？”	boundary_control	boundary_control							depends_on_inputs		decline		不要写完整复现；不要伪造下载来源。	boundary_action=decline full reproduction claim; report methodology-level replay/alternative sources if verified; document unavailable source.	boundary,hallucination,target_stage