| { |
| "task_id": "genome_004", |
| "domain": "KEGG_GENOME", |
| "autonomy_type": "ordered table", |
| "oracle_output_cardinality": 2, |
| "instruction": "我在为灵长类进化课准备一页讲义，想把“为什么这一支系必须从食物中获取维生素 C”的异常模式整理成一张两行对照表。请先在截至 2022 年底前已建立的灵长类基因组条目中，定位上游糖醛酸模块 M00014 仍然保留、但动物型维生素 C 合成模块 M00129 已在该下一级类群中缺失的异常类群；再核对与其对应的姐妹分支，确认该姐妹分支仍保留 M00129。最后，请输出两行对照表，列为 rank|clade_role|parent_clade|clade|anomaly_pathway|contrast_pathway|retained_upstream_module|vitamin_c_synthesis_module|vitamin_c_module_status|example_org|cutoff_year。第一行为 EXCEPTION_CLADE，第二行为 RETAINED_SISTER_CLADE；其中 vitamin_c_synthesis_module 固定填写 M00129，vitamin_c_module_status 分别写 LOST 和 RETAINED。示例物种请使用 KEGG organism code。", |
| "start_url": "https://www.genome.jp/kegg/kegg2.html", |
| "output_format": "请输出两行对照表，列为 rank|clade_role|parent_clade|clade|anomaly_pathway|contrast_pathway|retained_upstream_module|vitamin_c_synthesis_module|vitamin_c_module_status|example_org|cutoff_year。", |
| "oracle_answer": "1|EXCEPTION_CLADE|Primates|Haplorrhini|map00053|map00040|M00014|M00129|LOST|csyr|2022\n2|RETAINED_SISTER_CLADE|Primates|Strepsirrhini|map00053|map00040|M00014|M00129|RETAINED|oga|2022", |
| "metadata": { |
| "State-Gated Retrieval": [ |
| "只在截至 2022 年底已建立的灵长类基因组条目中筛选：保留上游糖醛酸模块 M00014、但缺失动物型维生素 C 合成模块 M00129 的异常下一级类群。", |
| "该异常类群必须能在同一上一级分裂下找到可对照的姐妹分支，且该姐妹分支仍保留 M00129。", |
| "最终输出要把异常分支和保留姐妹分支并排整理成两行对照表，并给出路径、模块与示例物种字段。" |
| ], |
| "dependency_type": "Data + Control", |
| "intra_chain": true, |
| "inter_chain": true, |
| "data_dependency": [ |
| "KEGG primate clade pages and genome entries yield candidate subclades and example species established through the cutoff year", |
| "pathway and module views yield M00014 and M00129 presence/absence evidence for the exception clade and its sister branch", |
| "final rows are produced only after the exception clade and retained sister are jointly validated under the same parent split and paired with example organisms" |
| ], |
| "control_dependency": [ |
| "the exception clade remains provisional until both the sister-branch contrast and the example-species checks succeed", |
| "the comparison pathway must make both retained M00014 and missing M00129 visible in the same view", |
| "the two output rows are emitted together only after the exception clade and retained sister branch are fixed under the same parent split" |
| ], |
| "freeze": { |
| "historical_window": "primate genome entries established on or before 2022, with current KEGG clade, pathway, and module pages used as relatively stable reference information for comparing retained M00014 against lost M00129" |
| }, |
| "answer_type": "multi-row ordered table" |
| }, |
| "rubric": { |
| "inclusion_conditions": [ |
| "只在截至 2022 年底已建立的灵长类基因组条目中筛选：上游糖醛酸模块 M00014 仍保留、但动物型维生素 C 合成模块 M00129 缺失的异常下一级类群。", |
| "该异常类群必须存在可对照的姐妹分支，且该姐妹分支仍保留 M00129。", |
| "最终输出必须把异常分支和保留姐妹分支并排整理成两行对照表，并给出路径、模块与示例物种字段。" |
| ], |
| "exclusion_conditions": [ |
| "排除停在 Simiiformes、没有继续检查更外层边界而漏掉 Haplorrhini 的结果。", |
| "排除使用不能同时展示 M00014 与 M00129 差异的 pathway 视图。", |
| "排除没有完成姐妹分支保留对照验证的候选类群。" |
| ], |
| "normalization": { |
| "field_separator": "|", |
| "record_separator": "\n", |
| "header_row": "omit the header row; emit data rows only", |
| "schema": [ |
| "rank", |
| "clade_role", |
| "parent_clade", |
| "clade", |
| "anomaly_pathway", |
| "contrast_pathway", |
| "retained_upstream_module", |
| "vitamin_c_synthesis_module", |
| "vitamin_c_module_status", |
| "example_org", |
| "cutoff_year" |
| ], |
| "rank": "emit 1 for EXCEPTION_CLADE and 2 for RETAINED_SISTER_CLADE", |
| "clade_role": [ |
| "EXCEPTION_CLADE", |
| "RETAINED_SISTER_CLADE" |
| ], |
| "pathway_normalization": "emit KEGG pathway ids with the map prefix", |
| "module_normalization": "emit KEGG module ids with the leading M", |
| "vitamin_c_module_status": [ |
| "LOST", |
| "RETAINED" |
| ], |
| "organism_code": "use bare KEGG organism codes in lowercase, not species names", |
| "cutoff_year": "use a four-digit year; this task is frozen at 2022", |
| "sorting_or_selection": "emit rows in the fixed order EXCEPTION_CLADE then RETAINED_SISTER_CLADE" |
| } |
| } |
| } |
|
|
