| { |
| "task_id": "genome_002", |
| "domain": "KEGG_GENOME", |
| "autonomy_type": "ordered table", |
| "oracle_output_cardinality": 2, |
| "instruction": "我在为学生准备一页介绍经典动物内共生案例的讲义，想在 KEGG 的宿主—共生体示例中找出符合以下条件的那个案例：截至 2005 年底已收录，其细菌共生体基因组含有已命名的额外复制子，且这些复制子的名称在宿主—共生体联合通路图中可直接对应到氨基酸合成模块。请按以下顺序处理：先在 KEGG 的宿主—共生体示例中，按细菌共生体 KEGG GENOME 条目的 Created 年份筛选出 2005 年底前已收录的组合；再保留其细菌共生体基因组中带有已命名额外复制子的案例；随后核对这些复制子名称在宿主—共生体联合通路图中的对应关系，确认其可直接对应到氨基酸合成模块；最后，在该宿主—共生体组合对应的联合通路图范围内，把该案例中所有符合条件的通路—模块列出，并输出一行字符串：<group>|<symbiont>|<pathway>|<module>|<replicon>|<created_year>（按 pathway 编号升序排列，英文逗号分隔；若无则输出 NONE）。", |
| "start_url": "https://www.genome.jp/kegg/genome/", |
| "output_format": "请输出一行字符串：<group>|<symbiont>|<pathway>|<module>|<replicon>|<created_year>（按 pathway 编号升序排列，英文逗号分隔；若无则输出 NONE）。", |
| "oracle_answer": "api+buc|buc|00290|M00432|pLeu|2000,api+buc|buc|00400|M00023|pTrp|2000", |
| "metadata": { |
| "State-Gated Retrieval": [ |
| "只保留宿主—共生体示例中，细菌共生体 KEGG GENOME Created 年份不晚于 2005 年底、且其基因组带有已命名额外复制子的案例。", |
| "这些复制子的名称必须能在宿主—共生体联合 pathway 页面上直接对应到氨基酸合成模块。", |
| "最终输出 surviving 案例中所有符合条件的 pathway-module-replicon 记录，并按 pathway 编号升序排列。" |
| ], |
| "dependency_type": "Data + Control", |
| "intra_chain": true, |
| "inter_chain": true, |
| "data_dependency": [ |
| "KEGG host-symbiont examples and symbiont genome pages yield the pre-2006 candidate pairs and named extra replicons", |
| "joint pathway maps, module pages, and genome annotations yield the pathway-module-replicon links attributable to the symbiont side", |
| "final rows are produced only after the surviving host-symbiont pair is validated against both replicon existence and module support on the joint pathway page" |
| ], |
| "control_dependency": [ |
| "only branches satisfying the named-plasmid requirement may be retained, so the bmy+wbm branch must be excluded when the wbm genome page fails that requirement", |
| "module retrieval must use the api+buc pathway state and the 00400 view, because that view is the one that actually exposes M00023", |
| "module support is valid only after symbiont-side evidence for both M00023 and M00432 is validated in the selected pathway state" |
| ], |
| "freeze": { |
| "historical_window": "KEGG host-symbiont examples whose symbiont GENOME Created year is on or before 2005; current joint pathway, module, and genome replicon annotations" |
| }, |
| "answer_type": "multi-row ordered table" |
| }, |
| "rubric": { |
| "inclusion_conditions": [ |
| "只保留宿主—共生体示例中，细菌共生体 KEGG GENOME Created 年份不晚于 2005 年底、且其基因组带有已命名额外复制子的案例。", |
| "这些复制子的名称必须能在宿主—共生体联合 pathway 页面上直接对应到氨基酸合成模块。", |
| "最终输出 surviving 案例中所有符合条件的 pathway-module-replicon 记录，并按 pathway 编号升序排列。" |
| ], |
| "exclusion_conditions": [ |
| "排除像 bmy+wbm 这样共生体 genome 页并没有满足命名 plasmid 要求的案例。", |
| "排除只按 pathway 名称沿 00380 等页面追查、没有回到联合 pathway 面核验 module 证据的结果。", |
| "排除复制子名称与模块关系不能在联合 pathway 图上直接成立的记录。" |
| ], |
| "normalization": { |
| "field_separator": "|", |
| "record_separator": ",", |
| "schema": [ |
| "group", |
| "symbiont", |
| "pathway", |
| "module", |
| "replicon", |
| "created_year" |
| ], |
| "group": "use the canonical host-symbiont group label from the source workflow, such as `api+buc`", |
| "symbiont": "use the bare lowercase KEGG organism code", |
| "pathway": "emit the numeric KEGG pathway ID without a `map` prefix", |
| "module": "normalize the KEGG module identifier to the `Mxxxxx` form", |
| "replicon": "preserve the named extra replicon exactly as displayed in the source, such as `pLeu` or `pTrp`", |
| "created_year": "emit the four-digit created year", |
| "sorting_or_selection": "pathway numeric ascending" |
| } |
| } |
| } |
|
|
