| { |
| "task_id": "genome_004", |
| "domain": "KEGG_GENOME", |
| "autonomy_type": "ordered table", |
| "oracle_output_cardinality": 2, |
| "instruction": "I am preparing a handout for a primate evolution course and want to summarize, in a two-row comparison table, the anomalous pattern behind why this lineage must obtain vitamin C from the diet. Among primate genome entries established by the end of 2022, identify the anomalous lower-level clade in which the upstream glucuronate module M00014 is still retained but the animal-type vitamin C biosynthesis module M00129 has been lost. Then verify the corresponding sister branch and confirm that it still retains M00129. Finally, output a two-row comparison table with columns 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. The first row should be EXCEPTION_CLADE and the second row RETAINED_SISTER_CLADE. In all rows, vitamin_c_synthesis_module is fixed as M00129; vitamin_c_module_status should be LOST for the first row and RETAINED for the second. Use KEGG organism codes for the example species.", |
| "start_url": "https://www.genome.jp/kegg/kegg2.html", |
| "output_format": "Output a two-row comparison table with columns 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": [ |
| "Search only among primate genome entries established by the end of 2022, and isolate the anomalous lower-level clade that retains the upstream glucuronate module M00014 but lacks the animal-type vitamin C biosynthesis module M00129.", |
| "That anomalous clade must be paired with a sister branch under the same higher-level split, and the sister branch must still retain M00129.", |
| "The final output must place the anomalous branch and the retained sister branch into a two-row comparison table, including the required pathway, module, and example-species fields." |
| ], |
| "dependency_type": "Data + Control", |
| "intra_chain": true, |
| "inter_chain": true, |
| "data_dependency": [ |
| "the KEGG primate clade pages and genome entries yield candidate subclades and example species established through the cutoff year", |
| "the 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 branch 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 view must make retained M00014 and missing M00129 visible together", |
| "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": [ |
| "Search only among primate genome entries established by the end of 2022, and isolate the anomalous lower-level clade that retains the upstream glucuronate module M00014 but lacks the animal-type vitamin C biosynthesis module M00129.", |
| "That anomalous clade must have a contrastable sister branch, and that sister branch must still retain M00129.", |
| "The final output must place the anomalous branch and the retained sister branch into a two-row comparison table, including the required pathway, module, and example-species fields." |
| ], |
| "exclusion_conditions": [ |
| "Exclude results that stop at Simiiformes without checking the broader boundary and therefore miss Haplorrhini.", |
| "Exclude pathway views that do not make the M00014 versus M00129 contrast visible together.", |
| "Exclude candidate clades that have not been validated against a retained sister branch." |
| ], |
| "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" |
| } |
| } |
| } |
|
|
