{"gene":"TG_240540","gene_symbol":"COG8","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG8, was identified and characterized in T. gondii tachyzoites; the COG complex plays an essential role in protein transport and is associated with novel partners critical for Golgi-mediated trafficking in this parasite.","method":"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (genetic/cell biological approaches implied by 'identified and characterized')","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single paper, abstract-level description with no explicit mechanistic detail specific to COG8; complex-level finding inferred from abstract","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"COG8 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, which plays an essential role in Golgi-mediated protein transport and glycosylation, with the parasite having expanded the complex's functional repertoire through novel partner proteins."},"narrative":{"mechanistic_narrative":"COG8 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, a complex that plays an essential role in Golgi-mediated protein transport and is associated with novel partner proteins critical for trafficking in this parasite [PMID:37966241]. Beyond this complex-level characterization [PMID:37966241], no further mechanistic detail specific to COG8 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether T. gondii possesses a functional COG complex and how it is organized was unknown; identification of the complex including COG8 established that this parasite maintains a COG-based Golgi trafficking machinery and has expanded it with novel partners.","evidence":"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites","pmids":["37966241"],"confidence":"Low","gaps":["Abstract-level description with no mechanistic detail specific to COG8's individual role within the complex","The specific novel partners and their interactions with COG8 are not resolved","No structural or biochemical assignment of COG8 function distinct from the complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":[],"other_free_text":["COG8 is a subunit of the T. gondii COG complex, which is essential for Golgi-mediated protein transport and is associated with novel parasite-specific partners [#0]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"37966241","id":"PMC_37966241","title":"Essential role of the conserved oligomeric Golgi complex in Toxoplasma gondii.","date":"2023","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/37966241","citation_count":7,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2723,"output_tokens":352,"usd":0.006724,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4929,"output_tokens":1103,"usd":0.02611,"stage2_stop_reason":"end_turn"},"total_usd":0.065582,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"re-read with subject anchor"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"The conserved oligomeric Golgi (COG) complex, which includes COG8, was identified and characterized in T. gondii tachyzoites; the COG complex plays an essential role in protein transport and is associated with novel partners critical for Golgi-mediated trafficking in this parasite.\",\n      \"method\": \"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (genetic/cell biological approaches implied by 'identified and characterized')\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single paper, abstract-level description with no explicit mechanistic detail specific to COG8; complex-level finding inferred from abstract\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"COG8 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, which plays an essential role in Golgi-mediated protein transport and glycosylation, with the parasite having expanded the complex's functional repertoire through novel partner proteins.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"COG8 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, a complex that plays an essential role in Golgi-mediated protein transport and is associated with novel partner proteins critical for trafficking in this parasite [#0]. Beyond this complex-level characterization [#0], no further mechanistic detail specific to COG8 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether T. gondii possesses a functional COG complex and how it is organized was unknown; identification of the complex including COG8 established that this parasite maintains a COG-based Golgi trafficking machinery and has expanded it with novel partners.\",\n      \"evidence\": \"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites\",\n      \"pmids\": [\n        \"37966241\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Abstract-level description with no mechanistic detail specific to COG8's individual role within the complex\",\n        \"The specific novel partners and their interactions with COG8 are not resolved\",\n        \"No structural or biochemical assignment of COG8 function distinct from the complex\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular activity, binding partners, and substrate-transport role of COG8 as an individual subunit within the T. gondii COG complex remain uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No COG8-specific interaction map\",\n        \"No characterization of COG8's contribution to Golgi glycosylation or trafficking independent of the complex\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006888\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"Conserved oligomeric Golgi (COG) complex\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"COG8 is a subunit of the T. gondii COG complex, which is essential for Golgi-mediated protein transport and is associated with novel parasite-specific partners [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_240540","name":"COG8","product":"conserved oligomeric Golgi complex subunit 8","uniprot_acc":"A0A125YTG0","chromosome":"TGME49_chrVI","start_pos":1311713},{"strain":"GT1","gene_id":"TGGT1_240540","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVI","start_pos":1284468},{"strain":"RH88","gene_id":"TGRH88_030600","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023087","start_pos":2395883},{"strain":"VEG","gene_id":"TGVEG_240540","name":null,"product":"putative oligomeric component 8","uniprot_acc":"V4ZGG9","chromosome":"TGVEG_chrVI","start_pos":1328825}]}