{"gene":"TG_273580","gene_symbol":"COG2","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG2, was identified and characterized in Toxoplasma gondii tachyzoites and shown to play an essential role in protein transport; the study also identified novel partners of the COG complex critical for this trafficking function.","method":"Functional characterization of the COG complex in T. gondii tachyzoites, including identification of novel COG-interacting partners","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab study characterizing the COG complex with functional readouts, but abstract does not detail orthogonal methods or COG2-specific experiments beyond complex-level characterization","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"COG2 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii, which is essential for protein transport and glycosylation in tachyzoites, with the complex associating with novel parasite-specific partners that adapt the trafficking machinery to the parasite's specific needs."},"narrative":{"mechanistic_narrative":"COG2 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii, which in tachyzoites is essential for protein transport [PMID:37966241]. The COG complex associates with novel parasite-specific partners that are critical for its trafficking function [PMID:37966241]. Beyond this complex-level characterization, no further COG2-specific mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether Toxoplasma gondii possesses a functional Golgi trafficking machinery analogous to the COG complex was unresolved; identifying and functionally characterizing the COG complex established it as essential for protein transport in tachyzoites and revealed parasite-specific interacting partners.","evidence":"Functional characterization of the COG complex in T. gondii tachyzoites with identification of novel COG-interacting partners","pmids":["37966241"],"confidence":"Medium","gaps":["No COG2-specific experiments distinguishing its individual role from the complex as a whole","The identities and mechanistic roles of the novel COG-interacting partners are not detailed at the COG2 level","No structural or biochemical data on how COG2 assembles into or contributes to the complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":[],"other_free_text":["COG2 is a subunit of the COG complex in Toxoplasma gondii tachyzoites, which is essential for protein transport and associates 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":387,"usd":0.006987,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4982,"output_tokens":1083,"usd":0.025993,"stage2_stop_reason":"end_turn"},"total_usd":0.065865,"stage1_batch_id":"msgbatch_015xmQKDRqnTh9anE4m7LiD6","stage2_batch_id":"msgbatch_01JLpkFTVhoQBNgqHCKFrVVU","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 COG2, was identified and characterized in Toxoplasma gondii tachyzoites and shown to play an essential role in protein transport; the study also identified novel partners of the COG complex critical for this trafficking function.\",\n      \"method\": \"Functional characterization of the COG complex in T. gondii tachyzoites, including identification of novel COG-interacting partners\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab study characterizing the COG complex with functional readouts, but abstract does not detail orthogonal methods or COG2-specific experiments beyond complex-level characterization\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"COG2 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii, which is essential for protein transport and glycosylation in tachyzoites, with the complex associating with novel parasite-specific partners that adapt the trafficking machinery to the parasite's specific needs.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COG2 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii, which in tachyzoites is essential for protein transport [#0]. The COG complex associates with novel parasite-specific partners that are critical for its trafficking function [#0]. Beyond this complex-level characterization, no further COG2-specific mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether Toxoplasma gondii possesses a functional Golgi trafficking machinery analogous to the COG complex was unresolved; identifying and functionally characterizing the COG complex established it as essential for protein transport in tachyzoites and revealed parasite-specific interacting partners.\",\n      \"evidence\": \"Functional characterization of the COG complex in T. gondii tachyzoites with identification of novel COG-interacting partners\",\n      \"pmids\": [\"37966241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No COG2-specific experiments distinguishing its individual role from the complex as a whole\",\n        \"The identities and mechanistic roles of the novel COG-interacting partners are not detailed at the COG2 level\",\n        \"No structural or biochemical data on how COG2 assembles into or contributes to the complex\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular function of COG2 within the COG complex, its direct binding partners, and its individual contribution to Golgi trafficking and glycosylation remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No COG2-specific molecular activity or substrate identified\",\n        \"No structural model of COG2 or its interfaces within the complex\",\n        \"Mechanism by which COG2 contributes to protein transport not dissected\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0015031\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Conserved oligomeric Golgi (COG) complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"COG2 is a subunit of the COG complex in Toxoplasma gondii tachyzoites, which is essential for protein transport and associates with novel parasite-specific partners [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_273580","name":"COG2","product":"conserved oligomeric Golgi complex subunit 2","uniprot_acc":"S8F590","chromosome":"TGME49_chrVIII","start_pos":3366153},{"strain":"GT1","gene_id":"TGGT1_273580","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":3363343},{"strain":"RH88","gene_id":"TGRH88_078450","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023089","start_pos":8474730},{"strain":"VEG","gene_id":"TGVEG_273580","name":null,"product":"hypothetical protein","uniprot_acc":"A0A125YM40","chromosome":"TGVEG_chrVIII","start_pos":3375709}]}