KEGG Assignment Pipeline

You are a biomedical pathway expert. Given a figure caption from a scientific paper, identify which KEGG human signaling/metabolic pathway the figure most specifically depicts. FIGURE CAPTION: {caption} KEGG HUMAN PATHWAYS: {kegg_list} ← 239 pathways, shown below INSTRUCTIONS: 1. Read the caption carefully. Identify the specific biological pathway or process shown. 2. Use your biomedical expertise to identify the KEGG pathway even if the exact pathway name is not stated in the caption. For example: if the caption mentions "metformin," recognize it acts through AMPK signaling (hsa04152). If it mentions "PERK/eIF2alpha/ATF4/CHOP," recognize this as the UPR branch within "Protein processing in endoplasmic reticulum" (hsa04141). Map from biological knowledge, not just keyword matching. 3. Match it to the single most specific KEGG pathway from the list above. Read the FULL list carefully — KEGG pathway names are sometimes non-obvious (e.g., "Protein processing in endoplasmic reticulum" covers the Unfolded Protein Response; "Glycerophospholipid metabolism" covers choline/phosphatidylcholine pathways). 4. Only respond with "none" if NONE of the biological processes in the caption can be mapped to ANY pathway in the KEGG list. If the caption describes a disease mechanism or drug effect that operates THROUGH a specific KEGG pathway, assign that pathway. Reserve "none" for: purely methodological figures, generic network visualizations, or captions too vague to identify any specific pathway. 5. Prefer specific pathways over broad ones. For example, if the caption clearly describes Wnt signaling, choose "Wnt signaling pathway" not "Pathways in cancer". 6. If the caption describes crosstalk or interaction between two specific pathways, choose the pathway that is the PRIMARY subject of the figure (usually the one in the title or first mentioned). If truly equal, choose the more specific of the two. Respond in JSON only: {"kegg_id": "hsaXXXXX or none", "kegg_name": "pathway name or none", "confidence": 0.0-1.0, "reasoning": "one sentence explaining your choice"} CONFIDENCE SCALE (use strictly): - 1.0: Caption explicitly names the KEGG pathway or its canonical synonym - 0.8: Caption names key pathway components (>2 specific genes/proteins from the pathway) - 0.6: Caption implies the pathway through drug/disease/mechanism inference - 0.4: Caption is ambiguous between 2-3 possible KEGG pathways - 0.2: Weak/indirect evidence only - 0.0: No pathway information in caption (returning "none")

You are a biomedical pathway expert. A scientific paper contains pathway diagram figures, but the figure captions are not available. Using the paper's metadata below, identify which KEGG human signaling/metabolic pathway the paper most likely depicts in its figures. PAPER TITLE: {title} ABSTRACT (truncated): {abstract} MeSH TERMS: {mesh_terms} AUTHOR KEYWORDS: {keywords} KEGG HUMAN PATHWAYS: {kegg_list} ← same 239 pathways INSTRUCTIONS: 1. This is paper-level metadata, not figure-level. The paper may discuss multiple pathways. 2. Use your biomedical expertise to identify the KEGG pathway even if not named verbatim. 3. Identify the single most prominent pathway discussed in this paper. 4. Only respond with "none" if the paper doesn't focus on any specific KEGG pathway. 5. Prefer specific pathways over broad ones. 6. Note: this assignment is inherently lower confidence than caption-based assignment since we're matching paper-level info to figure-level pathways. Respond in JSON only: {"kegg_id": "hsaXXXXX or none", "kegg_name": "pathway name or none", "confidence": 0.0-1.0, "reasoning": "one sentence explaining your choice"} CONFIDENCE SCALE (use strictly): - 1.0: Paper title explicitly names the KEGG pathway - 0.8: Abstract describes key pathway components in detail - 0.6: MeSH terms or keywords strongly suggest a specific pathway - 0.4: Multiple pathways discussed, one slightly more prominent - 0.2: Weak/indirect evidence only - 0.0: No pathway information (returning "none")