Okay, I need to figure out how the pathway enrichment analysis was conducted in this article. Let me start by looking through the Methods section and other parts of the paper for clues. First, the question is about the tool used for pathway enrichment. In the Statistical Analysis subsection under Methods, it mentions that metabolite enrichment was log-transformed and then subjected to pathway analysis in MetaboAnalyst version 4.0. So the tool is MetaboAnalyst, version 4.0. That answers the first two questions: tool is MetaboAnalyst, version is 4.0. Next, the gene set library. MetaboAnalyst typically uses databases like KEGG, HMDB, etc. The paper doesn't explicitly state which library, but since they mention pathways like "Alanine, aspartate, and glutamate metabolism" in the supplementary figures (like Figure S4), which is a KEGG pathway, it's likely they used KEGG. However, the exact library isn't specified in the text. Wait, in the Conclusions section, they mention "altered metabolism pathways using MetPA". MetPA is another tool, but maybe they used MetaboAnalyst with KEGG as the default? Hmm, the paper says MetaboAnalyst version 4.0. Let me check the references. The reference for MetaboAnalyst is [131], which is cited as "Xia Lab, McGill University... MetaboAnalyst". The user might not have access to the actual reference, but the main point is the article says MetaboAnalyst 4.0, and usually, MetaboAnalyst uses KEGG, but the exact library isn't mentioned here. Since the question asks what library was queried, but the text doesn't specify, maybe it's not described. Wait, in the results, they mention pathways by KEGG names? Let me check the Conclusions section again. They mention "Construction of the altered metabolism pathways using MetPA" in Figure S2 and S4. But the main text says MetaboAnalyst 4.0. The authors might have used KEGG pathways through MetaboAnalyst. However, the exact library isn't stated in the Methods, so maybe it's not described here. Wait, the question is about what was described in the article. The article's Methods section says they used MetaboAnalyst 4.0 for pathway analysis but doesn't specify the library. So the answer would be that it's not described? Or is KEGG the default? Hmm, maybe the authors didn't specify, so I should note that it's not described. Moving on, the third question: gene set library. Since they didn't specify, maybe the answer is "not described". Fourth question: was a background gene list defined? The Methods don't mention defining a background list. They talk about log-transforming metabolite enrichment and then using MetaboAnalyst. So probably not described. Fifth: statistical test used. The Methods section says they used MetaboAnalyst, but doesn't specify the statistical test. MetaboAnalyst usually uses Fisher's exact test or similar for enrichment. But since the authors didn't mention the exact test, so it's not described. Sixth: FDR correction. The Methods don't mention FDR correction. They talk about p-values but not correction. Unless it's part of MetaboAnalyst's default, but since they didn't specify, it's not described. Wait, but looking again at the Statistical Analysis section: "the metabolites obtained from global analysis were subjected to Kruskal–Wallis analysis, HCA, and AUC analysis..." Then pathway analysis via MetaboAnalyst. They mention using logistic regression with FDR? No, FDR isn't mentioned here. The only FDR mentioned is in the Supplementary Materials? Not in the main text. The question is about pathway enrichment specifically. Since the Methods don't mention FDR correction for the pathway analysis, the answer is no or not described. So compiling this: 1. Tool: MetaboAnalyst version 4.0. 2. Version: Yes, 4.0. 3. Library: Not described (since the text doesn't specify KEGG or another). 4. Background list: Not described. 5. Statistical test: Not described. 6. FDR correction: Not described. Wait, but in the references, maybe the MetaboAnalyst paper (Xia Lab's) uses certain defaults? But as per the article provided, the user can only go by what's written here. The authors didn't specify the library or statistical tests used within MetaboAnalyst. So according to the given text, those details aren't provided. So the answers are as above. 1. **Tool used for pathway enrichment analysis?** MetaboAnalyst version 4.0. 2. **Was a tool version number provided?** Yes, version 4.0. 3. **Gene set library queried (e.g., GO, KEGG, Reactome, or other)?** Not described. The article does not specify which library (e.g., KEGG, Reactome) was used within MetaboAnalyst. 4. **Was a background gene list defined for pathway enrichment analysis?** Not described. The methods do not mention defining a background list. 5. **Statistical test used for enrichment analysis?** Not described. The article does not specify the statistical test (e.g., Fisher’s exact test, hypergeometric test) employed within MetaboAnalyst. 6. **Was false discovery rate (FDR) correction used?** Not described. The methods do not mention FDR or multiple testing correction for pathway enrichment analysis.