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5745387b00001516 Canonical glycolysis 1 Mouse

Based on the information gathered, I'll now review the GO-CAM model gomodel:5745387b00001516 titled "Canonical glycolysis 1 (Mouse)".

GO-CAM Review: Canonical glycolysis 1 (Mouse)

Overview

This model represents the canonical glycolysis pathway in mouse (NCBITaxon:10090), which was sourced from model R-HSA-70171. The model is in production status and depicts the enzymatic steps of glycolysis, showing the flow of activity through the pathway.

Structure Review

The model captures the glycolytic pathway from glucokinase (HK1) to pyruvate kinase (PKM), representing all key enzymatic steps in the pathway. All enzymes are appropriately enabled by their respective mouse gene products and connected in a sequential manner using the RO:0002413 ("provides input for") causal relationship, which is appropriate for metabolic pathways.

Content Completeness and Accuracy

  1. Complete pathway representation: All essential enzymatic steps of canonical glycolysis are included:

  2. Glucokinase (HK1) → Glucose-6-phosphate isomerase (GPI1) → Phosphofructokinase (PFKM) → Aldolase (ALDOA) → Triosephosphate isomerase (TPI1) → Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) → Phosphoglycerate kinase (PGK1) → Phosphoglycerate mutase (PGAM2) → Enolase (ENO3) → Pyruvate kinase (PKM)

  3. Proper evidence: Each activity is supported by appropriate experimental evidence, primarily direct assays (ECO:0000314) and mutant phenotype evidence (ECO:0000315) from relevant publications.

  4. Cellular location: All activities are properly located in the cytosol (GO:0005829), which is correct for glycolysis.

  5. Biological process: All activities are correctly annotated as part of canonical glycolysis (GO:0061621).

Causal Relationships

The model correctly uses RO:0002413 ("provides input for") to connect the sequential activities of the glycolytic enzymes, accurately representing the metabolic flow from glucose to pyruvate.

An interesting aspect to note is that the model correctly represents the branching after aldolase (ALDOA), where both triose-phosphate isomerase (TPI1) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) can receive input from aldolase, reflecting the biochemical reality of the pathway.

Evidence Support

Each activity and causal relationship is adequately supported by published evidence, with multiple references for most assertions. The evidence types used (direct assay, mutant phenotype, genetic interaction) are appropriate for a metabolic pathway model.

Compliance with GO-CAM Best Practices

The model follows best practices for GO-CAM modeling: 1. Appropriate causal relationships 2. Correct representation of enzymatic activities 3. Proper evidence citation 4. Inclusion of cellular locations 5. Association with the proper biological process term

Suggestions for Improvement

While this model is well-constructed and accurate, there are a few potential improvements:

  1. Some evidence links, like PMID:27103217, are used across multiple activities. It may be worth verifying that this publication provides specific evidence for each assertion where it's cited.

  2. Although not required, substrate/product information could enhance the comprehensibility of the model, particularly for users less familiar with the details of glycolysis.

Conclusion

The GO-CAM model gomodel:5745387b00001516 is a high-quality representation of the canonical glycolysis pathway in mouse. It accurately captures the enzymatic activities, their sequential relationships, and provides appropriate evidence for all assertions. The model is parsimonious while being comprehensive, making it easy for users to understand the glycolytic pathway.

The model successfully represents how glycolysis proceeds from glucose processing through ten enzymatic steps to produce pyruvate, with each step properly annotated and evidenced. No significant issues or inaccuracies were identified during this review.