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622aace900000962 Pentose phosphate shunt 1 Mouse

Based on my review of the GO-CAM model gomodel:622aace900000962 titled "Pentose-phosphate shunt 1 (Mouse)", I'll provide a comprehensive assessment:

Model Summary

This model represents the pentose phosphate pathway (PPP) in mouse, focusing on the enzymatic activities and their connections in this essential metabolic pathway. The model includes both the oxidative and non-oxidative branches of the PPP.

Overall Assessment

The model is generally well constructed and adheres to GO-CAM best practices. It captures the key enzymatic reactions of the PPP and their causal relationships appropriately.

Strengths

  1. Appropriate molecular functions: Each enzyme is associated with the correct molecular function (e.g., G6PD with glucose-6-phosphate dehydrogenase activity).
  2. Proper cellular localization: The activities are correctly located in the cytosol (GO:0005829).
  3. Causal flow: The causal relationships between activities using "provides input for" (RO:0002413) accurately reflect the metabolic flow of the pathway.
  4. Evidence support: Most activities have appropriate evidence codes with relevant PMIDs.
  5. Taxon specificity: The model is properly specified for mouse (NCBITaxon:10090).

Areas for Improvement

  1. Inconsistent biological process annotations:
  2. Some activities are annotated to "pentose-phosphate shunt" (GO:0006098) while others to "pentose-phosphate shunt, oxidative branch" (GO:0009051)

  3. For clarity and consistency, it would be better to use the more specific terms throughout (distinguishing oxidative vs. non-oxidative branch activities)

  4. Missing evidence for some assertions:

  5. Some cellular localization evidence is missing (e.g., for MGI:MGI:105977 and MGI:MGI:1913421)

  6. Some biological process associations lack evidence (e.g., for MGI:MGI:105977)

  7. Potential redundancy:

  8. There are two separate activities for transketolase (Tkt) with the same function (GO:0004802) - gomodel:622aace900000962/622aace900000984 and gomodel:622aace900000962/622aace900000980

  9. This appears redundant and could be consolidated into a single activity

  10. Missing has_input associations:

  11. While "has_output" associations are included for some activities, the corresponding "has_input" associations are missing

  12. For example, NADP+ as input for G6PD activities, glucose-6-phosphate as input, etc.

  13. No complex annotations:

  14. The model doesn't include any protein complexes, which is appropriate since the PPP enzymes generally function as individual proteins, not as complexes

Biological Content Assessment

The model accurately represents the pentose phosphate pathway in mouse:

  1. The oxidative phase is represented by:
  2. G6PD (glucose-6-phosphate dehydrogenase) - G6pd2 and G6pdx
  3. PGLS (6-phosphogluconolactonase)

  4. PGD (6-phosphogluconate dehydrogenase)

  5. The non-oxidative phase is represented by:

  6. RPE (ribulose-5-phosphate-3-epimerase)
  7. RPIA (ribose-5-phosphate isomerase)
  8. TKT (transketolase)
  9. TALDO1 (transaldolase)

The causal flow correctly demonstrates how these enzymes work sequentially in the pathway, with appropriate outputs (NADPH, fructose-6-phosphate).

Recommendations

  1. Harmonize the biological process annotations - consistently use the specific branch terms (oxidative or non-oxidative) where appropriate.

  2. Add missing evidence for cellular location and biological process assertions.

  3. Consolidate redundant transketolase activities into a single representation.

  4. Add "has_input" associations to better represent the substrates for each reaction.

  5. Consider adding more detailed regulation information if available in the literature.

This model is scientifically accurate and generally well-constructed, requiring only minor improvements to better conform to GO-CAM best practices.