Skip to content

Based on my review of GO-CAM model 60ad85f700003015 "'de novo' GMP biosynthetic process (Mouse)", I can provide the following assessment:

GO-CAM Model Review: 'de novo' GMP biosynthetic process (Mouse)

gomodel:60ad85f700003015

Overview

This GO-CAM model represents the 'de novo' GMP biosynthetic process in mouse (NCBITaxon:10090). It's a comprehensive pathway model that depicts the sequential enzymatic steps involved in GMP biosynthesis from the beginning of purine synthesis.

Strengths

  1. Comprehensive pathway representation: The model successfully captures the multi-step process of de novo GMP biosynthesis, including all key enzymatic steps from the beginning of purine synthesis through to the final GMP production.

  2. Causal connections: The model correctly uses the "provides input for" (RO:0002413) predicate to show the sequential flow of enzymatic reactions through the pathway.

  3. Evidence quality: Each activity in the model is supported by appropriate evidence codes and literature references (PMIDs), providing solid support for the annotations.

  4. Cellular location: Some activities appropriately specify cellular location (e.g., cytosol/GO:0005829), which enhances the biological accuracy of the model.

  5. Species specificity: The model is properly specified for mouse with mouse gene identifiers (MGI IDs).

Areas for Improvement

  1. Input/output molecules: While the causal flow of activities is well represented, the model would benefit from explicitly stating the input and output molecules for each activity. This would make the model more informative for users who may not be familiar with these enzymatic activities.

  2. Visualization organization: The pathway flow would be easier to follow if the activities were organized in a linear or branched representation that visually matches the pathway's biological progression.

  3. Complex representation: For any steps where the enzymatic activity is carried out by protein complexes, the model should follow GO-CAM best practices for representing complexes. The current model doesn't indicate whether any of these activities involve complexes.

  4. Regulatory information: The model could be enhanced by including regulatory information about how this pathway is controlled (e.g., feedback inhibition by end products).

Biological Accuracy

The model accurately represents the de novo GMP biosynthetic pathway: - It begins with amidophosphoribosyltransferase (GO:0004044) by PPAT (MGI:MGI:2387203) - Proceeds through phosphoribosylamine-glycine ligase (GO:0004637) by GART (MGI:MGI:95654) - Includes key steps like phosphoribosylglycinamide formyltransferase (GO:0004644), phosphoribosylformylglycinamidine synthase (GO:0004642), and others - Shows the branching to GMP synthesis via IMP dehydrogenase activity (GO:0003938) and GMP synthase activity (GO:0003922)

The evidence cited from the literature supports these activities and their connections.

Conclusion

This appears to be a well-constructed GO-CAM model that accurately represents the de novo GMP biosynthetic process in mouse. The model is supported by appropriate evidence and follows the GO-CAM modeling guidelines. The suggested improvements would make the model more informative and easier to interpret, but the basic biological content and relationships are sound.

The model would be valuable for researchers studying purine biosynthesis in mouse models and could serve as a reference for understanding how this fundamental metabolic pathway is organized.