Skip to content

5fadbcf000000480 UMP catabolic process Mouse

Now I have enough information to proceed with a comprehensive review of GO-CAM model gomodel:5fadbcf000000480, titled "UMP catabolic process (Mouse)".

GO-CAM Review: UMP catabolic process (Mouse) - gomodel:5fadbcf000000480

Overall Assessment

This model represents the UMP catabolic process in mouse, showing multiple enzymatic activities involved in the pathway with their respective causal connections. The model depicts a biochemical pathway where UMP is catabolized through a series of enzymatic reactions.

Strengths

  1. Appropriate use of causal connections: The model uses RO:0002413 "provides input for" predicate to connect the activities in a logical sequence, which is appropriate for this metabolic pathway.

  2. Spatial organization: Most activities are annotated as occurring in the cytosol (GO:0005829), which is consistent with known cellular localization of this pathway. One activity is appropriately annotated to occur in the mitochondrion (GO:0005739).

  3. Evidence support: The model cites multiple PMIDs to support the activities and connections, showing a good level of literature support.

  4. Taxonomic specificity: The model is correctly specified for mouse (NCBITaxon:10090).

Issues and Recommendations

  1. Incomplete process annotations: Not all activities have "part_of" associations connecting them to the UMP catabolic process (GO:0046050). Specifically:
  2. The activity enabled by MGI:MGI:2146052 (Agxt2) lacks a part_of association to GO:0046050
  3. The activity enabled by MGI:MGI:1354954 (Nt5c) lacks a part_of association to GO:0046050
  4. The activity enabled by MGI:MGI:2143535 (Upb1) lacks a part_of association to GO:0046050

Recommendation: Add "part_of" associations to connect all relevant activities to GO:0046050 to ensure completeness.

  1. Missing evidence for spatial location: The cytosolic localization of MGI:MGI:2146052 (Agxt2) has no evidence. However, this protein is annotated as occurring in mitochondrion which may be correct, but evidence should be added.

Recommendation: Add evidence to support the subcellular localization.

  1. Pathway completeness: While the model covers key steps in UMP catabolism, there are some potential gaps in the pathway representation:
  2. The connection between MGI:MGI:2143535 (Upb1, beta-ureidopropionase) and any further metabolic steps is missing

Recommendation: Consider adding the complete catabolic path to show the final products of UMP degradation.

  1. Missing/incomplete evidence: Some of the causal connections have evidence from references that we were unable to verify due to lack of full text access (PMID:14715930, PMID:7744869).

Recommendation: Ensure all evidence is properly reviewed and documented.

  1. Potential inconsistency in gene product orthology: Some activities use evidence with "ECO:0000266" (sequence orthology evidence) referring to human proteins (e.g., UniProtKB:Q9H0P0, UniProtKB:Q8TCD5). While orthology-based annotation is valid, it would be better to directly cite mouse-specific evidence where available.

Recommendation: Where possible, replace orthology-based evidence with direct experimental evidence in the mouse model system.

GO-CAM Best Practice Conformance

Based on the GO-CAM best practices:

  1. Causal relationships: The model appropriately uses the "provides input for" predicate (RO:0002413) for metabolic pathways, which conforms to GO-CAM best practices.

  2. Complex representation: The model doesn't include any protein complexes, which is appropriate as the individual enzymatic activities are clearly attributed to specific gene products.

  3. Evidence quality: The model uses a mix of direct experimental evidence (ECO:0000314) and sequence orthology evidence (ECO:0000266), which is acceptable but could be improved with more direct evidence where possible.

Conclusion

This GO-CAM model effectively represents the UMP catabolic process in mouse with appropriate causal connections, evidence, and cellular localizations. With minor improvements to process annotations and evidence documentation, this would be an excellent model of this metabolic pathway. The model is parsimonious and should be understandable to a human viewer familiar with biochemical pathways.