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61f34dd300001044 Yeast ergosterol

GO-CAM Review for Model gomodel:61f34dd300001044 "Yeast ergosterol"

Summary:

This model represents the ergosterol biosynthetic pathway in yeast, showing the sequence of enzymatic activities that lead to the production of ergosterol. It contains 25 activities carried out by different enzymes, with each step converting specific chemical compounds as part of the GO:0006696 (ergosterol biosynthetic process).

Strengths:

  1. Comprehensive Pathway Representation: The model provides a detailed representation of the entire ergosterol biosynthetic pathway, with each enzymatic step properly annotated.

  2. Appropriate Evidence and References: Each activity is supported by evidence codes (ECO terms) and references to scientific literature (PMIDs).

  3. Clear Input/Output Relationships: Most activities clearly specify their chemical inputs and outputs with CHEBI terms, establishing the flow of metabolites through the pathway.

  4. Cellular Locations: Most activities specify where they occur within the cell (endoplasmic reticulum, vacuole, or mitochondrion).

Issues Identified:

  1. Limited Causal Connections: While the model represents a linear metabolic pathway, only two causal connections are explicitly defined:
  2. SGD:S000004741 (ERG29) causally upstream of (positive effect) the C-4 methylsterol oxidase activity (ERG25)
  3. The activity of SGD:S000002969 (ERG26) provides input for the 3-keto sterol reductase activity (ERG27)

The model would benefit from explicit causal connections between all steps in the pathway to clearly show the sequential nature of the reactions.

  1. Duplicate Inputs/Outputs: Some activities have duplicate entries for the same molecule:
  2. Activity gomodel:61f34dd300001044/61f34dd300001167 (ERG11) has three identical outputs of CHEBI:17813
  3. Activity gomodel:61f34dd300001044/61f34dd300001179 (ERG24) has duplicate inputs of CHEBI:17813

  4. Activity gomodel:61f34dd300001044/61f34dd300001208 (ERG26) has duplicate inputs of CHEBI:64925

  5. Taxonomic Discrepancy: The model's taxon is listed as "NCBITaxon:9823" (which is pig/Sus scrofa), but all gene products are from yeast (SGD identifiers). The taxon should be changed to a yeast taxon (likely NCBITaxon:4932 for S. cerevisiae).

  6. Missing Information for Some Activities: Some activities lack complete information:

  7. Activity gomodel:61f34dd300001044/6205c24300000094 (ERG29) has a general molecular_function (GO:0003674) rather than a specific one

Recommendations:

  1. Add Missing Causal Connections: Add "provides input for" (RO:0002413) connections between sequential activities in the pathway to clearly show the metabolic flow.

  2. Fix Taxonomic Information: Update the taxon to the correct yeast species (NCBITaxon:4932).

  3. Remove Duplicate Inputs/Outputs: Clean up the duplicate molecules in the activities mentioned above.

  4. Specify More Precise Function for ERG29: If possible, update the general molecular function (GO:0003674) for ERG29 to a more specific term.

  5. Ensure All Activities Have Location Information: Some activities may be missing cellular location information.

Overall, this is a well-constructed GO-CAM model that accurately represents the ergosterol biosynthetic pathway in yeast. With the suggested improvements, particularly adding causal connections between sequential steps, it would be even more valuable for representing the full pathway structure.