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663d668500000596 oxidative phosphorylation GO 0006119

Based on my review of the GO-CAM model and the relevant documentation, here is my assessment of the model gomodel:663d668500000596 on "oxidative phosphorylation":

Review Summary

This model represents the oxidative phosphorylation process in Schizosaccharomyces pombe (fission yeast), focusing on the electron transport chain components and their relationships.

Strengths:

  1. Appropriate use of protein complexes: The model correctly represents respiratory chain complexes II, III, and IV using ComplexPortal IDs and lists all constituent subunits as members, following the best practices for complex annotation.

  2. Correct molecular functions: Each complex or protein is assigned the appropriate molecular function:

  3. Complex II (CPX-566): electron transfer activity (GO:0009055)
  4. Complex III (CPX-9308): ubiquinol-cytochrome-c reductase activity (GO:0008121)
  5. Complex IV (CPX-9641): cytochrome-c oxidase activity (GO:0004129)
  6. NADH dehydrogenase (ndi1): NADH dehydrogenase activity (GO:0008137)

  7. Cytochrome c (cyc1): electron transfer activity (GO:0009055)

  8. Correct cellular localization: Components are appropriately placed in mitochondrial compartments:

  9. Complexes II, III, IV: mitochondrial inner membrane (GO:0005743)
  10. NADH dehydrogenase: mitochondrial matrix (GO:0005759)

  11. Cytochrome c: mitochondrial intermembrane space (GO:0005758)

  12. Appropriate causal relationships: The model captures the flow of electrons through the respiratory chain using the "provides input for" (RO:0002413) predicate.

Areas for Improvement:

  1. Incomplete evidence for some causal associations: I noticed several causal associations have no evidence annotations:
  2. The link from complex II to complex III
  3. The first link from cytochrome c to complex IV

  4. The link from complex II to cytochrome c

  5. Redundant causal associations: There are duplicate causal assertions between some components:

  6. Two identical causal associations from complex III to cytochrome c
  7. Two identical causal associations from cytochrome c to complex IV

This redundancy may make the model less clear and should be eliminated by keeping only one well-evidenced association.

  1. Missing complex I: While the model includes ndi1 (NADH dehydrogenase), there is no representation of the complete respiratory chain complex I. The comment in the model ("Add etf1 complex") suggests additional components are planned to be added.

  2. Model comments suggest incomplete work: The comments indicate the model is still under development:

  3. "Testing how a complex renders. Waiting for the other complexes to build electron transport chain"
  4. "Add etf1 complex"

Biological Accuracy:

The biological flow of electrons is generally correct, matching the established path in the electron transport chain: 1. NADH dehydrogenase (ndi1) → Complex II 2. Complex II → Complex III (though there's also a direct link to cytochrome c which may be redundant) 3. Complex III → cytochrome c 4. cytochrome c → Complex IV

The biological processes are also correctly annotated for each activity: - ndi1: mitochondrial electron transport, NADH to ubiquinone (GO:0006120) - Complex III: mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122) - Complex IV: mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)

Recommendations:

  1. Remove redundant causal links: Eliminate duplicate causal assertions between components.

  2. Add evidence to all causal associations: Ensure all causal links have appropriate evidence annotations.

  3. Complete the model: Add the ETF1 complex as mentioned in the comments, and consider adding ATP synthase (Complex V) to complete the oxidative phosphorylation pathway.

  4. Clean up comments: Once development is complete, update or remove the comments that indicate the model is still under development.

  5. Clarify the role of complex II: In the standard electron transport chain, NADH dehydrogenase (Complex I) typically leads to ubiquinone, which then interacts with Complex III, while Complex II (succinate dehydrogenase) is a separate input to ubiquinone. The current model shows ndi1 providing input to Complex II, which may need to be revisited for biological accuracy.

Overall, this is a mostly well-constructed model that represents the core components of oxidative phosphorylation in fission yeast, but would benefit from the improvements noted above to increase its biological accuracy and adherence to GO-CAM curation standards.