Skip to content

Based on the information gathered, I'll now provide my review of the GO-CAM model (gomodel:66187e4700001573) on RNA capping:

Review of GO-CAM Model: RNA capping (GO:0036260)

Model ID: gomodel:66187e4700001573

Overview

This model represents the RNA capping pathway in Schizosaccharomyces pombe (fission yeast), specifically focusing on the 7-methylguanosine mRNA capping process (GO:0006370). The model includes four key activities performed by different proteins:

  1. mRNA 5'-triphosphate monophosphatase activity (Pct1)
  2. mRNA guanylyltransferase activity (Ceg1)
  3. mRNA 5'-cap (guanine-N7)-methyltransferase activity (Pcm1)
  4. RNA polymerase II CTD regulatory activities (Rpb1 and Mcs6)

Biological Accuracy

The model correctly captures the key components of the RNA capping pathway in fission yeast. In contrast to budding yeast (S. cerevisiae) where the capping machinery enzymes interact directly with each other, the literature confirms that S. pombe capping enzymes don't necessarily interact with each other but can independently interact with RNA polymerase II.

The causal relationships between activities are supported by primary research literature, particularly: - The sequential process from Pct1 (triphosphatase) to Ceg1 (guanylyltransferase) to Pcm1 (methyltransferase) - The regulatory interactions of RNA Pol II (Rpb1) and the kinase Mcs6 in the process

Adherence to GO-CAM Best Practices

The model follows GO-CAM best practices in several areas:

  1. Activity representation: Each molecular function is appropriately associated with the protein that performs it
  2. Causal connections: The model uses appropriate causal relationship predicates: primarily RO:0002413 (provides input for) and RO:0002629 (directly positively regulates)
  3. Evidence: Each assertion is backed by appropriate evidence codes and PMIDs

Areas for Improvement

  1. Subcellular localization: The model includes cellular location information for some proteins (nucleus, P-TEFb-cap methyltransferase complex) but not all. This could be completed for the remaining proteins.

  2. Evidence details: Some of the PMIDs cited couldn't be retrieved in full, making it difficult to fully verify all supporting evidence. In particular, PMID:19328067 and PMID:11139608 couldn't be examined in detail.

  3. UniProt lookup issue: I attempted to look up the UniProt entries for some of the proteins, but encountered technical issues. It would be beneficial to confirm the precise functions of each protein from their UniProt entries.

  4. Redundant evidence: For some assertions, there are multiple identical pieces of evidence with the same PMID and contributor, which appears redundant.

Conclusion

The GO-CAM model (gomodel:66187e4700001573) is a biologically accurate and well-structured representation of the RNA capping process in S. pombe. It effectively captures the unique aspects of fission yeast capping machinery, where the enzymes operate independently rather than as a complex. The model correctly represents the sequential nature of the capping process and its regulation by RNA polymerase II.

The model adheres to GO-CAM best practices in terms of activity representation, causal relationships, and evidence citation. With minor improvements to complete subcellular localization information and consolidate redundant evidence, this would be an exemplary GO-CAM model.