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Let me review the model based on the information I have. I'll start by summarizing the activities and relationships in the model:

Review of GO-CAM Model: gomodel:623d156d00000939

Model Overview

  • Title: Glycogen catabolic process 3 (Mouse)
  • Taxon: NCBITaxon:10090 (Mouse)
  • Status: Production
  • Comments:
  • Automated change 2023-03-16: RO:0002213 replaced by RO:0002629
  • Sourced from: gomodel:R-HSA-70221

Model Content Summary

This GO-CAM model represents the glycogen catabolic process in mouse, involving various enzymes in the pathway of glycogen breakdown. The model includes:

  1. Phosphorylase kinase (Phkg1) - catalyzes phosphorylation of glycogen phosphorylase
  2. Glycogen phosphorylase (Pygm) - breaks down glycogen by cleaving α-1,4-glycosidic bonds
  3. Amylo-alpha-1,6-glucosidase (Agl) - removes branches in glycogen by cleaving α-1,6-glycosidic bonds
  4. Phosphoglucomutase (Pgm1, Pgm2) - converts glucose-1-phosphate to glucose-6-phosphate

Detailed Activity Breakdown

Activity 1 (gomodel:623d156d00000939/623d156d00000941)

  • Enabled by: MGI:MGI:97579 (Phkg1 - Phosphorylase kinase gamma 1)
  • Molecular Function: GO:0004689 (phosphorylase kinase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Causal relationship: Directly positively regulates (RO:0002629) Activity 4

Activity 2 (gomodel:623d156d00000939/623d156d00000949)

  • Enabled by: MGI:MGI:1924809 (Agl - Amylo-alpha-1,6-glucosidase)
  • Molecular Function: GO:0004134 (4-alpha-glucanotransferase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Causal relationship: Provides input for (RO:0002413) Activity 6

Activity 3 (gomodel:623d156d00000939/623d156d00000945)

  • Enabled by: MGI:MGI:97830 (Pygm - Muscle glycogen phosphorylase)
  • Molecular Function: GO:0008184 (glycogen phosphorylase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Causal relationships:
  • Provides input for (RO:0002413) Activity 7
  • Provides input for (RO:0002413) Activity 5
  • Provides input for (RO:0002413) Activity 2

Activity 4 (gomodel:623d156d00000939/623d156d00000945)

  • Enabled by: MGI:MGI:97830 (Pygm - Muscle glycogen phosphorylase)
  • Molecular Function: GO:0008184 (glycogen phosphorylase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)

Activity 5 (gomodel:623d156d00000939/623d156d00000953)

  • Enabled by: MGI:MGI:97565 (Pgm1 - Phosphoglucomutase-1)
  • Molecular Function: GO:0004614 (phosphoglucomutase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Has output: CHEBI:58225 (alpha-D-glucose 6-phosphate(2-))

Activity 6 (gomodel:623d156d00000939/623d156d00000947)

  • Enabled by: MGI:MGI:1924809 (Agl - Amylo-alpha-1,6-glucosidase)
  • Molecular Function: GO:0004135 (amylo-alpha-1,6-glucosidase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Causal relationship: Provides input for (RO:0002413) Activity 7

Activity 7 (gomodel:623d156d00000939/623d156d00000954)

  • Enabled by: MGI:MGI:97564 (Pgm2 - Phosphoglucomutase-2)
  • Molecular Function: GO:0004614 (phosphoglucomutase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Has output: CHEBI:58225 (alpha-D-glucose 6-phosphate(2-))

Activity 8 (gomodel:623d156d00000939/623d156d00000950)

  • Enabled by: MGI:MGI:97830 (Pygm - Muscle glycogen phosphorylase)
  • Molecular Function: GO:0008184 (glycogen phosphorylase activity)
  • Occurs in: GO:0005829 (cytosol)
  • Part of: GO:0005980 (glycogen catabolic process)
  • Causal relationships:
  • Provides input for (RO:0002413) Activity 7
  • Provides input for (RO:0002413) Activity 5

Review Assessment

Strengths

  1. The model correctly represents the key enzymes involved in glycogen catabolism in mouse.
  2. The spatial context (cytosol) is appropriately captured for all activities.
  3. The main biological process (glycogen catabolic process) is correctly linked to all activities.
  4. The causal relationships between activities generally follow the established biochemical pathway of glycogen breakdown.
  5. Evidence is provided for most of the activities with appropriate references to the literature.

Areas for Improvement

  1. Redundancy: There appears to be some redundancy in the representation of glycogen phosphorylase (Pygm) activities - Activities 3, 4, and 8 all describe the same molecular function (glycogen phosphorylase activity) by the same protein.

  2. Evidence Gaps: Some causal associations lack evidence annotations.

  3. Activity Disambiguation: The model would benefit from clearer distinction between the activities of the same enzyme in different contexts or steps of the pathway.

  4. Pathway Completeness: The model represents major steps in glycogen catabolism but could potentially include additional regulatory steps or connections to other metabolic pathways.

  5. Consistency with Literature: The evidence cited in PMID:24613482 strongly supports the roles of Agl in glycogen debranching, which is appropriately captured in the model.

Recommendations

  1. Consolidate Redundant Activities: Consider merging Activities 3, 4, and 8 (all representing glycogen phosphorylase activity by Pygm) into a single activity with appropriate causal relationships.

  2. Complete Evidence Documentation: Add evidence annotations to all causal associations.

  3. Clarify Activity Context: Provide more specific context for each activity if they represent different steps or conditions in the pathway.

  4. Expand Regulatory Relationships: Consider adding known regulatory relationships that control this pathway, such as hormonal regulation of glycogen metabolism.

Overall, this GO-CAM model provides a good representation of the glycogen catabolic pathway in mouse, with a logical flow of activities that matches the known biochemistry. With the suggested refinements, it could be an even more valuable resource for understanding glycogen metabolism.