Noctua Manual: General Guidelines for Model Titles

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  • All GO-CAM models require a title
  • While currently there are no strictly enforced rules for naming a model, curators should consider that the more informative the title is for end users, the easier it will be for them to browse a list of GO-CAM models and find what they're looking for
  • Since not all Noctua users create causal models every time they curate, we've created guidelines for naming different types of models.

Models Representing a Biological Process or Pathway

  • Include:
    • GO Biological Process term that best represents the biological process or pathway being modeled
    • Additional biological context, such as cells, tissues, specific genes, if not already represented in the GO BP term but helpful for distinguishing models
    • Species
      • If there are two species (host-symbiont), separate species with hyphen
    • Examples:
      • BMP signaling pathway via dpp-tkv/put (D.mel)
      • 'de novo' AMP biosynthetic process (Mouse)
      • Antifungal innate immune response in the hypodermis via transforming growth factor beta receptor signaling pathway (C. elegans)
      • Mumps-V inhibition of STAT1/STAT3 via DDB1/CUL4A (Human-Paramyxovirus)

Gene-Centric Models

  • Gene-centric models are generated by manual annotation, or as part of the imports project, in which annotation groups import all of their 'standard' manual GO annotations into Noctua.
  • These models are named enabled by 'Gene X' (Species), or Gene X (ID)