Noctua model curation tracking table

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Contributor(s) Broad Category Pathway WBProcess Noctua Model Title Genes GO Term(s), IDs Module(s) Noctua Model URL Model Status Annotation Issues To Do
Kimberly Apoptosis Execution phase Apoptotic process involved in development - C. elegans NSM sister cell death Development
Kimberly Apoptosis Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways Localization - C. elegans apoptotic cell engulfment ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1 Development
Kimberly Axon regeneration Rac module; upstream of JNK-MAPK C. elegans regulation of axon regeneration Development
Kimberly Dosage Compensation C. elegans X chromosome dosage compensation Development
EGF Signaling
FGF Signaling
Kimberly Distal tip cell migration Glycosylation The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme Development
Kimberly Dauer GPCR Signaling Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. Development
Jae, Jane, Kimberly Egg laying GPCR Signaling GRK-2 egg laying regulation JM Development 1 Finish up annotations for other genes in the paper
Kimberly Innate immune response GPCR Signaling The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity. Development
Kimberly Innate immune response GPCR Signaling and MAPK signaling C_elegans_defense_response_to_fungus Development
Kimberly Heterochronic pathway Control of C. elegans larval developmental timing - the heterochronic pathway Development
Kimberly Insulin Signaling Signaling - C. elegans insulin receptor signaling Development
Kimberly Germ line stem cell maintenance Notch Signaling C. elegans germline stem cell maintenance - Notch pathway Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648) Development
Kimberly Neuronal morphogenesis - AFD thermosensory neuron Receptor guanylyl cyclase Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape Development
Kimberly Olfactory behavior Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) Development
Kimberly Thermosensory behavior Cyclic nucleotide-gated ion channels C. elegans CNG-3 in non-motile cilium of AFD (same reference) cng-3 Development 1) How should we annotate different evidence for CC vs tissue? 2) Annotation extensions that don't use the same evidence code should not appear in the GPAD output. 3) Add relations for positive and negative effect for causally upstream of or within.
RTK Ras MAPK signaling Development
Kimberly Striated muscle mitochondrial patterning Receptor tyrosine phosphatase The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1 Development
Kimberly Germ line stem cell maintenance TGFbeta Signaling Linking the environment, DAF-7/TGFβ signaling and LAG-2/DSL ligand expression in the germline stem cell niche Development
Kimberly DA/DB motor neuron axon outgrowth Wnt Signaling The ENU-3 protein family members function in the Wnt pathway parallel to UNC-6/Netrin to promote motor neuron axon outgrowth in C. elegans. Development
Chris Q neuroblast descendant migration Wnt Signaling Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration canonical Wnt signaling pathway (GO:0060070), cell migration (GO:0016477), transcription from RNA polymerase II promoter (GO:0006366) Development

Annotations Issues

  1. What is the correct relation to use between an upstream MF that creates or removes a small molecule that is the input of a downstream MF?
  2. What is the correct way to evidence a CC when there is experimental data for expression at the tissue- or cellular level, but no subcellular localization?
  3. Where do the binding activities of a ligand and its receptor occur?
  4. How should the MFs of protein complexes and their constituent members be represented in GO-CAMs?