Difference between revisions of "Noctua model curation tracking table"

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| Apoptosis
 
| Apoptosis
 
| Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways
 
| Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways
 +
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| Localization - C. elegans apoptotic cell engulfment  
 
| Localization - C. elegans apoptotic cell engulfment  
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| ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1
 
| ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1
 
|  
 
|  
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| Axon regeneration
 
| Axon regeneration
 
| Rac module; upstream of JNK-MAPK
 
| Rac module; upstream of JNK-MAPK
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| C. elegans regulation of axon regeneration
 
| C. elegans regulation of axon regeneration
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| Kimberly
 
| Kimberly
 
| Dosage Compensation
 
| Dosage Compensation
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| C. elegans X chromosome dosage compensation
 
| C. elegans X chromosome dosage compensation
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| Distal tip cell migration
 
| Distal tip cell migration
 
| Glycosylation
 
| Glycosylation
 +
|
 
| The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme  
 
| The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme  
 
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| Dauer
 
| Dauer
 
| GPCR Signaling
 
| GPCR Signaling
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| Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans.  
 
| Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans.  
|
 
 
|  
 
|  
 
|
 
|
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| Egg laying
 
| Egg laying
 
| GPCR Signaling
 
| GPCR Signaling
 +
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| GRK-2 egg laying regulation JM  
 
| GRK-2 egg laying regulation JM  
 
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|
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| Innate immune response
 
| Innate immune response
 
| GPCR Signaling
 
| GPCR Signaling
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| The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity.  
 
| The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity.  
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|  
 
|  
 
|
 
|
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| Innate immune response
 
| Innate immune response
 
| GPCR Signaling and MAPK signaling
 
| GPCR Signaling and MAPK signaling
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| C_elegans_defense_response_to_fungus  
 
| C_elegans_defense_response_to_fungus  
 
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|
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|
 
|
 
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| Kimberly
 
| Kimberly
 
| Heterochronic pathway
 
| Heterochronic pathway
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|
 
|
 
| Control of C. elegans larval developmental timing - the heterochronic pathway  
 
| Control of C. elegans larval developmental timing - the heterochronic pathway  
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|
 
|
 
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|  
 
|  
 
| Insulin Signaling
 
| Insulin Signaling
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| Signaling - C. elegans insulin receptor signaling  
 
| Signaling - C. elegans insulin receptor signaling  
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|
 
|
 
|
 
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| Germ line stem cell maintenance
 
| Germ line stem cell maintenance
 
| Notch Signaling
 
| Notch Signaling
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| C. elegans germline stem cell maintenance - Notch pathway
 
| 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)
 
| Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459),  positive regulation of stem cell proliferation (GO:2000648)
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| Neuronal morphogenesis - AFD thermosensory neuron
 
| Neuronal morphogenesis - AFD thermosensory neuron
 
| Receptor guanylyl cyclase
 
| Receptor guanylyl cyclase
 +
|
 
| Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape
 
| Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape
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|
 
|
 
|  
 
|  
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| Olfactory behavior
 
| Olfactory behavior
 
|  
 
|  
 +
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| Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255)
 
| Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255)
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|
 
|
 
|  
 
|  
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| Thermosensory behavior
 
| Thermosensory behavior
 
| Cyclic nucleotide-gated ion channels
 
| Cyclic nucleotide-gated ion channels
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| C. elegans CNG-3 in non-motile cilium of AFD (same reference)
 
| C. elegans CNG-3 in non-motile cilium of AFD (same reference)
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| cng-3
 
| cng-3
 
|  
 
|  
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| Striated muscle mitochondrial patterning
 
| Striated muscle mitochondrial patterning
 
| Receptor tyrosine phosphatase
 
| Receptor tyrosine phosphatase
 +
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| The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1  
 
| The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1  
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|  

Revision as of 18:00, 19 March 2018

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 http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001432 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 http://noctua.berkeleybop.org/editor/graph/gomodel:56aac7ad00000175 Development
Kimberly Axon regeneration Rac module; upstream of JNK-MAPK C. elegans regulation of axon regeneration http://noctua.berkeleybop.org/editor/graph/gomodel:591f58ab00000003 Development
Kimberly Dosage Compensation C. elegans X chromosome dosage compensation http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000147 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 http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000138 Development
Kimberly Dauer GPCR Signaling Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000454 Development
Jae, Jane, Kimberly Egg laying GPCR Signaling GRK-2 egg laying regulation JM http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000287 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. http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000158 Development
Kimberly Innate immune response GPCR Signaling and MAPK signaling C_elegans_defense_response_to_fungus http://noctua.berkeleybop.org/editor/graph/gomodel:564622cc00000003 Development
Kimberly Heterochronic pathway Control of C. elegans larval developmental timing - the heterochronic pathway http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000246 Development
Kimberly Insulin Signaling Signaling - C. elegans insulin receptor signaling http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696 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) http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750 Development
Kimberly Neuronal morphogenesis - AFD thermosensory neuron Receptor guanylyl cyclase Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000192 Development
Kimberly Olfactory behavior Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) http://noctua.berkeleybop.org/editor/graph/gomodel:59237a3c00000026 Development
Kimberly Thermosensory behavior Cyclic nucleotide-gated ion channels C. elegans CNG-3 in non-motile cilium of AFD (same reference) cng-3 http://noctua.berkeleybop.org/editor/graph/gomodel:5900dc7400001096 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.
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 http://noctua.berkeleybop.org/editor/graph/gomodel:5970219a00000566 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 http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000074 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. http://noctua.berkeleybop.org/editor/graph/gomodel:598826eb00000296 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) http://noctua.berkeleybop.org/editor/graph/gomodel:595a9ee700000584 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?