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Table 2 Outline of ontology search strategies

From: Genome-wide analysis of pain-, nerve- and neurotrophin -related gene expression in the degenerating human annulus

Pain Ontologies:
A. Biological Process:
1. Sensory perception
 a. Sensory perception of pain:
  I. Regulation of sensory perception of pain
  II. Detection of chemical stimulus involved
  III. Detection of temperature stimulus involved
  IV. Detection of mechanical stimulus involved
2. Ion transport
3. Inflammatory response
4. Behavior
5. Response to pain:
 a. Behavioral response to pain
6. G-protein coupled receptor (protein) signaling pathway
7. Transmission of nerve impulse
8. Fatty acid catabolic process
B. Molecular Function:
1. 1. Carboxyl- or carbamoyl-transferase activity
2. Opioid peptide activity
3. Signal transducer activity
 a. G-protein coupled receptor activity
 b. Galanin receptor activity
 c. Bradykinin receptor activity
 d. Opioid receptor activity
 e. Adrenergic receptor activity
4. Voltage-gated channel activity
5. G-protein coupled receptor binding
C. Cellular component
1. Plasma lipoprotein particle
2. Axon
Nerve Ontologies:
A. Biological Process:
1. Neuron death
 a. Neuron apoptosis
  i. Positive regulation of neuron apoptosis
  ii. Negative regulation of neuron apoptosis
 a. Neurotrophin production
  iii. Neuroprotection
2. Neuropeptide signaling pathway
3. Transmission of nerve impulse
4. Nervous system development:
 a. Nerve development
 b. Neurogenesis
  i. Regulation of neurogenesis
   a. Positive regulation of neurogenesis
   b. Negative regulation of neurogenesis
  ii. Neuron differentiation
   a. Neuron projection development
  i. Axonogenesis regulation:
   a. Positive regulation of axonogenesis
   b. Negative regulation of axonogenesis
  iii. Neuroblast differentiation
  iv. Neuroblast proliferation
  v. Neuron migration
B. Molecular function:
1. Neurotrophin binding:
 a. Nerve growth factor binding
2. Neurotrophin receptor activity
3. Neurotransmitter receptor activity
 a. Substance P receptor activity
4. Calcitonin receptor binding
5. Vascular endothelial growth factor (-activated) receptor activity
6. Protein kinase activity
7. Neuropeptide hormone activity
8. Neuropeptide binding
9. Ciliary neurotrophic factor receptor binding
10. Neurotrophin receptor binding:
 a. Nerve growth factor receptor binding
C. Cellular component:
1. Neuron projection:
 a. Axon
 b. Dendrite
2. Endoplasmic reticulum lumen
3. Nuclear outer membrane