SourceForge meeting 2015-12-14

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Reinstating DNA supercoiling activity

https://github.com/geneontology/go-ontology/issues/12197

TG requests

  • response to nitroglycerin
  • cellular response to nitroglycerin
  • response to microwave radiation
  • response to psychosocial stress
  • response to hypobaric hypoxia
  • sperm head plasma membrane
  • structural constituent of ascospore wall
  • meiotic double-strand break repair

Synapse Project

work on the synapse terms: problems arising from work + questions about general strategy.

Partitioning synaptic transmission

'synaptic transmission' is_a 'cell-cell signaling' but what are the pre and post-synaptic parts of this process?

'synaptic transmission: "The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse."


post_synaptic part = signal transduction ?

most of the pre-synaptic part is secretion (exocytosis). But there are some upstream bits. Re-use 'synaptic vesicle secretory pathway'? But what general classification should we have for this?

Some pattern questions

Does this pattern and naming look OK?

[Term] id: GO:0099551 name: trans-synaptic signaling by neuropeptide, modulating synaptic transmission namespace: biological_process def: "Cell-cell signaling between presynapse and postsynapse via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse." [GOC:dos] subset: goslim_synapse is_a: GO:0099540 ! trans-synaptic signaling by neuropeptide intersection_of: GO:0099537 ! trans-synaptic signaling intersection_of: mediated_by CHEBI:16670 ! peptide intersection_of: regulates GO:0007268 ! chemical synaptic transmission is_a: GO:0050804 { is_inferred = 'true' } | modulation of synaptic transmission

Note, added: 'regulation of biological process': EquivalentTo: biological_process that regulates some biological_process


Use of regulated_by

[Term] id: GO:0017156 name: calcium ion regulated exocytosis namespace: biological_process def: "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels." [GOC:go_curators] comment: Note that the calcium regulated exocytosis pathway can be leaky: some level of exocytosis via this pathway occurs spontaneously. This phenomenon underlies spontaneous neurotransmitter release from presynapses. This phenomenon is distinct from the unregulated, calcium independent exocytosis pathway. synonym: "calcium ion-dependent exocytosis" EXACT [] is_a: GO:0045055 ! regulated exocytosis intersection_of: GO:0045055 ! regulated exocytosis intersection_of: regulated_by GO:0007204 ! positive regulation of cytosolic calcium ion concentration

[Term] id: GO:1990504 name: dense core granule exocytosis namespace: biological_process def: "The secretion of molecules (e.g. neuropeptides, insulin-related peptides or neuromodulators such as serotonin and dopamine) contained within a membrane-bounced dense core granule by fusion of the granule with the plasma membrane of a cell in response to increased cytosolic calcium levels." [GOC:kmv, PMID:17553987, PMID:24653208] synonym: "dense core vesicle exocytosis" EXACT [] is_a: GO:0017156 ! calcium ion regulated exocytosis intersection_of: GO:0045055 ! regulated exocytosis intersection_of: has_input GO:0031045 ! dense core granule intersection_of: regulated_by GO:0007204 ! positive regulation of cytosolic calcium ion concentration

calcium ion transport and regulation of calcium ion concentration in cytosol

https://github.com/geneontology/synapse/issues/46#issuecomment-161320244

In GO, we embed the assumption that 'calcium ion transport into cytosol' increases the concentration of calcium ions in the cytosol:

  positive regulation of cytosolic calcium ion concentration
     <-- is_a calcium ion transport into cytosol
         <-- is_a  release of sequestered calcium ion into cytosol

This doesn't fit with the patterns proposed by VU

  positive regulation of cytosolic calcium ion concentration
     <-- part_of release of sequestered calcium ion into cytosol involved in positive regulation of cytosolic calcium ion concentration