Ontology meeting 2023-10-09

• Group members: Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, Chris, Paul
• Present: Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
• Regrets: David,

Guidelines needed

Cross references for obsolete terms

should we keep cross-references and def cross references? I have been removing them, since it can be confusing, but we dont have official guidelines can we remove comments about transferred EC: 'Formerly EC:x.x.x.x'? I dont think this is up to GO to maintain that history; also, some ECs get transferred multiple times, this information is very inconsistent.

DECISIONS

• only link to valid EC terms (using BROAD and NARROW xreferences as needed)
• Can keep the xref on an obsolete GO term (or move it to a more general valid GO term)
• Will not keep EC's history, ie remove 'Formerly EC:xxx'

Enzymatic directional reactions

See https://github.com/geneontology/go-ontology/issues/26213#issuecomment-1748877420 David: "Historically, if the reaction was thought to never proceed in both directions, we made the MF directional." ... was this practice changed? ie when we decided to use non-directional RHEA ?

• Some directionality was changed here for bi-directional
• If we use a directional reaction, do we map to the RHEA directional?
• Most reactions are directional, physiologically, right?

DECISION If opposite reactions are known to occurs physiologically and be catalyzed by different enzymes, then we create two GO terms and link to directional RHEAs.

Discussion points

Switching from has in/output to has primary in/output

• TBC OK to merge, in the sense that the inferences are no worse than current and no equivalent terms are being created
• Need to disallow use of 'has input'

Issues has input

• Need guidelines to complete changes for 'signaling receptor activity', see

https://github.com/geneontology/go-ontology/issues/26217

Issues has output

New inferences: https://github.com/geneontology/go-ontology/commit/38646a101ca1dd104f8bf57b76442c38944ec4c4#commitcomment-129159526

• Some 'assembly' terms use 'has output' rather than 'results in assembly of' >> inconsistent with DP
  • GO:0044571 [2Fe-2S] cluster assembly
  • GO:0044572 [4Fe-4S] cluster assembly
  • GO:0007596 blood coagulation
  • GO:0031412 gas vesicle organization
  • GO:0016226 iron-sulfur cluster assembly
  • GO:0031163 metallo-sulfur cluster assembly
• Budding: is 'has (primary) output' correct?
  • GO:0048194 Golgi vesicle budding
  • GO:0070142 synaptic vesicle budding
• Biogenesis: is 'has (primary) output' correct? should we use 'results in formation of'?
  • GO:0017126 nucleologenesis
  • GO:0043164 Gram-negative-bacterium-type cell wall biogenesis
  • GO:0042546 cell wall biogenesis
  • GO:0160031 endoplasmic reticulum membrane biogenesis
  • GO:0044091 membrane biogenesis
  • GO:0101025 nuclear membrane biogenesis
  • GO:0016557 peroxisome membrane biogenesis
  • GO:0031671 primary cell septum biogenesis
  • GO:0045313 rhabdomere membrane biogenesis
  • GO:1990344 secondary cell septum biogenesis
• Odd balls
  • GO:0036440 citrate synthase activity
  • GO:0002537 nitric oxide production involved in inflammatory response
  • GO:1990417 snoRNA release from pre-rRNA

Cell to cell signaling terms

Request was to

• Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling (Single EXP to PMID:14511481)
• Replace "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation GO:0021937, with: cerebellar Purkinje cell-granule cell precursor cell signaling (def: Any process that mediates the transfer of information from Purkinje cells to granule cell precursors.) (9 EXP)

Some example terms:

• neuron-glial cell signaling
• epithelial-mesenchymal cell signaling
• mesenchymal-epithelial cell signaling
• astrocyte-dopaminergic neuron signaling
• ectoderm and mesoderm interaction
• mesodermal-endodermal cell signaling
• glial cell-neuron signaling

There are also terms for which the cells signaling to each other are not specified:

• cell-cell signaling involved in amphid sensory organ development
• cell-cell signaling involved in cardiac conduction
• cell-cell signaling involved in cell fate commitment
• cell-cell signaling involved in kidney development
• cell-cell signaling involved in lung development

etc

• The question is, is 'cell x to cell y' signaling a biological process relevant for GO?
• Issues:
  • orthogonal to other signaling pathways
  • For example: neuron-glial cell signaling is defined as "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine."
    • acetylcholine receptor signaling pathway is not a child of cell-cell signaling
    • dopamine receptor signaling pathway is a has_part child, with the relation 'has part 'synaptic transmission, dopaminergic'
    • We dont have noradrenaline signaling, but we have synaptic transmission, noradrenergic
    • >> but none of these are linked to neuron-glial cell signaling, which is probably OK, since these pathways may be taking place in various cell types
    • >>> It seems these terms are BPs that contain CC information, and this information should be captured with 'occurs in'

• Terms are not much used:
  • cell-cell signaling involved in cell fate commitment 9 EXP
  • epithelial-mesenchymal cell signaling 4 EXP
  • glutamate secretion, neurotransmission 4 EXP
  • mesenchymal-epithelial cell signaling 4 EXP
  • mesodermal-endodermal cell signaling 2 EXP
  • neuron-glial cell signaling 5 EXP

• Chris's slides: Decomposition of macro biological processes in GO