Meeting minutes/2010-08-24 RDTF relations discussion
From Program on Ontologies of Neural Structures
Attendees: Alan, David, Alex, Terry, and Jyl
Contents |
Agenda
1. synapsed_to vs NRTF contacts – are they the same?
2. capable_of vs has_function_in – What’s the difference. Do we need both. Need relation that works for functions realized by process cell participates as well as one cell can carry our completely. Perhaps 2 relations?
3. Recording neurotransmitter: OK to use capable_of, rather than predefined releases_neurotransmitter relation?
CL now using secretion terms FBbt using releases_neurotransmitter defined in terms of GO neurotransmitter secretion – more specific than just secretion.
NRTF - using has_molecule. Can we reconcile this with other approaches? - Do we have a way to infer one from other?
4. Recording neuron sensory function
Which target GO terms ?
Discussion
Does NRTF makes_contact_to map to synapses_to ?
Alan worries that it may not because:
* Giorgio's last e-mail on this mentions that it can be (is being?) used for connection via gap junctions too (the currently defined synapses_to relation is just for chemical synapses). * May also be used for cell class to region.
David: I suspect that the gap junction connections are all electrical synapses. This would suggest the property hierarchy:
synapses_to
- electrically_synapses_to
- chemically_synapses_to
with synapses_to mapping to the NRTF relation.
Note: Haven’t yet come up with a good definition of electrical synapsing. Need more expert input.
Alan: Would like to reference the gap junction connectivity directly:
=> a property (poly)hierarchy something like this:
coupled_by_gap_junction (or perhaps has_gap_junction_contact?)
- electrically_synapsed_to
synapses_to
- electrically_synapses_to
- chemically_synapses_to
(OK?)
ACTION ITEM: Alan to contact Giorgio to check whether gap junction connectivity covered by connected_to relations always implies electrical synapsing. Also are gap-junctions / electrical synapses directional?
Defining electrical synapsing:
David: I've been assuming we need a functional definition based on electrical coupling between neurons. Not sure we can point to a structure and call it an electrical synapsed in the way we can point to an individual chemical synapse.
Alex: in GO, Synapse should be divided into electrical and chemical.
David: But what is the object you’re calling an electrical synapse? Can a single gap junction be called an electrical synapse?
Alex and Jyl: Maybe it can.
capable_of vs has_function_in
functions realized by process intrinsic to cell vs functions realized by process that cell participates in.
There are two issues here:
- CL uses capable_of, fly anatomy uses has_function_in. We need to agree whether both are necessary and if so when to use each, or whether it is better to standardize on one.
- Purely by its name – capable_of sounds wrong if used for processes a neuron participates in – e.g.- behavior. So, we either need a general relation that covers both, or two specific relations.
Alex: I think we can usually distinguish the two clearly. Perhaps only occasionally difficult to decide which applies.
Alan: I believe the current thinking is that bearer of should be used for dispositions. *only* difference between function and disposition is selective pressure.
David: Here're the current definitions from RO:
capable_of: capable_of P <-> bearer_of (some realized_by only P).
has_function_in: has_function_in P <-> has_function (some realized_by only P).
bearer_of is a relation that applies between a continuant and a dependent continuant. Functions and dispositions are both dependent continuant sin BFO, therefore has_function_in is subproperty of capable_of by this definition and bearer_of of is agnostic about whether its target is a function or a disposition. i.e.- capable_of doesn't make commitment to whether the participant the process was under selective pressure to be able to do so.
Jyl: Just on the name, couldn’t we use ‘has_role_in’ – biologists would say that a neuron has a role in a behavior.
David: Agree that this is a good name for biologists. Unfortunately ‘role’ has other meanings to ontologists.
David: Based on the definition, are either of these any good for functions or dispositions of a cell realized by a process does not take place completely within that cell? e.g.- could they be used to record the roll of a clock neuron in control of circadian behavior or of a neuron in some reflex (jump response in flies)?
Alan: Not sure (?)
David: Would this work?
capable_of_participation_in P <-> bearer_of some (realized_by only participates_in some P)
Alan: No, (participates_in some P) is not a process, but target_of realized_by needs to be a process.
David: Ahhh, OK.
ACTION ITEM: Alan will try to draft a couple of possibilities for these
Alan notes in chat window: distinction desired is where x is part of X that bears a function F, and realization of x's function f is part of realization of F. Relation we want is between x and F
Has role in some function
e.g body has jumping function. cell is part of body has some function f. Realization of jumping function has cell realizing f. (we don't necessarily know what f is)
realization of f is part of realization of jumping
Recording neurotransmitter
Fly anatomy using relation ‘releases_neurotransmitter’ with target – CHEBI term. The relation ‘releases_neurotransmitter’ is defined using the GO term for neurotransmitter secretion. Would be happy to use capable_of to some suitable GO term and let GO do the hard work of making cross-products using CHEBI terms.
CL now using capable_of with target = general secretion terms from GO. Not necessarily children of neurotransmitter secretion (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007269, formerly neurotransmitter release). Neurotransmitter secretion as defined by GO is more specific than simply secretion. It involves secretion into the synaptic cleft.
David: I think that being a neurotransmitter is a role that a molecule has when it is secreted by a presynaptic cell into the synaptic cleft and binds to receptors on the postsynaptic membrane. The same molecule secreted generally and acting as a paracrine hormone is not a neurotransmitter. So, we need a set of terms in GO for subclasses of neurotransmitter secretion. These should be used as targets of capable_of for recording what neurotransmitter a cell releases.
Alex: Some of these terms already exist, e.g. serotonin secretion, neurotransmitter. Perhaps we should use this as model for defining other neurotransmitter secretion terms.
David: Agree. Can you request the terms or should I?
ACTION ITEM: Alex & Terry to request GO terms for secretion of specific neurotransmitters – to be children of GO neurotransmitter secretion.
NRTF - using has_molecule.
Definition is has_part has_molecule. (so it’s also used for things that are not neurotransmitters, e.g.- parvalbumin).
Giorgio’s not comfortable recording neurotransmitter release on the basis of simply knowing that a molecule or its biosynthetic enzyme is present. Something can’t be secreting a molecule if it’s not expressed there. Can make the logical step from has neurotransmitter to has_molecule, but not the other way around.
If we define a relation for releases_neurotransmitter, then we can make this a subproperty_of has_molecule => the inference we need.
But – we just agreed not to use a specific relation for this, but to use capable_of with GO neurotransmitter release subclass as a target
ACTION ITEM: ALAN - challenge: state C capable_of X_neurotransmitter_release and then imply C has_molecule X
Recording neuron sensory function
Which target GO terms ?
CL is using child detection of stimulus, which isn’t necessarily sensory perception. General agreement to use children of:
Detection of stimulus involved in sensory perception http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050906
