mcoenca / obo-relations

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Align neuroanatomical relations with those used in FMA #12

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
See
http://www.jbiomedsem.com/content/5/1/1/abstract

Specifically table 1:

Innervate
a connectivity relation where a neurite of one neuron synapses with a neurite 
or a region of the soma of another neuron or a region of a muscle cell or a 
gland cell.
Synapse_with
a connectivity relation where there is apposition between the presynaptic 
membrane of a neurite of one neuron and the postsynaptic membrane of one or 
more neurites of another neuron or a region of a muscle cell or a gland cell 
and some form of neurotransmission is evident between them.
Projects_to
a connectivity relation where individual axons comprising a fiber tract 
originating from one or more brain regions synapse_with neurites or somas of a 
collection of neurons located in one or more other brain regions. This relation 
may be synonymous with ‘terminate_in’.
Projects_from
a connectivity relation where individual axons comprising a fiber tract are 
parts of a collection of neurons located in one or more brain regions. This 
relation may be synonymous with ‘originate_in’.
Sends_output_to
a subproperty of project_to relation where neurotransmission is sent from one 
brain region to one or more other brain regions.
Receives_input_from
a subproperty of project_from relation where neurotransmission is received by 
one brain region from one or more other brain regions.
Has_pathway
a connectivity relation where a collection of neurons located in brain region A 
sends_output_to a collection of neurons located in B via axons comprising the 
fiber tract from

Original issue reported on code.google.com by cmung...@gmail.com on 14 Jan 2014 at 12:55

GoogleCodeExporter commented 9 years ago

Original comment by cmung...@gmail.com on 14 Jan 2014 at 12:56

GoogleCodeExporter commented 9 years ago
FMA innervate maps to RO synapsed_to.  Not clear to me how synapse_with differs 
from this.

Projects_to maps roughly to RO innervates - although not strictly as innervates 
requires synapsing by the neurons involved in the target regions.

Projects_from doesn't map easily.   tract that connected_to some neuropil 
domain would give correct answer.

RO doesn't have  relatinos corresponding to sends_output_to & 
recieves_input_from. Superficially one might think that property chains of 
innervated_by/innervates could work, but these are unsafe because tracts may 
branch.
Could define wrt chains of synapsed neurons.  This would fit with planned work 
on circuits for VFB

Original comment by dosu...@gmail.com on 7 Dec 2014 at 12:19