obsolete: visceral muscle (as it is a cell type)

[cmungall]

[Term]
id: UBERON:6005070
name: visceral muscle
xref: FBbt:00005070
def: "The visceral musculature comprises circular and longitudinal fibers which surround the entire intestinal tract, with the exception of the recurrent layer of the proventriculus. The circular fibers derive from a bilaterally symmetrical band of mesodermal cells extending continuously throughout most of the germ band. The longitudinal fibers derive from clusters of mesodermal cells which appear during stage 12 at the posterior end of the embryo and migrate anteriorly." [FlyBase:FBrf0064793, FlyBase:FBrf0089570]
is_a: CL:0000187 ! muscle cell
relationship: part_of UBERON:0000383 ! muscle system

so far we haven't put any cell types in the UBERON ID space - it complicates some things to do this.

I can obsolete and add a consider to:

[Term]
id: CL:0008007
name: visceral muscle cell
def: "A muscle cell that is part of some visceral muscle" [GOC:dos]
is_a: CL:0000187  ! muscle cell

but this doesn't tell us in the OWL what a visceral muscle is.

we have had this horribly underspecified class in uberon for a while:

[Term]
id: UBERON:0007094
name: visceral musculature
xref: BILA:0000132 ! visceral muculature
is_a: UBERON:0000383 ! musculature of body

[dosumis]

FBbt classification may be wrong. Somatic muscles in arthropods are (mostly?) single syncytia. Pretty sure this is not true of visceral muscle. Will check.

Given def of FBbt term, general class could be gut muscle, rather than visceral. In arthropods, unlike vertebrates, thus is striated.

On 8 Sep 2016 00:40, "Chris Mungall" notifications@github.com wrote:

[Term] id: UBERON:6005070 name: visceral muscle xref: FBbt:00005070 def: "The visceral musculature comprises circular and longitudinal fibers which surround the entire intestinal tract, with the exception of the recurrent layer of the proventriculus. The circular fibers derive from a bilaterally symmetrical band of mesodermal cells extending continuously throughout most of the germ band. The longitudinal fibers derive from clusters of mesodermal cells which appear during stage 12 at the posterior end of the embryo and migrate anteriorly." [FlyBase:FBrf0064793, FlyBase:FBrf0089570] is_a: CL:0000187 ! muscle cell relationship: part_of UBERON:0000383 ! muscle system

so far we haven't put any cell types in the UBERON ID space - it complicates some things to do this.

I can obsolete and add a consider to:

[Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle" [GOC:dos] is_a: CL:0000187 ! muscle cell

but this doesn't tell us in the OWL what a visceral muscle is.

we have had this horribly underspecified class in uberon for a while:

[Term] id: UBERON:0007094 name: visceral musculature xref: BILA:0000132 ! visceral muculature is_a: UBERON:0000383 ! musculature of body

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/8, or mute the thread https://github.com/notifications/unsubscribe-auth/AAG4x8EkIa8YyUw4b9WIVUskNujQRfR2ks5qn0tmgaJpZM4J3d5X .

[dosumis]

CC @mmc46

[mmc46]

At least in larva, visceral muscles are arranged as two layers of striated, mononucleated fibres.

[dosumis]

IIRC - the issue here is what counts as a muscle - a whole sheet, or a single mononucleated fiber (= a single cell), or something in between? Don’t think that was ever very clear from the lit so we may need to decide by fiat.

On Sep 8, 2016, at 1:07 PM, Marta Costa notifications@github.com wrote:

At least in larva, visceral muscles are arranged as two layers of striated, mononucleated fibres.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/8#issuecomment-245577069, or mute the thread https://github.com/notifications/unsubscribe-auth/AAG4x-OIQfJS4ZiGsQdnJ02WJSsFnV_hks5qn_qKgaJpZM4J3d5X.

[mmc46]

Our terms define muscle as the whole sheet. And we have a few terms to designate individual muscle fibres of different types. But I don’t currently know enough on this subject to know if that follows common convention.

On 8 Sep 2016, at 13:44, David Osumi-Sutherland notifications@github.com wrote:

IIRC - the issue here is what counts as a muscle - a whole sheet, or a single mononucleated fiber (= a single cell), or something in between? Don’t think that was ever very clear from the lit so we may need to decide by fiat.

On Sep 8, 2016, at 1:07 PM, Marta Costa notifications@github.com wrote:

At least in larva, visceral muscles are arranged as two layers of striated, mononucleated fibres.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/8#issuecomment-245577069, or mute the thread https://github.com/notifications/unsubscribe-auth/AAG4x-OIQfJS4ZiGsQdnJ02WJSsFnV_hks5qn_qKgaJpZM4J3d5X.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/8#issuecomment-245585153, or mute the thread https://github.com/notifications/unsubscribe-auth/AByQ03Awp5YZTNEiwm2mIy4Fzkozjj4Nks5qoAM2gaJpZM4J3d5X.