obophenotype/c-elegans-gross-anatomy-ontology

C. elegans Gross Anatomy Ontology

c-elegans-gross-anatomy-ontology's Issues

Add PVR and male ciliated neurons as subclass of "ciliated neuron"

According to this page at WormAtlas:

https://www.wormatlas.org/postembryonicneurons.htm

We are missing the following neurons/classes (and respective subclasses) from the "ciliated neuron" class:

PVR
CEM
HOA
HOB
PCA
ray neuron type A
ray neuron type B
SPD
SPV

Oddly FLP is missing from the WormAtlas list. I will notify David Hall.

@raymond91125
I'm happy to make the change in the ontology file if it's OK with you.

WBbt:0005780, wrong 'is_a' relationship

Hi Wormbase team,

I would like to draw your attention to this error:

[Term]
id: WBbt:0005780
name: non-striated muscle
is_a: WBbt:0003675 ! muscle cell => a muscle is not a cell

Kind regards,

Anne Niknejad
bgee.org curator
UNIL University of Lausanne

Bodywall muscle cell naming difference between WB and WA

There was apparently some discrepancy of muscle cell names between WB and WormAtlas (https://www.wormatlas.org/hermaphrodite/musclesomatic/jump.html?newLink=mainframe.htm&newAnchor=Developmentofsomaticmuscle3).

Make 'somatic nervous system' and 'pharyngeal nervous system' subclasses of 'nervous system'

The terms:

pharyngeal nervous system (WBbt:0005440)
somatic nervous system (WBbt:0005760)

should be made subclasses of:

nervous system (WBbt:0005735)

Updating cryptic term labels

There are several term labels that are quite cryptic to anyone unfamiliar with the anatomy ontology and should probably be more user-friendly:

Some initial (high priority?) terms would be:

hmc (WBbt:0004697) -> ‘head mesodermal cell’
gon_herm_dtc_A ( WBbt:0004520 ) -> ‘anterior distal tip cell’
gon_herm_dtc_P ( WBbt:0004506 ) -> ‘posterior distal tip cell’
dtc (WBbt:0006865) -> ‘distal tip cell’
gon_male_dtc anterior (WBbt:0005064) -> ‘anterior distal tip cell male’
gon_male_dtc posterior (WBbt:0005063) -> ‘posterior distal tip cell male’

Additional terms could also use a label update:

arc ant DL
arc ant DR
arc ant V
arc post D
arc post DL
arc post DR
arc post V
arc post VL
arc post VR
exc_gl_L nucleus
exc_gl_R nucleus
gon herm dish A
gon herm dut
gon herm prsh A
gon herm prsh P
gon herm sujn
gon herm vut (5L)
gon herm vut (5R)
gon herm vut
gon male sves
gon male vdef 1L
gon male vdef 4L
gon male vdef
gon_male_sves Z1 or Z4
gon_herm_dish_P
mu_int_L
mu_int_R
mu_male_diag
proct
rect_D
rect_VL
rect_VR
se_male
se seam

It can probably be argued for some of these (e.g. "sujn"?) that the acronym used is already understood by the community. There has also been a request to possibly create a "common name" or "public name" that might be distinct from the primary label that represents how the community references the anatomy object in the literature.

Review OBO artefact (WBBT)

Review the OBO release artefact. You should download it, then download the old wbbt.obo then diff them (for example with the command line or whatever other tool you use.

There will be differences, that is for sure! The question is whether they are acceptable. We will talk about your findings during the next meeting.

'rectum' subclassof 'hermaphrodite-specific'?

It appears that the term 'rectum' is a child of the term 'hermaphrodite-specific'; was this intentional? Can it be a subclass of 'organ' instead? This is causing some strange inferences in the phenotype ontology.

Missing g1 precursor cells

There are missing precursor cells (before fusion into syncytium).
Pharyngeal g1AR (MS papaapaa) https://www.wormatlas.org/pharynxatlas/pharynx7g1AR.html
Pharyngeal g1P (MS aaaaapap) https://www.wormatlas.org/pharynxatlas/pharynx8g1P.html

Potential anatomy term name change

AB -> embryonic founder cell AB
EMS -> embryonic founder cell EMS -> should the definition of EMS be changed from ‘Embryonic cell’ to ‘Embryonic founder cell’? See WormAtlas founder cell definition.
C -> embryonic founder cell C
D -> embryonic founder cell D
E -> embryonic founder cell E
MS -> embryonic founder cell MS
Psub1 -> embryonic founder cell Psub1 (or simply embryonic founder cell P1)
Psub2 -> embryonic founder cell Psub2
Psub3 -> embryonic founder cell Psub3
Psub4 -> germline founder cell Psub4
Pn.p hermaphrodite -> Pn.p hermaphrodite vulval precursor cell. e.g. P3.p hermaphrodite (WBbt:0008112) -> P3.p hermaphrodite vulval precursor cell
G1 -> Postembryonic blast cell G1
G2 -> Postembryonic blast cell G2

Add "bursa" / "male tail" term

For new term requests, please provide the following information:

Preferred term label

bursa

Synonyms

male tail

Textual definition

From WormAtlas:

"The adult male tail including the the lateral fan and rays."

https://www.wormatlas.org/glossary/bglossary.htm#bursa

Suggested parent term

male-specific (WBbt:0005757)

g1AR and g1P may not fuse

According to PMID:18927627 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000222
phat-5 is expressed exclusively in g1AR and g1AL but not g1P.
"Previous reports have suggested that the g1AR and g1P cells are fused [9], yet we see no passage of phat-5-expressed YFP from g1AR to g1P, suggesting either that YFP is restricted from diffusing between these cells or that the two cells are not fused."

'amphid process' part_of AWC issue

@raymond91125
I've run into an issue with a recent help desk inquiry (that you have already answered) regarding finding genes expressed in the AWC neuron. The issue is that the anatomy term "amphid process" is considered "part of" the AWC neuron, and therefore any genes annotated to "amphid process" in any context (in any amphid neuron) are being returned by WOBr as being expressed in AWC, which isn't necessarily correct. In fact, on the "amphid process" page:

https://wormbase.org/species/all/anatomy_term/WBbt:0005393#041--10

the "Associations" widget displays five genes annotated to "amphid process", three of which (hda-4, pam-1, and arrd-6) have no annotations to AWC, AWCL, or AWCR, yet these three genes will always be returned as expressed in AWC with the current logic.

I would like to suggest that we make "amphid process" only a "part of" the "amphid neuron" term. We could create an "AWC amphid process" - "part of" - "AWC" axiom if we wanted, but I think the current construction will return incorrect results in WOBr.

'intestinal muscle' part_of intestine?

@raymond91125
I noticed that the term:

intestinal muscle (WBbt:0005796)

is asserted to be "part of" the intestine (WBbt:0005772). I wouldn't have considered the intestinal muscle to be part of the intestine, but rather part of the alimentary system as a whole. The definition of "intestine" does not appear to accommodate the "intestinal muscle" as part. I would suggest/request that we remove the "part_of intestine" axiom for "intestinal muscle" and instead add the "part_of alimentary_system" axiom.

This comes up because a user is asking for genes expressed in the intestine, but if I use the WormBase Ontology Browser to get the list of genes expressed in the intestine or any of its parts, this will include genes expressed in the intestinal muscle, which I don't think is what they are looking for.

What do you think?

Quality control: Fix errors

Quality control flagged up a significant number of errors.

https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/blob/master/reports/wbbt-edit-obo-report.tsv

Check the tsv file. But only address this issue after issue 1 is closed!

Add PDHL/R male neuron

Preferred term label

PHD
PDHL
PDHR

Synonyms

Phasmid D neuron
Phasmid D neuron left
Phasmid D neuron right

Textual definition

PHD
A neuron class of 2 bilateral, cholinergic, peptidergic, male-specific, ciliated neurons generated by transdifferentiation from a male PHso1 glial cell in the late L4 larval stage of a male C. elegans animal.

PHDL
The left PHD neuron of the pair of bilateral PHD neurons in a male C. elegans animal.

PHDR
The right PHD neuron of the pair of bilateral PHD neurons in a male C. elegans animal.

Paper in review at eLife; BoRXiv preprint here:
https://www.biorxiv.org/content/biorxiv/early/2019/05/01/285320.full.pdf

"Together, these data demonstrate that the male PHso1 glial cells transdifferentiate into a novel class of ciliated neurons which we have termed phasmid D neurons (PHDs)."

"The data presented here extend John Sulston’s original observations and demonstrate that male PHso1 cells undergo a direct glia-to-neuron transdifferentiation to produce a novel class of bilateral cholinergic, peptidergic and ciliated sensory neurons, the phasmid D neurons."

Suggested parent term

ciliated neuron (WBbt:0006816)
male-specific (WBbt:0005757)
cholinergic neuron (WBbt:0006840)

Create 'gonad arm' class that is a superclass of both 'anterior gonad arm' and 'posterior gonad arm'

For new term requests, please provide the following information:

Preferred term label

gonad arm

Textual definition

One arm (males) or one of two arms (anterior or posterior in hermaphrodites) of the gonad, generally consisting of a core of germline cells surrounded by an outer somatic epithelium (somatic gonad), comprised of the gonad sheath (ovary), spermatheca, uterus (oviduct) and vulva in the hermaphrodite, or gonadal sheath, seminal vesicle and cloaca in the male.

https://www.wormatlas.org/glossary/gglossary.htm#gonad

Tissue (WBbt:0005729)

redundant ventral uterine precursor

There are two terms for ventral uterine precursor cell WBbt:0006780 and WBbt:0005154. WBbt:0005154 does not have annotations, should probably merge into WBbt:0006780.

Why is the IRI of the obo release .owl?

http://purl.obolibrary.org/obo/wbbt.obo/wbbt/releases/2019-04-18/wbbt.obo.owl

Hypodermal cell alignment with WormAtlas

https://www.wormatlas.org/hermaphrodite/hypodermis/Hypframeset.html
On WormAtlas, each hypodermal cell precursor (prior to fusion into syncytium) has a name based on location.