incorrect parentage: "cell migration" not a type of "cell motility"

[krchristie]

While curating Wang et al. 2020 that indicates that Pdilt is involved in the same process as Lypd4 to mature Adam3, a sperm cell surface protein involved in the process of fertilization:

• Wang D, et al. LYPD4, mouse homolog of a human acrosome protein, is essential for sperm fertilizing ability and male fertility. Biol Reprod. 2020 Apr 24;102(5):1033-1044. PMID: 32040177.

I noticed that Tokuhiro et al. 2012 is cited as the source of an annotation of Pdilt to "sperm motility" though both of these two papers indicate that mutations in either Lypd4 or Pdilt do NOT cause defects in sperm motility, but instead in "migration of sperm from uterus to oviduct":

• Tokuhiro K, et al. Protein disulfide isomerase homolog PDILT is required for quality control of sperm membrane protein ADAM3 and male fertility [corrected]. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3850-5. PMID: 22357757

Looking in Noctua, I see that the curator actually chose the term "cell migration", but that the logic over the GO term, extensions, and relationships has come up with the term "sperm motility":

I think it is INCORRECT to say that "cell migration" is a "cell motility". The definition of "cell migration" includes the fact that the movement of the cell is guided by molecular cues.

It seems that the CORRECT relationship is that "cell migration" _haspart "cell motility" where "cell motility" refers to methods of cell motility, e.g.:

• actin polymerization-dependent cell motility (GO:0070358)
• cell gliding (GO:0071976)
• cilium or flagellum-dependent cell motility (GO:0001539)
• ameoidal-type cell motility ** this term does not exist, but we do have "ameboidal-type cell migration" (GO:0001667) & "amoeboid sperm motility" (GO:0097723)
• cytoskeleton-mediated cell swimming (GO:0071979)
• substrate-dependent cell motility ** this term does not exist, but we do have "substrate-dependent cell migration" (GO:0006929)
• type IV pilus-dependent motility (GO:0043107)

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These direct child terms of "cell motility" might actually be intended to be migration terms and probably merit a closer look:

• cell motility in response to calcium ion (GO:0097231)
• cell motility in response to potassium ion (GO:0097230)
• cell motility involved in camera-type eye morphogenesis (GO:0003411)
• cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)
• cell movement involved in somal translocation (GO:0021805)

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For reference, here are portions of the stanzas for each of these two terms:

id: GO:0048870 name: cell motility namespace: biological_process def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] synonym: "cell locomotion" EXACT [] synonym: "cell movement" RELATED [] synonym: "movement of a cell" EXACT [] is_a: GO:0009987 ! cellular process

id: GO:0016477 name: cell migration namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] is_a: GO:0048870 ! cell motility

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@ukemi - your thoughts on this issue would be greatly appreciated

[krchristie]

It seems that the CORRECT relationship is that "cell migration" _haspart "cell motility"

Actually, I think it might NOT be correct to code any absolute relationship between "cell migration" and "cell motility", at least not between these two terms, though it may be appropriate to code relationships between specific types of cell motility and specific cell migrations.

Quotes from: Barton LJ, LeBlanc MG, Lehmann R. Finding their way: themes in germ cell migration. Curr Opin Cell Biol. 2016 Oct;42:128-137. PMID: 27484857

The translocation of germ cells from the place of origin to the developing somatic gonad involves several processes including passive movements with underlying tissues, transepithelial migration, cell adhesion dynamics, the establishment of environmental guidance cues and the ability to sustain directed migration.

and regarding one phase of embryonic germ cell migration in some organisms:

In Drosophila and Xenopus, the translocation with endodermal tissue is a passive process and known to require germ cell adhesion to underlying endodermal epithelium

[pgaudet]

@krchristie 'passive' processes do not apply to GO, since no genes mediate them. All protein-mediate migration likely involves motililty.

[krchristie]

@krchristie 'passive' processes do not apply to GO, since no genes mediate them. All protein-mediate migration likely involves motililty.

In embryonic germ cell migration, the passive stages of migration appear to be mediated by adhesion molecules that allow the primordial germ cells to stick to other cells that are moving, so it would not true to say that "embryonic germ cell migration" always has_part "motility of primordial germ cells".

[krchristie]

@krchristie 'passive' processes do not apply to GO, since no genes mediate them. All protein-mediate migration likely involves motililty.

@pgaudet - Why did you close this?

This comment about whether or not it is true to say that "cell migration" always has some "cell motililty" or not (depending on whether you want to talk about whether or not the migrating cells are motile cells, or are "riding" on other cells that do have cell motility) has no impact on the fact that it is not true to say that "cell migration" is_a "cell motility.

"cell migration" is a process that includes additional signalling processes in addition to cell motility.

This incorrect relationship is causing some incorrect inferred annotations.

"cell migration" needs to become a direct child of "cellular process" so that it will be a sibling of "cell motility", not a child of it.