cilium motion

[gocentral]

For the annotation of RSPH9 Q9H1X1 and RSPH4A Q5TD94, mutations in these genes lead to nasal cilia with abnormal motility PMID:19200523

Currently wrongly annotated to ciliary cell motility: Cell motility due to the motion of one or more cilia., but the nasal cell itself isn’t moving just the cilia.

This could be a child of GO:0006928 cell motion and a parent of GO:0060287 cilium motion involved in determination of left/right asymmetry

Tx

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/6577

[gocentral]

Actually, I think you've highlighted a bit of a gap in the ontology here Ruth. We don't have any term for movement of something that isn't an organism or cell. The definition of locomotion is:

Self-propelled movement of a cell or organism from one location to another.

And 'cell motion' is:

Any process involved in the controlled movement of a cell.

There's no generic 'motion' parent where you can have an 'organelle motion' or similar term.

I reckon we could have a generic 'biological motion' term as a child of bp and parent to 'cell motion' then we could have a term 'cilium motion' or something as another child (perhaps 'organelle motion' as a parent as there are probably several cell projections that move).

I'm not sure how this might overlap with 'locomotion' though, so I'd like to suggest we have a clinic item about this:

http://gocwiki.geneontology.org/index.php/GO\_clinic\_late\_2009

Original comment by: jl242

[gocentral]

• status: open --> open-later

Original comment by: jl242

[gocentral]

Hi,

when you do make these new terms, please could you include something to describe:

"ciliary beat pattern" for annotation of human, mouse and zebrafish RSPH9 "flagellar beat frequency" for annotation of Chlamydomonas RSP9 also from PMID:19200523

Thanks, Varsha

Original comment by: vkhodiyar

[gocentral]

This is a good idea, please let Varsha and I know when you plan to discuss this

Ruth

Original comment by: RLovering

[gocentral]

Also note that the original request here is largely redundant with SF 2801480, which is open and assigned to David (the older item cited therein, SF 1766338, is also relevant). This is probably closer to being sorted than Jane realized, and just needs to percolate nearer the top of the priority heap. It may not have to go to a clinic.

Varsha requested 'ciliary beat frequency' in SF 1968619, and David added GO:0060296 'regulation of cilium beat frequency involved in ciliary motility'. Presumably the new beat pattern and beat frequency terms should follow that model.

Links: https://sourceforge.net/tracker/index.php?func=detail&aid=2801480&group\_id=36855&atid=440764 https://sourceforge.net/tracker/index.php?func=detail&aid=1766338&group\_id=36855&atid=440764 https://sourceforge.net/tracker/index.php?func=detail&aid=1968619&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> ukemi
• status: open-later --> open

Original comment by: mah11

[gocentral]

David and I have discussed this - he had added 'cilium movement involved in ciliary motility ; GO:0060294' with the beat freq children but it is still part_of 'ciliary cell motility' (i.e. the cell itself moving) so that doesn't work for Ruth's nasal cilia which stay still.

So we still need a generic parent to 'cilium movement involved in ciliary motility ; GO:0060294' which itself I think needs a generic movement parent (it's currently under microtubule-based movement but that won't work for everything - flagella for example). So we need 'cillium movement' then maybe 'cell projection movement' then I'm not sure - cell part movement? And the ultimate is_a parent is tough - can't go under locomotion which would be the obvious place because the def is 'Self-propelled movement of a cell or organism...'. So perhaps we do need a generic 'biological movement' term as originally suggested - this could be a parent to locomotion...?

Original comment by: jl242

[gocentral]

Hi Jane,

I think that we need a generic cilium motion term to cover Ruth's annotation. However, I do not think that microtubule-based movement is wrong. As far as I know, all cilia are MT-based. Not all flagella are, but these can be distinguished by being MT-containing flagella and flagellin-containing flagella. I'm jut not sure what having a generic movement parent would buy us. It seems like that term would not give us any real information.

David

Original comment by: ukemi

[gocentral]

Well, we know the mechanism for cillia and flagella, but what about movement where we don't know the underlying mechanism? I'm sure I can come up with a bacterial example for you ;-)

(I don't think the microtubule-based movement term is wrong, btw, I just think it needs another, generic movement parent)

Original comment by: jl242

[gocentral]

Okay - following another long discussion with David, we may have a possible solution.

Briefly, the main problem with any sort of generic movement term is that a lot of things move and it's hard restricting the term so it doesn't cover everything. So we decided we could restrict it to just the movement of cellular components (which includes whole cells). There is actually a term that's supposed to encompass this: cell motion ; GO:0006928 but the definition was made too restrictive. It has a child 'cell motility ; GO:0048870' which is the movement of whole cells.

So, the challenge is to define and rename 'cell motion ; GO:0006928' such that it includes the movement of whole cells and cell components but excludes transport. Here's a stab at it:

cellular component movement The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore.

(if we need to define movement itself we could call it 'the change in position or location' - not sure if we need to do this)

It would also mean altering the definition of transport to:

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism by means of some external agent such as a transporter or pore.

What do you think?

Original comment by: jl242

[gocentral]

Hey Jane,

I like this! Let's give it a few days to percolate and then implement it. I will also retain the cell motion string as a synonym. What do you think, related?

David

Original comment by: ukemi

[gocentral]

I agree this is looking excellent, thanks for putting so much time into this issue.

So all current child/grandchild terms of cell motion will become child/grandchild terms for cellular component movement, ie the cell doesn't 'move' without a cellular component moving?

Definitely want cell motion as a synonym, as current synonyms for cell motion are: exact cell movement related cell locomotion Couldn't we have cell motion as an exact synonym?

Ruth

So that

Original comment by: RLovering

[gocentral]

OK. Done. Note that I only changed the definition of the root transport term. It seemed easier than it should have, so please check. Jane, do you think we need to do them all? Maybe we could automate it the change through the graph in some way. D

Original comment by: ukemi

[gocentral]

• status: open --> closed-fixed

Original comment by: ukemi

[gocentral]

I think we should change all the transport child defs too. I can probably do that automatically though - I'll have a stab...

Ruth - in GO, a cell is classed as a cellular component (confusing, huh?) so that's why it's okay to have 'cellular component movement' as the top term. Might be worth putting in a comment to explain that actually, as it's not exactly intuitive.

Original comment by: jl242

[gocentral]

Okay - fixed all the transport defs.

Original comment by: jl242