Cilia: new terms and links - cellular component branch

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We are in contact with John van Dam, Toby Gibson and colleagues to add/revise terms related to cilia (CC and BP). Here is a first list of suggested edits from John:

"...In the end I've removed a lot of terms from my list because I found out they already existed as part of the axoneme term, which itself was not connected to the cilium. I've missed these terms using the graphical viewer in OBO-edit. Please find attached an excel file with the new terms, a short definition, reference data and relationships. I've also added some new connections for existing terms as well as identified some issues that need some rewiring of the terms. I am sure that in terms of is_a and part_of relationships there are more issues to solve. I will try and figure those out this December, as well as figure out the biological processes part. One of these things is the fact that some terms define areas through which other components cross, like "ciliary transition zone" and "axoneme", in the excel file I've made "axoneme" part_of "ciliary transition zone", but I'm not quite sure if it is the way to go."

The excel file is called "New GO terms - Nov2013" and is attached.

Paola

Reported by: paolaroncaglia

Original Ticket: geneontology/ontology-requests/10553

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Original comment by: paolaroncaglia

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Hi, I was going to request a new term, transition fibre, this morning but saw this SourceForge item where transition fiber is included as a new term to add to the CC.

Here is a possibly revised definition for that term:

A nine-bladed, propeller-like protein structure that links the distal end of the basal body and the cilium to the plasma membrane. Functions in protein sorting and gating (i.e. active and passive transport of proteins in and out of the cilium).

References: PMID:24231678 (new paper describing localization of specific proteins to this structure) PMID:22653444 PMID:5064817

Thanks, --Kimberly

Original comment by: vanaukenk

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To start with, I've added these new terms:

id: GO:0097537 name: Y-shaped link def: "A Y-shaped protein complex in the ciliary transition zone that connects the cilium axoneme to the ciliary necklace. Both protein sorting and protein gating occur at this point in the cilium allowing some, but not all proteins to enter the cilium." [GOC:cilia, PMID:22653444, PMID:4554367] synonym: "membrane-microtubule complex" RELATED [] synonym: "Y-link" RELATED [] synonym: "Y-link structure" RELATED [] synonym: "Y-shaped assemblage" RELATED [] synonym: "Y-shaped fiber" RELATED [] synonym: "Y-shaped fibre" RELATED [] synonym: "Y-shaped linker" RELATED [] is_a: GO:0043234 ! protein complex is_a: GO:0044441 ! cilium part relationship: part_of GO:0035869 ! ciliary transition zone

id: GO:0097538 name: ciliary necklace def: "A protein complex located on the cilium membrane in the ciliary transition zone; it is connected to the cilium axoneme via Y-shaped links." [GOC:cilia, PMID:22653444, PMID:4554367] synonym: "cilium necklace" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044441 ! cilium part relationship: part_of GO:0035869 ! ciliary transition zone relationship: part_of GO:0060170 ! cilium membrane

id: GO:0097539 name: ciliary transition fiber def: "A nine-bladed, propeller-like protein complex that links the distal end of the basal body and the cilium to the plasma membrane. Functions in protein sorting and gating (i.e. active and passive transport of proteins in and out of the cilium)." [GOC:cilia, GOC:kmv, PMID:22653444, PMID:24231678, PMID:5064817, PMID:5335827] synonym: "ciliary transition fibre" EXACT [] synonym: "cilium transition fiber" EXACT [] synonym: "cilium transition fibre" EXACT [] synonym: "transition fiber" BROAD [] synonym: "transition fibre" BROAD [] is_a: GO:0043234 ! protein complex is_a: GO:0044441 ! cilium part

(John, we tend to use US spelling in GO hence the 'ciliary transition fiber', but I've used the wording 'fibre' in exact synonyms, so you'll still be able to retrieve the GO term if you search for the 'fibre' wording.)

Thanks, Paola

Original comment by: paolaroncaglia

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Looks wonderful Paola! Thanks. US spelling is fine for me if that is your default. I always get confused anyway between the UK and US spelling.

Original comment by: johnvandam

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Hi Paola,

This is great that you're working on improving ciliary terms. I've recently started a project to annotate ciliary genes in mouse, so I've noticed a number of times that the term I need exists, but the term name uses "flagellar" and there is no synonym that includes the word "cilia" or "cilium", so these terms are sometimes quite hard to find.

Thanks for working on this!

-Karen

Original comment by: krchristie

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Hi Karen,

Thanks for pointing that out; John made a similar note in his spreadsheet, so I'll work on standardizing names/adding synonyms too.

Paola

Original comment by: paolaroncaglia

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A bit more work:

merged 'cilium axoneme' into 'axoneme'; made 'axoneme' a 'cilium part'; moved 'cilium part' under 'organelle part' (rather than 'intracellular organelle part'); worked on some synonyms.

Original comment by: paolaroncaglia

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I've also merged 'cilium axoneme assembly' into 'axoneme assembly'.

Original comment by: paolaroncaglia

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This is great Paola! This was the biggest issue within the existing ontology that needed to be resolved.

Thanks, John

Original comment by: johnvandam

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Hi John,

Wrt your comment in your initial request: "some terms define areas through which other components cross, like "ciliary transition zone" and "axoneme", in the excel file I've made "axoneme" part_of "ciliary transition zone", but I'm not quite sure if it is the way to go."

The axoneme extends beyond the ciliary transition zone, so in GO speak we can't make it part_of it. The statement "axoneme part_of ciliary transition zone" would mean that an axoneme can only exist when it's embedded in the ciliary transition zone and nowhere else, which is incorrect.

Is the portion of the axoneme located in the ciliary transition zone structurally/functionally/compositionally any different than the rest of the axoneme as far as you know? I could create a term to indicate the portion of the axoneme located within the transition zone, if it's useful/meaningful, and make it part_of both terms. If not, I'd suggest annotating proteins located there to both terms.

Let me know if this doesn't make any sense... cheers, Paola

Original comment by: paolaroncaglia

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More done: standardized names and synonyms; edited defs. accordingly. So e.g. 'flagellar pocket' is now 'ciliary pocket' ('flagellar pocket' stays as an exact synonym). Opted to use the adjective 'ciliary' in all primary names, for consistency with other parts of the ontology ('ciliary part' rather than 'cilium part', similarly to 'nuclear part'). Added/kept 'cilium' in synonyms; also added 'cilial' synonyms.

Original comment by: paolaroncaglia

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Hi Paola,

There are some differences between the axoneme in the transition zone and the axoneme in the ciliary shaft. Most notably the central pair starts just above the TZ towards the tip, but there is no central pair observed within the TZ. I am not sure if this is also the case for the inner and outer dynein arms, radial spokes, etc. I don't think research in general make a distinction though, so I think you are right in solving it this way.

Original comment by: johnvandam

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Before I forget - standardized all ciliary names/synonyms in the Process and Component branch. The only instance where the primary name still contains 'flagellum' rather than cilium is 'sperm flagellum', based on community/literature usage, but I've given it a 'cilium' synonym.

Original comment by: paolaroncaglia

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Thanks for your reply John. So for the time being I'll leave 'axoneme' and TZ as they are, but I'll do more work on this next week (sorry, I'm not in tomorrow).

Best, Paola

Original comment by: paolaroncaglia

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Hi John and Karen,

I have a question about this note from John that I hope you may help me with:

"GO:0030990 [intraciliary transport particle, also called 'intraflagellar transport complex' or IFT complex] - I don't think that the IFT complex and its components are part of the axoneme. It is a higly dynamic complex that moves up and down the complex, but never realy becomes part of the core structure."

The current def. of GO:0030990 says "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.". For children of 'protein complexes', such as this one, we use the part_of relationship to give some structure to the node and indicate where the complex is found. Do you know of any experimental evidence whereby the IFT has been found somewhere other than the axoneme? I could make it part_of cilium, but this would be too broad based on the current def.

Thanks, Paola

Original comment by: paolaroncaglia

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Hi Paola,

I've been looking up the BP terms for cilia related things and I found them to be rather limited. I expect to supply you with a set of new terms, hopefully next week as I am still trying to get the hang of the specific BP ways of defining terms and subterms. I think we can borrow a lot of logic and terms from the nucleocytoplasmic transport process for the ciliary transport processes.

What immediately caught my eye in the BP, is that it also suffers from disconnected axoneme/cilium terms. "cilium exoneme assembly" is_a "axoneme_assembly", but should be a synonym. Also "axoneme assembly" is currently not part_of "cilium assembly".

I'll try to get back on this a.s.a.p.

Cheers, John

Original comment by: johnvandam

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Hi Paola,

In response to your question about the IFT complex, I agree that the IFT complexes are not part_of the axoneme, but rather complexes that interact with the axoneme to move along it, with the IFT-B subcomplex providing anterograde transport activity and the IFT-A subcomplex providing retrograde transport.

However, I have seen some suggestions that at least some IFT complex subunits have roles outside of the cilium. Follit et al. 2009 talk about an Golgi IFT complex that may be involved in transport of sorting of cilium membrane proteins and the and Bhogaraju et al. review talks about that too. The Taschner et al. review also talks about roles of some IFT complex proteins outside the cilia.

Since the IFT complex seems to be required for properly assembled and functioning cilia, perhaps it would work to say that the "cilium" has_part "IFT complex".

-Karen

Follit JA, Xu F, Keady BT, Pazour GJ. Characterization of mouse IFT complex B. Cell Motil Cytoskeleton. 2009 Aug;66(8):457-68. doi: 10.1002/cm.20346. PubMed PMID: 19253336

Taschner M, Bhogaraju S, Lorentzen E. Architecture and function of IFT complex proteins in ciliogenesis. Differentiation. 2012 Feb;83(2):S12-22. doi: 10.1016/j.diff.2011.11.001. Epub 2011 Nov 25. Review. PubMed PMID: 22118932.

Bhogaraju S, Engel BD, Lorentzen E. Intraflagellar transport complex structure and cargo interactions. Cilia. 2013 Aug 14;2(1):10. doi: 10.1186/2046-2530-2-10. PubMed PMID: 23945166

Original comment by: krchristie

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Hi John,

As per your comment: " "cilium exoneme assembly" is_a "axoneme_assembly", but should be a synonym. Also "axoneme assembly" is currently not part_of "cilium assembly"."

Actually, these links are now in place - as I wrote down here last week, I merged 'cilium axoneme assembly' into 'axoneme assembly'. So 'cilium axoneme assembly' is now in GO only as a synonym of 'axoneme assembly'. And 'axoneme assembly' is indeed part_of 'cilium assembly'. Unfortunately you won't be able to see the new links (or the new terms) unless you update your copy of the ontology to the latest one, which I believe might have been the issue here.

Please feel free to post here any feedback you may have on BP terms, this will be a work in progress as we work through. And let me know if you need any assistance with files or if anything I write is unclear :-)

Thanks! Paola

Original comment by: paolaroncaglia

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Hi Karen (and John),

Karen's suggestion "Since the IFT complex seems to be required for properly assembled and functioning cilia, perhaps it would work to say that the "cilium" has_part "IFT complex"."

makes sense to me. What we'd be saying with this link is that a functional cilium must necessarily contain an IFT complex. At the same time we would not be ruling out that IFT complexes can be observed outside the cilium. John, if this works for you too, I'll remove the link 'intraciliary transport particle' is_a 'axoneme part', I will add instead a link "cilium" has_part "IFT complex", and I'll add Karen's PMID references to 'cilium'.

Thanks, Paola

Original comment by: paolaroncaglia

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Hi Paola,

Yes, of course! I now remember. Sorry about that. I'll download the latest version now.

Original comment by: johnvandam

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Hi Paola,

The "cilium" has_part "IFT complex" makes total sense. The role of IFT components in coated vesicle transport is just beginning to emerge, specifically for vesicle transport towards the neural synapse.

Original comment by: johnvandam

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To start with:

Removed link 'intraciliary transport particle' is_a 'axoneme part'; Added link 'cilium' has_part 'intraciliary transport particle'; 'intraciliary transport particle B': added PMID: 19253336 and 'IFT complex B' as an exact synonym; 'intraciliary transport particle': added PMID: 22118932 and PMID: 23945166; 'axoneme part': added exact synonym 'axonemal part'.

More soon...

Original comment by: paolaroncaglia

[gocentral]

Added new terms (full stanzas below for details):

GO:0097540 axonemal central pair GO:0097541 axonemal basal plate GO:0097542 ciliary tip GO:0097543 ciliary inversin compartment GO:0097544 ciliary shaft GO:0097545 axonemal outer doublet

Here are the full ontology stanzas for your reference (John, I've edited your suggested definitions slightly, but their meaning was kept the same) (and Karen, I've added 'flagellar' synonyms where appropriate):

[Term] id: GO:0097540 name: axonemal central pair namespace: cellular_component def: "Part of the axoneme consisting of the inner two microtubule doublets of the 9+2 axoneme occurring in most motile cilia." [GOC:cilia, PMID:24283352] synonym: "axonemal microtubule central pair" EXACT [] synonym: "axoneme central pair" EXACT [] synonym: "axoneme microtubule central pair" EXACT [] synonym: "central pair" BROAD [] synonym: "central-pair microtubules" RELATED [] is_a: GO:0044447 ! axoneme part created_by: paola creation_date: 2013-12-12T11:07:09Z

[Term] id: GO:0097541 name: axonemal basal plate namespace: cellular_component def: "Part of the axoneme consisting of a highly electron-dense region at the distal end of the ciliary transition zone within the axonemal lumen at which the axonemal central pair of microtubules is connected to the rest of the axonemal structure." [GOC:cilia, PMID:23352055, PMID:4554367] synonym: "axoneme basal plate" EXACT [] synonym: "basal plate" BROAD [] is_a: GO:0044447 ! axoneme part created_by: paola creation_date: 2013-12-12T11:10:39Z

[Term] id: GO:0097542 name: ciliary tip namespace: cellular_component def: "Part of the cilium where the axoneme ends. The ciliary tip has been implicated in ciliary assembly and disassembly, as well as signal transduction." [GOC:cilia, PMID:23970417] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "cilial tip" EXACT [] synonym: "cilium tip" EXACT [] synonym: "flagellar tip" EXACT [] synonym: "flagellum tip" EXACT [] is_a: GO:0044441 ! ciliary part created_by: paola creation_date: 2013-12-12T11:12:22Z

[Term] id: GO:0097543 name: ciliary inversin compartment namespace: cellular_component def: "Proximal part of the ciliary shaft to which the inversin protein (also called Inv) specifically localizes. The inversin compartment appears to have a different protein composition than the rest of the cilium, although there is no structure that separates it form the distal part of the cilium." [GOC:cilia, PMID:19050042] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "cilial inversin compartment" EXACT [] synonym: "cilium inversin compartment" EXACT [] synonym: "flagellar inversin compartment" EXACT [] synonym: "flagellum inversin compartment" EXACT [] synonym: "Inv compartment of the cilium" EXACT [] synonym: "inversin compartment" BROAD [] is_a: GO:0044441 ! ciliary part created_by: paola creation_date: 2013-12-12T11:14:36Z

[Term] id: GO:0097544 name: ciliary shaft namespace: cellular_component def: "The mid part of a cilium between the ciliary base and ciliary tip that extends into the extracellular space." [GOC:cilia, PMID:19866682] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "cilial shaft" EXACT [] synonym: "cilium shaft" EXACT [] synonym: "flagellar shaft" EXACT [] synonym: "flagellum shaft" EXACT [] is_a: GO:0044441 ! ciliary part created_by: paola creation_date: 2013-12-12T11:17:30Z

[Term] id: GO:0097545 name: axonemal outer doublet namespace: cellular_component def: "Part of an axoneme consisting in a doublet microtubule. Nine of these outer doublets form the 9+0 axoneme, while the 9+2 axoneme also contains a central pair. Dynein arms attached to the doublets provide the mechanism of movement of the cilium." [GOC:cilia, http://en.wikipedia.org/wiki/Axoneme, PMID:5044758, PMID:5664206] synonym: "axoneme outer doublet" EXACT [] synonym: "outer doublet" BROAD [] synonym: "outer-doublet microtubules" RELATED [] is_a: GO:0044447 ! axoneme part created_by: paola creation_date: 2013-12-12T11:19:29Z

Thanks, more later, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi again John (and Karen),

I have a question on your suggested term 'ciliary base'. Your suggested definition is:

"Proximal part of the cilium. Often used to refer to a collective localization of proteins to the basal body and transition zone. May or may not also include pheripheral centromal matrix."

I'm wondering if this should be a proper component term or rather a related synonym for 'ciliary basal body' and 'ciliary transition zone'. In the former case, I'd add it as follows, please let me know if this is correct (I'm basing on Fig. 1 in PMID:23352055):

GO:NEW ciliary base is_a ciliary part Def: Proximal part of the cilium that includes the ciliary basal body, ciliary transition fibers and ciliary transition zone. has_part ciliary basal body, ciliary transition fibers and ciliary transition zone [but does the basal body include the peripheral centriolar matrix? As this is said not to always be the case for the ciliary base in John's suggested def.]

Note that the def. of 'ciliary shaft' refers to 'ciliary base' currently, so I may have to edit that based on the outcome.

Let me know what you think, thanks! Paola

Original comment by: paolaroncaglia

[gocentral]

One more question: is the invertin compartment located in primary cilia only, as PMID:19050042 suggests?

(In general, we'll need to look at cilia, primary cilia and motile cilia as we have them in GO now, to make sure they're correct, and we'll also need to decide if we want to add axoneme children for the 9+0 and 9+2 types, but let's keep these issues aside for today, my aim today was to get you all the missing terms so your colleagues may start annotation when they wish. Other than 'ciliary base', all terms in John's list are in now.)

Thanks, Paola

Original comment by: paolaroncaglia

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Thanks Paola! This is great! I am in contact with the annotation people in CCNet and they are going to start their first annotation pilots focussing on the transition zone.

All the newly added terms look perfect, thanks! Regarding your other questions:

Regarding "Ciliary base": It is not a proper component term, but it has value to exist in one form or another. In many publications researchers use microscope technology and control proteins that diminish resolution. I.e. it is not clear if the protein localizes specifically to the basal body or TZ or both, but it is clear that it localizes at the base of the cilium, and does not enter the cilium proper. In order to capture that information I thought that having "ciliary base" as a term would be useful. However I can also appreciate that you would want to keep the gene ontology as clean as possible and not "invent" terms that do not specifically refer to a tangible structure or compartment. To be clear, it is not a specific component by itself. If it can be solved by a shared synonym between basal body and transition zone, that would be sufficient. Although I do not know how this in practise would work. Could you maybe explain how that would work in practise?

Regarding the "inversin compartment" and Motile vs. primary cilia... That's a difficult one. Given PMID: 22206729 where inversin is mentioned conjoined with motile cilia, I think that PMID:19050042 only talks about primary cilia, because that is the type they've been looking at. So that doesn't exclude the inversin compartment being present in motile cilia. This is a big issue within the cilia field. Not many take effort to distinguish between primary or motile cilia, but just report on what they found in cilia of type X. Things like making a difference for 9+0 and 9+2 axonemes suffer from notable exceptions to the rules. There is at least one case of motile cilium that does not have a central pair (the nodal cilium, currently in GO as "motile primary cilium"), and one that is considered "primary" but has a 9+2, sometimes 9+4, axoneme (kinocilium).

I will send an email to some of our consortium partners to ask about the inversin compartment and get that straight.

Thanks!

John

Original comment by: johnvandam

[gocentral]

Hi John,

Thanks for your comments. If I add 'ciliary base' as a synonym to basal body and TZ, if you annotate a paper that can't distinguish between the two locations, you'd have to make a choice - annotate to one, to both, or to 'cilium'. In the first two cases, your annotation may end up being incorrect. In the third case, your annotation would be correct, but not as granular as it could be. Since it's used in the literature, I'd add the term in its own right, and explain the resolution issue in a definition comment, to warn curators (the idea is you'd want them to refer to a more specific ciliary part if at all possible, otherwise fine to use 'ciliary base'). I hope this makes sense. I'll add the term next week - I'll be on leave tomorrow and Monday, but feel free to leave any comment here and I'll get back to you next week.

Thanks! Paola

Original comment by: paolaroncaglia

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Hi Paola,

Sounds good! I've just quickly checked for myself again how it is used in the literature. Definitions differ slightly, but in general cover distal part of basal body + centriolar appendages, transition fibers and transition zone. PMID:22653444 gives a good overview. I do want to change the definition to make it more precise and in line with literature. I'll put it here before you get back.

John

Original comment by: johnvandam

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Hi Paola,

Here is a slightly longer definition for the ciliary base, also explaining the annotation issues.

Area of the cilium/flagellum where the basal body and axoneme is anchored to the plasma membrane. It encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium and many proteins localize specifically to this area. Due to resolution issues researchers are often unable to assign protein localisation to the more specific ciliary compartments and instead refer to ‘ciliary base’. The compartments ‘Basal body’, ‘transition fibers’ and ‘transition zone’ represent strictly defined compartments at the ciliary base and should be used for annotation whenever possible.

I hope this helps.

Cheers, John

Original comment by: johnvandam

[gocentral]

Hi John, Thanks for your feedback on the ciliary base. I've added the term as follows, I hope it's ok:

[Term] id: GO:0097546 name: ciliary base namespace: cellular_component def: "Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area." [GOC:cilia, PMID:22653444] comment: Due to resolution issues, researchers are often unable to assign protein localization to more specific ciliary compartments such as the basal body, transition fibers or transition zone, and instead refer to 'ciliary base'. The terms GO:0036064 'ciliary basal body', GO:0097539 'ciliary transition fiber' and GO:0035869 'ciliary transition zone' represent strictly defined compartments at the ciliary base and should be used for annotation whenever possible. Also, note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "cilial base" EXACT [] synonym: "cilium base" EXACT [] synonym: "flagellar base" EXACT [] synonym: "flagellum base" EXACT [] is_a: GO:0044441 ! ciliary part

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi again John,

(Karen, may I please have your feedback on this one too?)

As for your second-last note in the spreadsheet you provided:

"GO:0005932 microtubule basal body. I think this term is redundant to GO:0036064 cilium basal body. It has only one child term (ciliary basal body), and the definition overlaps."

I think you're right - this probably dates back to when GO differentiated between cilia and eukaryotic flagella. I could merge 'microtubule basal body' and 'ciliary basal body', leaving the latter as the primary name and the former as a synonym. However, 'microtubule basal body' has 139 direct manual experimental annotations, and I'd need to get a feel if they'd all be correct under 'ciliary basal body'. My assumption is yes, but I'd like to ask Karen Christie, a curator at Mouse Genome Informatics, if she'd agree based on the MGI annotations (which are >50% of the 139 above), or if she'd have different suggestions.

Thanks, Paola

Original comment by: paolaroncaglia

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I've also added a definition comment to 'ciliary shaft' based on the last line in the spreadsheet:

"Note that 'ciliary shaft' is sparingly used in the literature to denote the projecting part of the cilium; many authors would refer to the axoneme instead. However, the definition of GO:0005930 'axoneme' is rather stringent, and the localization of many ciliary proteins would not fit that definition."

Original comment by: paolaroncaglia

[gocentral]

Looks perfect! Thanks!

Original comment by: johnvandam

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Hi Paola,

Sure, I can take a look at some of the MGI annotations to develop an opinion on the question of merging "GO:0005932 - microtubule basal body" with "GO:0036064 - cilium basal body". I'm sure that will take me a few days, but I'll post my thoughts here.

-Karen

Original comment by: krchristie

[gocentral]

• summary: Cilia: new terms and links --> Cilia: new terms and links - cellular component branch

Original comment by: paolaroncaglia

[gocentral]

Hi Karen (and John),

Thanks. Sure, I'll keep this ticket open, so feel free to add comments later on - I'd like to do one last check of existing terms and links to make sure they're all correct, and I hope to do that by the end of the week. At any rate the priority was to add all of John's terms and take into account all of his comments on the spreadsheet and that's all done now. John, I think we should keep this ticket for cellular component terms only, and open a new one when you have suggestions for the biological process branch, so it's easier to find information. Simply email me later on with your requests/comments on ciliary process terms, and I'll make a new ticket. Thanks!

Paola

Original comment by: paolaroncaglia

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Hi Paola,

I have looked through all of the mouse annotations to "microtubule basal body" for 28 mouse genes from 21 papers.

In all cases, I think annotations to "microtubule basal body" could be transferred to "ciliary basal body" or (for a very small number) were just wrong. I have already updated the annotations that were made by MGI. I did not come across anything that would distinguish those two terms.

I also came across a couple papers (listed below) that deal with sterocilia (I know, not actual cilia) and the associated kinocilium and talk about "the basal body" in this context. From those papers, I have developed the impression that there are proteins that are found in the basal bodies of kinocilia, but not of other cilia. So, I think we should consider adding an additional term for "kinociliary basal body" to distinguish these from "regular" ciliary basal bodies.

PMID:15855039 Leibovici et al. 2005 PMID:15882574 Lagziel et al. 2005

-Karen

Original comment by: krchristie

[gocentral]

Many thanks to Karen for her work and suggestions. I'll add the new term after the holidays, and will look into merging "microtubule basal body" and "ciliary basal body".

Other than this, I think that the only pending questions about the cellular component branch of cilial terms are about

1) the only is_a children (and grandchildren) of 'cilium', i.e. 'motile cilium' and 'primary cilium'. Are their placement, definitions, links correct? Currently, 'ciliary transition zone' is part_of 'nonmotile primary cilium': is this correct or is it too restrictive?

2) Do we need additional axoneme terms to describe 9+0, 9+2, etc.?

I have the feeling based on John's comments that both these points may not be straightforward. I'm happy to leave the ontology structure as is, provided the existing links are correct; we may add new terms as/if the need arises. When you have a chance, please take a look at the most updated version of the cilium component ontology (I did a couple more edits today too), and let me know if you have any comments.

I'll be on leave for a couple of weeks now, so very happy holidays and speak to you next year!

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Paola and Karen,

Just some remarks and answers before Christmas (feel free to ignore until after the festivities :-) )

Karen has a good point, in that each particular "type" of cilium likely has its own unique composition of the various sub-compartments like the TZ and basal body. I am just wondering if there is a better way of creating duplicate terms for every sub-type? Because it will inflate the number of terms greatly. Would it also work to annotate proteins as "cilium basal body" and "kinocilium"? However for some cilium types there are widely used different names for the same thing. I only just realized this: The term GO:0032391 Photoreceptor connecting cilium is actually the transition zone of that highly modified cilium, while the "photoreceptor outer segment" GO:0001750 is actually a highly modified ciliary shaft and tip. The term connecting cilium is however a widely used term in literature and has specific meaning in that context. Currently "photoreceptor connecting cilium" has not been linked to "transition zone". So we already do have some "type" specific naming of particular subcompartments. Not sure what to do with the other types... What are your thoughts?

Regarding Paola's questions: 1) The definition of "primary cilium" is rather poor, but both terms are regarded as a very important main distinction of cilia into two sub-categories. I've also heard somebody say that the transition zone may be substantially different between the two, but of course I can not find a reference for that nor recollect the person who I think said that... The transition zone is definitely part of both types, not just the primary cilium! PMID:1706225 is a paper from 1990 states: "Based on morphological similarities, the photoreceptor connecting cilium is thought to be homologous to the transition zone of the motile cilium. As such, we have stained oviduct epithelium with the K26 monoclonal antibody. Immunoreactivity is restricted to the region of the transition zone at the base of motile cilia." I could not find anything older or more specific that this one at this time, but it appears that the TZ was actually first described for motile cilia (my bet is on the flagella of the algae Chlamydomonas). I am having trouble with coming up with a better definition of the primary cilium (other than that they are supposed to be non-motile). I'll email one of the experts within cilia and ask them what they can come up with. That one will be more likely to represent the opinion of the research field. I'll get back to you on that after the holidays.

2) Concerning the 9+0 and 9+2 terms. That might be very useful indeed. In that way it will be easier to make distinction in the various axonemal terms that are specific for one or the other. These would then be child terms for "axoneme"?

Ok, that's it for now. I have not been able to work much on the BP terms because I am racing to get a large grant proposal finished, my apologies. Happy holidays to you and Rachel and thank you both for all your hard work. I'll speak with you next year!

Best, John

Original comment by: johnvandam

[gocentral]

Dear Karen and John,

Today I merged 'ciliary basal body' and 'microtubule basal body', keeping the former as primary name and the latter as a synonym. I also renamed 'microtubule basal body organization' and 'microtubule basal body duplication' accordingly. Lastly, I emailed authors of manual annotations to the 'microtubule' terms asking them to double-check that those annotations are indeed still ok under 'ciliary' terms. (Karen, QuickGO shows 3 MGI annotations left...?)

Next, I'll add Karen's suggested term and will look carefully into John's latest comment. John, if there's any edit you need urgently, please let me know. Otherwise I'll resume work on this next week.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

That all sounds great! There's no hurry. Next week I'll attend one of our consortium meetings and I have a presentation slot specifically for this project. I hope I get a lot of input there.

Best, John

Original comment by: johnvandam

[gocentral]

I've added GO:1902636 kinociliary basal body

Note for self: I still need to look into John's comment from just before Christmas.

Cheers, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi John and Karen,

I've been quite busy with other projects lately and haven't had a chance to look into John's comment yet, but FYI I wanted to let you know that I'm working on adding a bunch of cellular component terms needed to annotate proteins in the intestinal parasite Giardia. Some of the terms the Giardia community needs are for cilia and cilial parts (they need to be able to differentiate among the 8 Giardia flagella as this has relevance for pathogenesis). In case you're interested, there's a separate ticket for this work where the terms added so far are listed:

https://sourceforge.net/p/geneontology/ontology-requests/10642/

Thanks, and I'll be in touch again as soon as I manage. Of course John you're more than welcome to update this ticket for cilial cellular components, or to email me when you have requests for process terms and I'll make a separate ticket for those.

Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

The same goes for me as well. That said, I am determined to figure out the correct way to represent 9+0 and 9+2 axonemes and figure out how to incorporate the motile vs non-motile cilia subclasses. I will not manage to do this this week unfortunately. I will update this thread when I have something.

Concerning the Giardia project, that sounds great! If I or SYSCILIA can play any role in defining species specific or more general terminology, please let me know.

Best, John

Original comment by: johnvandam

[gocentral]

Thanks John! Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: New term request, Other term-related request --> New term request, Other term-related request, Cilia/flagella

Original comment by: paolaroncaglia

[gocentral]

• labels: New term request, Other term-related request, Cilia/flagella --> New term request, Other term-related request, Cilia/flagella, mini-project

Original comment by: paolaroncaglia

[gocentral]

Hi John, hope all is well with you!

While I'm hoping to be able to do some more work on this later this summer, I just wanted to add a comment that, with regard to these issues:

"I am determined to figure out the correct way to represent 9+0 and 9+2 axonemes and figure out how to incorporate the motile vs non-motile cilia subclasses."

Karen and Chris have some useful comments in this other ticket: https://sourceforge.net/p/geneontology/ontology-requests/10951/

Thanks, Paola (will be away on leave for some time now)

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

I am very well! Thank you! How are you? I have been slightly overburdened lately. Which is also why I have been silent. My sincerest apologies. I hope stuff will settle down in the holidays a bit so I will be able to work on the 9+0 9+2 thing. I say hope because due to issues with extending my contract things have become rather complex at the moment. I will do my best.

Best, John

Original comment by: johnvandam

[gocentral]

Hi John, thanks for replying so promptly. I'm doing fine thanks; like you, quite busy, so I understand. I'm sorry to hear there are troubles and I hope we'll be in touch soon. Your feedback on cilia matters is much appreciated. So, for now I wish you all my best, and speak soon.

Thanks! Paola

Original comment by: paolaroncaglia