Cilium terms

[gocentral]

I needed to annotate a C. elegans odorant receptor to the cellular component term cilium, GO:0005929, but realized that the definition did not apply to the type of cilia to which this protein localizes. I'd like to propose a change to the cilium definition and the addition of three is-a cilium child terms.

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Relevant references for these suggested changes include:

Scholey JM. Intraflagellar transport. Annu Rev Cell Dev Biol. 2003;19:423-43. Review. PMID: 14570576

Praetorius HA, Spring KR. A physiological view of the primary cilium. Annu Rev Physiol. 2005;67:515-29. PMID: 15709968

McGrath J, Somlo S, Makova S, Tian X, Brueckner M. Two populations of node monocilia initiate left-right asymmetry in the mouse. Cell. 2003 Jul 11;114(1):61-73. PMID: 12859898

Pazour GJ, Witman GB. The vertebrate primary cilium is a sensory organelle. Curr Opin Cell Biol. 2003 Feb;15(1):105-10. Review. PMID: 12517711

Mitchell DR. Speculations on the evolution of 9+2 organelles and the role of central pair microtubules. Biol Cell. 2004 Dec;96(9):691-6. PMID: 15567523

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1) The current definition of cilium states that a cilium is a specialized eukaryotic locomotor organelle that consists of a filiform extrusion of the cell surface. In eukaryotes, however, there are at least three types of cilia, one of which is nonmotile. Therefore, can we remove the term "locomotor" from the cilium definition and create three is-a cilium child terms that are specific for each type?

GO term: cilium

GO id: GO:0005929

Current Definition: A specialized eukaryotic locomotor organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.

Suggested New Definition: A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.

2) The proposed additions/changes to the ontology would be:

cellular component -cell ---cell projection ----cilium -----motile primary cilium -----nonmotile primary cilium ------photorecetor outer segment -----motile secondary cilium

The new terms:

term: motile primary cilium synonym: motile monocilium goid: new definition: A specialized primary cilium that contains a 9 + 0 arrangement of microtubules, radial spokes, and a dynein apparatus, but no inner doublet microtubules. Motile primary cilia display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface. definition_reference: WB:KVA

term: nonmotile primary cilium synonym: sensory cilium goid: new definition: An immotile primary cilium that may be missing the central pair of microtubules, or the central pair of microtubules and outer dynein arms. Some primary cilium also have altered arrangements of outer microtubules (fewer than nine and/or not always present as doublets). Nonmotile primary cilia typically function as sensory organelles that concentrate and organize sensory signaling molecules. definition_reference: WB:KVA

Note: The existing photoreceptor outer segment term would be an is-a child of nonmotile primary cilium.

term: motile secondary cilium synonym: motile cilium goid: new definition: A cilium that consists of a 9 + 2 arrangement of microtubules, radial spokes, and a dynein apparatus. Motile cilia, found on cells that line the lumenal ducts of various tissues, beat with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface.
definition_reference: WB:KVA

There are some Biological Process terms involving cilia that may also need to be revised if these additions to Cellular Component are approved. I believe those changes would be quite straightforward, but will take a look to make sure that's true.

Thanks, Kimberly

Reported by: vanaukenk

Original Ticket: "geneontology/ontology-requests/2588":https://sourceforge.net/p/geneontology/ontology-requests/2588

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

added motile primary cilium GO:0031512 nonmotile primary cilium GO:0031513 motile secondary cilium GO:0031514

and adjusted def of cilium as suggested

Original comment by: mah11

[gocentral]

• milestone: --> WormBase
• status: open --> closed-accepted

Original comment by: mah11