Cilia morphology and function

[obophenotype-user]

I've found that our MP lacks some general cilia morphology and function terms. Would it be possible to add some under cellular phenotype? Some times general cilia function and morphology is tested in culture and the tissue type is either not given or used as a representative tissue. Could we also add some general term for tracheal epithelium cilia morphology and function? I don't have the numbers on the frequency of use but it seems I've come across this issue a few times. Currently I am annotating PMID 19675306 in which the function of tracheal epithelium cilia function in culture and I had to back off the annotation term to abnormal respiratory system physiology [MP:0002133]. We do have a term for mucociliary clearance but that is a specific function of the respiratory system cilia.

Reported by: michknow

Original Ticket: obo/mammalian-phenotype-requests/520

[obophenotype-user]

This will probably turn into a "big thing". An initial survey of annotations containing the word "cilia" returned a huge number of alleles. There are a lot of tissues that I can think of that are ciliated, and defects in the cilia would definitely impair function (ventricular ependyma, respiratory tissues, etc..)

Original comment by: cindyJax

[obophenotype-user]

• assigned_to: nobody --> cynthiasmith

Original comment by: cindyJax

[obophenotype-user]

Since the initial comment, GO has added some terms as children of GO:0005929. Time to revisit this ticket.

GO term: cilium GO id: GO:0005929 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.

GO term: motile primary cilium
Synonym: motile primary cilia
Synonym: nodal cilium
GO id: GO:0031512
Definition: A primary cilium which may contain a variable array of axonemal microtubules and also contains molecular motors. Motile primary cilia display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization.
Comments Note that this term should not be confused with 'motile cilium ; GO:0031514': Motile primary cilia are distinct from motile cilia (GO:0031514) that are typically present on epithelial cells in multiple copies and move in a whip-like, as opposed to rotational, manner.
GO term: nonmotile primary cilium
Synonym: immotile primary cilium
Synonym: nonmotile primary cilia
Synonym: sensory cilium
GO id: GO:0031513
Definition: A primary cilium which contains a variable array of axonemal microtubules but does not contain molecular motors. Nonmotile primary cilia are found on many different cell types and function as sensory organelles that concentrate and organize sensory signaling molecules.

GO term: primary cilium
GO id: GO:0072372
Definition: A cilium found on many different cell types that is typically present in a single copy per cell. A primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors.

GO term: motile cilium
Synonym: motile cilia
Synonym: motile secondary cilium
GO id: GO:0031514
Definition: A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may also function as sensory organelles.
Comments Note that this term should not be confused with 'motile primary cilium ; GO:0031512': Motile cilia are distinct from motile primary cilia (GO:0031512) that are typically present during embryogenesis in a single copy per cell, affect asymmetric body plan organization, and move in a rotational manner, as opposed to a whip-like, manner.

Original comment by: cindyJax

[obophenotype-user]

See new respiratory cilia terms added (ID: 3279349).

Note that we already have terms for "embryonic cilium" (="motile primary cilium"); the definitions for MP:0008933, MP:0004131, and MP:0004132 were revised and synonyms derived from GO:0031512 were added.

Also added:

abnormal ependyma motile cilium morphology [MP:0011059]

abnormal brain ependyma motile cilium morphology [MP:0011056]

absent brain ependyma motile cilia [MP:0011057]

abnormal spinal cord motile cilium morphology [MP:0011058]

id: MP:0011060 name: abnormal kinocilium morphology

id: MP:0011061 name: abnormal inner hair cell kinocilium morphology

id: MP:0011062 name: abnormal outer hair cell kinocilium morphology

id: MP:0011063 name: absent inner hair cell kinocilia

id: MP:0011064 name: abnormal vestibular hair cell kinocilium morphology

id: MP:0011065 name: abnormal kidney epithelial cell primary cilium morphology

id: MP:0011066 name: abnormal renal tubule epithelial cell primary cilium morphology

More terms are pending and may be added after another annotation survey when these updates are completed.

Original comment by: cindyJax

[obophenotype-user]

• status: open --> pending-accepted

Original comment by: cindyJax

[obophenotype-user]

More terms from tracker ID: 2414432

abnormal ependyma motile cilium physiology [MP:0011068]

abnormal brain ependyma motile cilium physiology[MP:0011069]

abnormal spinal cord motile cilium physiology [MP:0011070]

Original comment by: cindyJax

[obophenotype-user]

Also added new terms for oviduct motile cilia, see tracker 3512958

id: MP:0011644 name: abnormal oviduct epithelium motile cilium morphology

id: MP:0011645 name: absent oviduct epithelium motile cilium

Original comment by: cindyJax

[obophenotype-user]

Closing this ticket. Several physiology and ciliary motility terms have also been added recently.

Original comment by: cindyJax

[obophenotype-user]

• status: pending-accepted --> closed-accepted

Original comment by: cindyJax