cilium/flagellum

[gocentral]

[Term] id: GO:0005929 name: cilium namespace: cellular_component def: "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." [GOC:kmv, ISBN:0198547684] comment: See also the cellular component term 'cilium ; GO:0005929'. subset: goslim_generic ! Generic GO slim subset: goslim_pir ! PIR GO slim synonym: "microtubule-based flagellum" RELATED [] xref: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium is_a: GO:0042995 ! cell projection is_a: GO:0043231 ! intracellular membrane-bounded organelle

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/10193

[gocentral]

I followed the instructions in the comment field, now I'm stuck in a loop...

It seems something odd happened with the flagellum obsoletion.

• flagellum has no consider/replaced_by
• cilium lacks synonyms that might be useful such as "flagellum" - consider a taxon-specific synonym

Original comment by: cmungall

[gocentral]

we should also update the taxon constraints. We have:

[Term]
id: GO:0009434
name: microtubule-based flagellum
relationship: only_in_taxon NCBITaxon:2759 {id="GOTAX:0000118"} ! Eukaryota

But this ID has been merged into

[Term]
id: GO:0031514
name: motile cilium
namespace: cellular_component
alt_id: GO:0009434
def: "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." [GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998]
comment: MERGED COMMENT:\nTARGET COMMENT: MERGED COMMENT:\nTARGET COMMENT: 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.\n--------------------\nSOURCE COMMENT: See also the cellular component term 'cilium ; GO:0005929'.\n--------------------\nSOURCE COMMENT: See also the cellular component term 'cilium ; GO:0005929'.
synonym: "microtubule-based flagellum" RELATED []
synonym: "motile cilia" EXACT [GOC:curators]
synonym: "motile secondary cilium" RELATED [GOC:curators]
is_a: GO:0005929 ! cilium

Original comment by: cmungall

[gocentral]

What about archaea-type flagella?

Original comment by: cmungall

[gocentral]

Does this need revising in light of the decision to obsolete flagellum?

--is_a GO:0048870 ! cell motility [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."]
----is_a GO:0001539 ! ciliary or flagellar motility ***  [DEF: "Cell motility due to movement of cilia or flagella."]
------is_a GO:0060285 ! ciliary cell motility [DEF: "Cell motility due to the motion of one or more cilia."]
------is_a GO:0060286 ! flagellar cell motility [DEF: "Cell motility due to the motion of one or more flagella."]

The decision to have a grouping class for motility is defensible given that this is a functional definition. But it suggests that a grouping of the structure based on function is also defensible.

Even if the above structure is OK, the labels and text defs need to be changed, presumably to:

--is_a GO:0048870 ! cell motility [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."]
----is_a GO:0001539 ! ciliary or *bacterial-type* flagellar motility   [DEF: "Cell motility due to movement of cilia or *bacteria-type* flagella."]
------is_a GO:0060285 ! ciliary cell motility [DEF: "Cell motility due to the motion of one or more cilia."]
------is_a GO:0060286 ! *bacteria-type* flagellar cell motility [DEF: "Cell motility due to the motion of one or more *bacteria-type* flagella."]

Original comment by: cmungall

[gocentral]

What structure is this referring to?

[Term]
id: GO:0036142
name: flagellum movement
namespace: biological_process
def: "The directed, self-propelled movement of a flagellum." [GOC:BHF, GOC:vk]
synonym: "flagellar motility" RELATED []
synonym: "flagellar movement" EXACT [GOC:bf]
is_a: GO:0006928  ! cellular component movement

Original comment by: cmungall

[gocentral]

What should the logical def for this be?

GO:0042073 ! intraflagellar transport [DEF: "The bidirectional movement of large protein complexes along microtubules within a cilium or flagellum, mediated by motor proteins."]

This is_a microtubule based transport, and the text def states microtubules specifically. I assume the intent is that this is referring to a GO:0005929 ! cilium (aka "microtubule-based flagellum").

If so, the label should either be "interciliary transport" or if that is too weird, how about "intraflagellar microtubule-based transport".

The text def should be changed. I believe the disjunction "cilium or flagellum" intends to capture what GO calls a cilium, the disjunction is terminological not logical. I would replace this disjunction with "cilium".

Also: add a logical def when done

Original comment by: cmungall

[gocentral]

Chris this is still in progress - it's a pretty massive set of changes so couldn't get it done in one go...

Original comment by: jl242

[gocentral]

Here's the open ticket:

https://sourceforge.net/p/geneontology/ontology-requests/9885/

I'll see if I can get it finished today...

Original comment by: jl242

[gocentral]

I think all the consider tags and synonyms now in place. I'll take a look at the taxon constraints...

Original comment by: jl242

[gocentral]

Moved the taxon constraint up to cilium:

[Term] id: GO:0005929 name: cilium relationship: only_in_taxon NCBITaxon:2759 {id="GOTAX:0000118"} ! Eukaryota

Also resolved all the merged comment tags!

Original comment by: jl242

[gocentral]

Yes these are structurally different to bacterial flagella (convergent evolution - archaeal flagella actually look to be homologous to bacterial type IV pili - PMID:21482178) so will require their own component terms. I'll make a ticket.

Original comment by: jl242

[gocentral]

Term labels fixed.

I'd be happy with grouping the structures based on function - I've seen 'motility organelle' used in the literature which we might want to use in cc. I think it's biologically interesting to group that way.

Original comment by: jl242

[gocentral]

Was merged with 'cilium movement'.

Original comment by: jl242

[gocentral]

This is always referred to as 'intraflagellar transport' in the literature so I wouldn't want to change the name. You're right though it means transport within a cilium.

I've taken flagellum out of the def, and made it part_of cilium organization.

Logical def could be:

cytoskeleton-dependent intracellular transport occurs_in cilium?

Original comment by: jl242

[gocentral]

On Jun 12, 2013, at 4:48 AM, Jane Lomax wrote:

This is always referred to as 'intraflagellar transport' in the literature so I wouldn't want to change the name. You're right though it means transport within a cilium.

I've taken flagellum out of the def, and made it part_of cilium organization.

Logical def could be:

cytoskeleton-dependent intracellular transport occurs_in cilium?

Agreed

Original comment by: cmungall

[gocentral]

Added cytoskeleton-dependent intracellular transport occurs_in cilium as logical def for intraflagellar transport

Original comment by: jl242

[gocentral]

• status: open --> closed-fixed

Original comment by: jl242