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SPKW mapping #451

Closed gocentral closed 9 years ago

gocentral commented 17 years ago

SP_KW:KW-0206 cytoskeleton SP_KW:KW-0760 structural molecule activity

these keywords appear in all actin family members, but not all actin family members are structural molecule activity cytoskeleton

some actin family are members of chromatin remodelling complexes (SWI?SNF, RSC etc).

The mapping, or the keywords, need removeing

(I think this was done before but has 'reappeared' ??)

Is there any way to stop these being 'reestablished after they have been removed?)

Thanks

Val

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/451":https://sourceforge.net/p/geneontology/annotation-issues/451

gocentral commented 17 years ago

Original comment by: mah11

gocentral commented 17 years ago

Logged In: YES user_id=1647919 Originator: NO

Hi Val,

In the Spkw2go tool I only see a mapping from SPKW cytoskeleton to GO cytoskeleton term, GO:0005856 and NOT to structural molecule activity, honest..

is it possible that you have used an old mapping file...

unless another kw2go mapping is creating the structural molecule activity term...if you send me some accessions I'll check then out..

cheers, Evelyn

Original comment by: camon

gocentral commented 17 years ago

Logged In: YES user_id=516865 Originator: YES

sorry its Structural protein

heres one: Q09849

Original comment by: ValWood

gocentral commented 17 years ago

Logged In: YES user_id=1647919 Originator: NO

Hi Val,

Thanks for all this feedback, I'm really grateful.

Here is the spkw definition of structural protein:

Proteins that serve as supporting filaments, cables or sheets, to give biological structures strength or protection.

and here the GO definition for 'structural molecule activity' The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell.

ok so the GO term def looks very particular to complex assembly while the kw seems to refer to biological structure integrity however the children of 'structural molecule activity' seem to refer also 'biological structure integrity'..

I'm wondering whether the def for 'structural molecule activity' is correct???? Im going to cc this sourceforge item to GO editors mailing list for further advice...

Evelyn

Original comment by: camon

gocentral commented 17 years ago

Logged In: YES user_id=516865 Originator: YES

I actually think 'structural molecule activity' is a bit of a crap GO term. It seems to be used liberally, for example, for ribosomal proteins which haven't got any other identified molecular function terms. Then it is used for things like actin tubulin etc because of its cytoskeletal role. Also for subunits of complexes which appear to be 'scaffold proteins'

my issue with actin is that many actin related proteins are not cytoskeletal proteins at all, they are part of chromatin remodelling complexes (like RSC/SWISNF and SAGA). In fact, actin itself has dual functionality and is a member of both SWR1 and INO80, and its role here may not be 'structural' but this doesn't matter so much as 'canonical actin' it clearly always has a structural role.

For the other actin related proteins, I'm not sure there is evidence that they do.

But with the current def, maybe it would be hard to exclude any complex member from having this annotation!

Original comment by: ValWood

gocentral commented 17 years ago

Logged In: YES user_id=436423 Originator: NO

> I actually think 'structural molecule activity' is a bit of a crap GO > term.

I tend to agree; the child terms are even worse, because they mention cellular components and anatomical structures -- stuff that's not supposed to be in the function ontology. But I think we're stuck with at least the parent for the duration ... and some gene prods really do seem to be important because they help hold structures together, so the term isn't totally bogus.

That doesn't address whether it's a good term to use for actin, let alone for actin-related proteins ...

m

Original comment by: mah11

gocentral commented 17 years ago

Original comment by: edimmer

gocentral commented 16 years ago

Original comment by: sf-robot

gocentral commented 16 years ago

Original comment by: mah11

gocentral commented 13 years ago

I think this is fixed.....

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: ValWood