GO cellular component

[Frank Gibson]

Hi,

I though I explicitly raised this issue before NOT to import GO:cellular_component into OBI, somehow it has sneaked in. If you look at the definition, it should be obvious why "The part of a cell or its extracellular environment in which a gene product is located." This includes any part of a cell and an environment. At the very least we cant assert this under material, can we please un-import this class.

Cheers

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

[Bjoern Peters]

From an ontological perspective, I agree that inclusion of 'extracellular environment' and other things that look like sites is problematic.
From a practical perspective, trying to fix this may continue to cause problems, as we will end up having to think about the correct place for each GO:cellular_component subclass we want to import. I don't think we should spend our time improving GO at this point.

If cellular component is not currently used, I am okay with importing all its unproblematic immediate children instead. If the need for cellular component for now is just to have a parent for 'membrane bounded organelle', then importing 'organelle' instead is fine with me (which seems an unproblematic material entity, just as 'protein complex', our other current cellular component child term.

- bjoern






Importing GO:organi
For now, we ca

[Frank Gibson]

On Thu, Jul 16, 2009 at 6:01 PM, Bjoern Peters <bpe...@liai.org> wrote:

From an ontological perspective, I agree that inclusion of 'extracellular environment' and other things that look like sites is problematic.
From a practical perspective, trying to fix this may continue to cause problems, as we will end up having to think about the correct place for each GO:cellular_component subclass we want to import. I don't think we should spend our time improving GO at this point.

agreed
 

If cellular component is not currently used, I am okay with importing all its unproblematic immediate children instead. If the need for cellular component for now is just to have a parent for 'membrane bounded organelle', then importing 'organelle' instead is fine with me (which seems an unproblematic material entity, just as 'protein complex', our other current cellular component child term.

That was the origional suggestion, get rid of the class cellular_component and import stuff directly under material. We needed the membrane_bound_organelle class, not the cellular_component class.

tut tut Alan, how did you miss this in your OBO foundry review, its not like there are 25,000 terms or anything :)



Frank

 

- bjoern






Importing GO:organi
For now, we ca

----- Original Message -----
From: "Frank Gibson" <fgi...@gmail.com>
To: "OBI Developers" <obi-...@lists.sourceforge.net>, obi-bio...@googlegroups.com
Sent: Thursday, July 16, 2009 6:39:04 AM GMT -08:00 US/Canada Pacific
Subject: [obi-biomaterial] GO cellular component

Hi,

I though I explicitly raised this issue before NOT to import GO:cellular_component into OBI, somehow it has sneaked in. If you look at the definition, it should be obvious why "The part of a cell or its extracellular environment in which a gene product is located." This includes any part of a cell and an environment. At the very least we cant assert this under material, can we please un-import this class.

Cheers

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

[kir...@ebi.ac.uk]

Hello,

IMHO either (1) "cellular component" as GO use it is a misnomer, or (2)
the definition should be corrected in GO to get rid of "its extracellular
environment" (to make it consistent with common sense, Wikipedia etc.)
Since
GO:0005576 ! extracellular region is_a: GO:0005575 ! cellular_component
GO:0019012 ! virion is_a: GO:0005575 ! cellular_component, etc.
I think it is more the case of (1), thus GO:0005575 is a useless class.

Kirill

[Alan Ruttenberg]

On Thu, Jul 16, 2009 at 1:08 PM, Frank Gibson<fgi...@gmail.com> wrote:
> That was the origional suggestion, get rid of the class cellular_component
> and import stuff directly under material. We needed the
> membrane_bound_organelle class, not the cellular_component class.

Yes.

> tut tut Alan, how did you miss this in your OBO foundry review, its not like
> there are 25,000 terms or anything :)

:)

For the review I selected some *new* problems that haven't been
complained about for years :)

-Alan