DV: ...process in another organism

[gocentral]

disjointness_violation:

GO:0051672-cell wall peptidoglycan catabolic process in another organism

is both cellular and MOP, through it's is_a parentage to

GO:0016998-cell wall catabolic process

It looks like this has the general pattern for solving these kinds of problems: http://sourceforge.net/tracker/index.php?func=detail&aid=1732046&group\_id=36855&atid=440764

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/4627":https://sourceforge.net/p/geneontology/ontology-requests/4627

[gocentral]

Logged In: YES user_id=436423 Originator: NO

yep, we know what all the disjoint violations are ...

seems this would work for GO:0051672:

MOP [i] degradation of cell wall in other organism (or 'catabolism' instead of 'degradation'?) GO:new --[p] cell wall peptidoglycan catabolic process in other organism GO:0051672

Do you have any clever ideas about the detection of/response to other organism terms? m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=631592 Originator: NO

In the past, we have solved the organism interaction processes by making the parent a multicellular organism process and then creating children that reflected the host and the symbiont. So in this case it would look something like this:

multi-organism process ... [i] cell wall peptidoglycan catabolic process in other organism ; GO:0051672 [P] cell wall peptidoglycan catabolic process by host organism [P] cell wall peptidoglycan catabolic process by symbiont

cellular process ... cell wall catabolic process ; GO:0016998 [i] cell wall peptidoglycan catabolic process by host organism [i] cell wall peptidoglycan catabolic process by symbiont

I think this might work for most of these.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=436423 Originator: NO

David - I don't think that makes sense

1) The 'by host' and 'by symbiont' terms would be is_a, not part_of, 'cell wall peptidoglycan catabolic process in other organism'.

2) I still think cell wall peptidoglycan catabolic process in other organism is a type of cell wall peptidoglycan catabolic process, so I don't think simply removing that relationship is a good solution to the DV. We need to figure out what type of multi-organism process cell wall peptidoglycan catab. is part of.

Also, are we sure that cell wall peptidoglycan catabolism in other organism is always in the context of symbiosis (it probably is ... but I'm not confident to make that call myself)?

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=631592 Originator: NO

Hi Midori,

1) The 'by host' and 'by symbiont' terms would be is_a, not part_of, 'cell wall peptidoglycan catabolic process in other organism'.

It depends. I'm not sure I know enough about exactly how this works, but if both organisms are contributing to the breakdown, then is would be a part_of relationship. Otherwise, if only one organism is doing the whole thing, then I don't think it is a multi-organism process. One organism is doing the whole process, but the target is in another organism. I think if we say something is a multi-organism process, then both organisms should be contributing to the process in a way other than just providing the substrate.

3) Also, are we sure that cell wall peptidoglycan catabolism in other organism is always in the context of symbiosis (it probably is ... but I'm not confident to make that call myself)?

Hmm. I'm not sure now either. How about when we break down bacterial cell walls, or lysozyme breaks down bacterial cell walls in a chicken egg.

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=436423 Originator: NO

> if both organisms are contributing to the breakdown, then is > would be a part_of relationship.

But they're not both the "other organism"! Should the organism whose cell wall is being degraded really have its gene products annotated to cell wall catab. in other organism? That just seems really weird to me.

> I think if we say something is a multi-organism process, then both > organisms should be contributing to the process in a way other than > just providing the substrate.

We should definitely check with Jane, Amelia and the PAMGO curators, but looking over existing terms and the PAMGO notes makes me think they haven't imposed this constraint. Most of the terms do fit the criterion, but there are a few exceptions (e.g. membrane disruption in another organism, and perhaps the cell killing terms).

That said, removing the multi-organism process parent from GO:0051672 would eliminate the disjoint violation!

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

This has been fixed ...

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11