defense response and double taxon id

[gocentral]

Hi,

Can we make...

cellular defense response to xxxxxxx

a

child of

'response to other organism'...

so that the extra taxon can be added to name the pathogen..

for example if I wanted to document that a chicken immune gene was involved in the defense response to Eimeria (intracellular protozoan)..

I could annotate GO term 'defense resonse to protozoa' and have first taxon as chicken, second as Eimeria..

it seems to me that alot of immunologists particularly farm animal ones are pathogen focussed for their work

Evelyn

Reported by: camon

Original Ticket: "geneontology/ontology-requests/4251":https://sourceforge.net/p/geneontology/ontology-requests/4251

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Evelyn,

As I mentioned by email, I think "response to other organism" is rather the appropriate term to apply dual-inheritance to, to have both "response to stimulus" and "multi-organism process" as parents. In this way we allow a wider range of responses to other organism to have access to dual-taxon annotations, and the defense response terms that refer to specific types of organisms gain the dual inheritance by default.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=451873 Originator: NO

Yes, I agree with Alex that "response to other organism" is the term to be copied under "multi-organism process", then all the other 'defense response to ...' terms will be children too.

Would that be okay Ev, or did you specifically want a 'defense response to other organism' term?

Jane

Original comment by: jl242

[gocentral]

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Yes Jane,

that suggestion works very well for me..

thanks

Evelyn

Original comment by: ecamon

[gocentral]

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Great. I've now made this change (i.e. Copied 'response to other organism' (GO:0051707) (as OBO_REL:is_a), to 'multi-organism process' (GO:0051704)).

Jane

Original comment by: jl242

[gocentral]

• assigned_to: nobody --> jl242
• status: open --> closed-works-for-me

Original comment by: jl242

[gocentral]

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Hi All,

I may be wrong here, but it may be time to take a look at these terms carefully and how they integrate with terms that PAMGO helped to add under the parent term "symbiosis, encompassing mutualism through parasitism." At least for the example Evelyn gave, it seems that there is a response in the host (chicken) to a symbiont (a pathogen), so it seems that these particular response terms belong under symbiosis. If so, then it's time to make sure they integrate in a meaningful way with the other terms PAMGO worked on. As the trees there were built, we tried to make terms to cover 2 organisms of equal size affecting each other as well as a symbiont (smaller organism) affecting a host (larger one), and vice versa. We have been focusing mostly on using the terms to annotate genes in microbes, but we knew that others would want terms to be used to annotate host genes involved in interactions with pathogens or other types of symbionts. We haven't really completed that part, in part because of being aware of many terms for host genes already in GO. But it may be time to start making sure that the terms, old and new, fit together in a way that makes sense.

Candace

Original comment by: ccollmer

[gocentral]

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Hi Candace - yes, I totally agree - we do really need to think about how these types of terms fit together before we start annotating to them. I wonder whether it might be worth organising a 'virtual' content meeting some time to discuss this? (We've been doing this a lot recently - we use WebEx (it's very easy to use) so we can all look at the same desktop while one person 'drives' OBO-Edit, combined with Skype for voice).

What do you think? Would you also be interested in participating Evelyn?

Jane

Original comment by: jl242

[gocentral]

• status: closed-works-for-me --> open

Original comment by: jl242

[gocentral]

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Jane,

I would like to participate in such a meeting, as I have similar annotation interests to Evelyn.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

• status: open --> closed-later

Original comment by: jl242