fix parentage of MOP metabolism terms

[gocentral]

To do when I have time:

The MOP process metabolism terms (e.g. metabolism by symbiont of host macromolecule ; GO:0052174) do not all have parentage under generic metabolic process terms - they should have. In some cases it will be straightforward, but in other cases it will require new 'cellular' and generic processes will be required.

See especially the protein modification terms.

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/5777":https://sourceforge.net/p/geneontology/ontology-requests/5777

[gocentral]

Probably need a new term 'multi-organism metabolic process'.

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242

[gocentral]

• status: closed-accepted --> open

Original comment by: jl242

[gocentral]

So GO:0052414 ! metabolism by host of symbiont glucan

would be a subtype of GO:0006073 ! glucan metabolic process

If you like, you can go ahead an add synonyms such as: GO:0052414 ! metabolism by host of symbiont glucan "glucan metabolism by host in symbiont"

Then using obol we can add the xps then run the reasoner to determine the correct parentage

I know these synonyms look a little odd but I think they are kind of implied if we accept 52414 as a subtype of the core GO process type.

Alternatively, I can extend the obol grammar such that it captures the xp from the synonym as-is. But this is a bit more complicated as it relies on CHEBI, and then bp_xp_chebi to "put things back together" as it were.

Option 3 is I extend the grammar such that it can recognize these terms without chebi, by effectively shuffling connecting together the disparate terms "metabolism" and "glucan", then using that as the process term. Should be doable.

Original comment by: cmungall

[gocentral]

here's the latest bp_xp_MOP reasoner results. I leave the induction ones in even though they are wrong - kind of as a signal for us to do something here. I think we should be univocal. This came up in a separate item with DavidH answering Mike Bada. I think we should rename GO:0031128.

[ GO:0019087 ! transformation of host cell by virus ] is_a [ GO:0019088 ! immortalization of host cell by virus ] [ GO:0034054 ! negative regulation by symbiont of host defense-related programmed cell death ] is_a [ GO:0052037 ! negative regulation by symbiont of host defense response ] [ GO:0034055 ! positive regulation by symbiont of host defense-related programmed cell death ] is_a [ GO:0052509 ! positive regulation by symbiont of host defense response ] [ GO:0052288 ! induction by organism of induced systemic resistance in other organism during symbiotic interaction ] is_a [ GO:0052382 ! induction by organism of innate immunity in other organism during symbiotic interaction ] [ GO:0052289 ! induction by organism of systemic acquired resistance in other organism during symbiotic interaction ] is_a [ GO:0052382 ! induction by organism of innate immunity in other organism during symbiotic interaction ] [ GO:0052330 ! positive regulation by organism of programmed cell death in other organism during symbiotic interaction ] is_a [ GO:0052529 ! upregulation by organism of programmed cell death in other organism during symbiotic interaction ] [ GO:0012504 ! induction of non-apoptotic programmed cell death by other organism ] is_a [ GO:0052045 ! upregulation by symbiont of host programmed cell death ] [ GO:0019050 ! suppression by virus of host apoptosis ] is_a [ GO:0033668 ! negative regulation by symbiont of host apoptosis ] [ GO:0019051 ! induction by virus of host apoptosis ] is_a [ GO:0052045 ! upregulation by symbiont of host programmed cell death ] [ GO:0019051 ! induction by virus of host apoptosis ] is_a [ GO:0060139 ! positive regulation of apoptosis by virus ] [ GO:0052068 ! negative regulation by symbiont of host jasmonic acid-mediated defense response ] is_a [ GO:0052037 ! negative regulation by symbiont of host defense response ] [ GO:0052075 ! positive regulation by symbiont of host jasmonic acid-mediated defense response ] is_a [ GO:0052509 ! positive regulation by symbiont of host defense response ] [ GO:0052144 ! negative energy taxis within host ] is_a [ GO:0052244 ! negative energy taxis within other organism during symbiotic interaction ] [ GO:0052147 ! positive energy taxis within host ] is_a [ GO:0052247 ! positive energy taxis within other organism during symbiotic interaction ] [ GO:0052263 ! induction by organism of defense-related nitric oxide production in other organism during symbiotic interaction ] is_a [ GO:0052558 ! induction by organism of immune response of other organism during symbiotic interaction ] [ GO:0052348 ! positive regulation by organism of defense-related reactive oxygen species production in other organism during symbiotic interaction ] is_a [ GO:0052510 ! positive regulation by organism of defense response of other organism during symbiotic interaction ] [ GO:0052369 ! positive regulation by symbiont of defense-related host reactive oxygen species production ] is_a [ GO:0052509 ! positive regulation by symbiont of host defense response ] [ GO:0052382 ! induction by organism of innate immunity in other organism during symbiotic interaction ] is_a [ GO:0052251 ! induction by organism of defense response of other organism during symbiotic interaction ] [ GO:0052390 ! induction by symbiont of host innate immunity ] is_a [ GO:0052509 ! positive regulation by symbiont of host defense response ] [ GO:0045881 ! positive regulation of sporulation resulting in formation of a cellular spore ] is_a [ GO:0075303 ! positive regulation of basidiospore formation ] [ GO:0052311 ! negative regulation by organism of defense-related cell wall callose deposition in other organism during symbiotic interaction ] is_a [ GO:0052310 ! modulation by organism of defense-related cell wall callose deposition in other organism during symbiotic interaction ] [ GO:0075073 ! autophagy of symbiont cells on or near host surface ] is_a [ GO:0051701 ! interaction with host ] entailed: [ GO:0075073 ! autophagy of symbiont cells on or near host surface ] part_of [ GO:0051701 ! interaction with host ] [ GO:0006948 ! induction by virus of cell-cell fusion in host ] is_a [ GO:0031128 ! induction ] [ GO:0009689 ! induction of phytoalexin biosynthetic process ] is_a [ GO:0031128 ! induction ] [ GO:0019054 ! modification by virus of host cellular process ] is_a [ GO:0065007 ! biological regulation ] [ GO:0043921 ! modulation by host of viral transcription ] is_a [ GO:0046782 ! regulation of viral transcription ] [ GO:0043922 ! negative regulation by host of viral transcription ] is_a [ GO:0032897 ! negative regulation of viral transcription ] [ GO:0043923 ! positive regulation by host of viral transcription ] is_a [ GO:0050434 ! positive regulation of viral transcription ] [ GO:0052043 ! modification by symbiont of host cellular component ] is_a [ GO:0051851 ! modification by host of symbiont morphology or physiology ] [ GO:0052204 ! negative regulation of molecular function in other organism during symbiotic interaction ] is_a [ GO:0065007 ! biological regulation ] [ GO:0052215 ! energy taxis in environment of other organism during symbiotic interaction ] is_a [ GO:0009453 ! energy taxis ] [ GO:0052218 ! positive energy taxis in environment of other organism during symbiotic interaction ] is_a [ GO:0052128 ! positive energy taxis ] [ GO:0052219 ! negative energy taxis in environment of other organism during symbiotic interaction ] is_a [ GO:0052129 ! negative energy taxis ] [ GO:0052221 ! positive chemotaxis in environment of other organism during symbiotic interaction ] is_a [ GO:0050918 ! positive chemotaxis ] [ GO:0052223 ! negative chemotaxis in environment of other organism during symbiotic interaction ] is_a [ GO:0050919 ! negative chemotaxis ] [ GO:0052251 ! induction by organism of defense response of other organism during symbiotic interaction ] is_a [ GO:0031128 ! induction ] [ GO:0052400 ! induction by organism of programmed cell death in other organism during symbiotic interaction ] is_a [ GO:0031128 ! induction ] [ GO:0052558 ! induction by organism of immune response of other organism during symbiotic interaction ] is_a [ GO:0031128 ! induction ]

Original comment by: cmungall

[gocentral]

Hi Chris -

"So GO:0052414 ! metabolism by host of symbiont glucan

would be a subtype of GO:0006073 ! glucan metabolic process"

Yes, exactly. Can we have a go at option 3, see what we get?

Original comment by: jl242

[gocentral]

I'm adding the new high-level terms now though, so probably best to wait until those are in.

Original comment by: jl242

[gocentral]

Okay, I've added the new parentage and some new terms:

GO:0044033 multi-organism metabolic process GO:0044034 multi-organism biosynthetic process GO:0044035 multi-organism catabolic process GO:0044036 cell wall metabolic process GO:0044037 multi-organism cell wall metabolic process GO:0044038 cell wall biosynthetic process GO:0044039 cellular cell wall catabolic process GO:0044040 multi-organism carbohydrate metabolic process GO:0044041 multi-organism carbohydrate catabolic process GO:0044042 glucan metabolic process GO:0044043 multi-organism glucan metabolic process

was incredibly complicated and confusing. Do you want to see if you can use obol to add the xps then, Chris?

Original comment by: jl242

[gocentral]

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

Original comment by: jl242