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Add taxon constraints for taxon-specific terms #11313

Closed gocentral closed 7 years ago

gocentral commented 9 years ago

Add taxon constraints for cases where the taxonomic group is cited in the term name e.g. bacterial degradosome, plant-type vacuole, nematode larval development.

Reported by: jl242

Original Ticket: geneontology/ontology-requests/11136

gocentral commented 9 years ago

Original comment by: jl242

gocentral commented 9 years ago

Should be only in Bacteria: bacterial-type RNA polymerase regulatory region DNA binding transcription from bacterial-type RNA polymerase promoter Gram-positive-bacterium-type cell wall Gram-negative-bacterium-type cell wall bacterial nucleoid bacterial nucleoid DNA packaging bacterial pre-replicative complex bacterial-type DNA replication Gram-negative-bacterium-type cell wall biogenesis Gram-negative-bacterium-type cell outer membrane assembly bacterial-type flagellum organization Actinobacterium-type cell wall biogenesis bacterial-type flagellum-dependent cell motility bacterial-type EF-P lysine modification bacterial cellulose biosynthetic process bacterial degradosome

Should be never in Eukaryotes: archaeal or bacterial-type flagellum-dependent cell motility

Should be only in Archaea: archaeal-type flagellum-dependent cell motility archaeal-specific GTP cyclohydrolase activity archaeal-type flagellum

Original comment by: paolaroncaglia

gocentral commented 9 years ago

Note for self: still need to look at non-prokaryotic terms.

Original comment by: paolaroncaglia

gocentral commented 9 years ago

bacterial degradosome: should have restriction :) Birgit

Original comment by: bmeldal

gocentral commented 9 years ago

Thanks Birgit.

Note for self - Karen says suggested taxon rules for transcription- and cilial-related terms look good to her, and other rules make sense too.

Original comment by: paolaroncaglia

paolaroncaglia commented 8 years ago

Started working on 'Should be only in Bacteria' list above. Done so far:

bacterial-type RNA polymerase regulatory region DNA binding transcription from bacterial-type RNA polymerase promoter Gram-positive-bacterium-type cell wall Gram-negative-bacterium-type cell wall bacterial nucleoid bacterial nucleoid DNA packaging bacterial pre-replicative complex bacterial-type DNA replication Gram-negative-bacterium-type cell wall biogenesis Gram-negative-bacterium-type cell outer membrane assembly

paolaroncaglia commented 8 years ago

Hi Tanya @tberardini

As agreed for the taxonomy JBMS paper, could you please help me with adding taxon rules to plant-related terms if any are missing? The idea is

"Add taxon constraints for cases where the taxonomic group is cited in the term name [or definition, or definition comment] e.g. bacterial degradosome, plant-type vacuole, nematode larval development."

Any question or comment let me know, and thanks again for your help!

Paola

paolaroncaglia commented 8 years ago

'Should be only in Bacteria' list above: done:

bacterial-type flagellum organization Actinobacterium-type cell wall biogenesis bacterial-type flagellum-dependent cell motility bacterial-type EF-P lysine modification bacterial cellulose biosynthetic process bacterial degradosome

Next up, 'Should be never in Eukaryotes' from list above etc.

cmungall commented 8 years ago

Some of the gross anatomy related ones should come from PO

E.g. https://en.wikipedia.org/wiki/Flowering_plant

On 27 Oct 2015, at 9:11, paolaroncaglia wrote:

Hi Tanya @tberardini

As agreed for the taxonomy JBMS paper, could you please help me with adding taxon rules to plant-related terms if any are missing? The idea is

"Add taxon constraints for cases where the taxonomic group is cited in the term name [or definition, or definition comment] e.g. bacterial degradosome, plant-type vacuole, nematode larval development."

Any question or comment let me know, and thanks again for your help!

Paola

Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/11313#issuecomment-151553984

tberardini commented 8 years ago

Does PO have taxon constraints? Ah, see the PO issue now.

tberardini commented 8 years ago

Should we defer to PO then for the TCs for anatomical related stuff and I'll look at other branches of GO?

cmungall commented 8 years ago

I think anything subcellular would still be the domain of GO, just punt on development of gross structures to PO

tberardini commented 8 years ago

Which constraint? Should I be evaluating these on a one-by-one basis by looking in the literature? If any parent term (regardless of is_a, part_of, regulates) has the constraint, do I need to add the constraint to the children terms?

Existing plant-y constraints:

relationship: only_in_taxon NCBITaxon:33090 {id="GOTAX:0000422"} ! Viridiplantae (green plants) relationship: only_in_taxon NCBITaxon:3398 {id="GOTAX:0000418"} ! Magnoliophyta (flowering plants)

Note that there are various GOTAX:ids for both Viridiplantae (95 ids) and Magnoliophyta (32 ids), all with the same NCBITaxon:id. Which one is correct or are they all valid? Why are there so many?

To do list: (has 'plant' in primary term name) - many of these are already constrained but I haven't checked systematically. _italicization means there is a TC, *_means an ancestor has the TC

_name: plant-type vacuole name: plant-type vacuole lumen name: plant-type cell wall name: plant-type cell wall organization name: plant-type vacuole membrane _name: plant-type cell wall modification _name: plant-type cell wall loosening _name: plant-type cell wall modification involved in multidimensional cell growth _name: plant-type cell wall biogenesis _name: plant-type primary cell wall biogenesis _name: plant-type secondary cell wall biogenesis name: cell plate formation involved in plant-type cell wall biogenesis _name: plant-type cell wall cellulose catabolic process _name: plant-type spore development name: seed germination on parent plant name: plantlet formation on parent plant _name: plant-type cell wall cellulose biosynthetic process _name: plant-type cell wall cellulose metabolic process _name: plant-type cell wall assembly _name: plant-type cell wall loosening involved in abscission _name: regulation of plant-type cell wall cellulose catabolic process _name: negative regulation of plant-type cell wall cellulose catabolic process _name: positive regulation of plant-type cell wall cellulose catabolic process _name: regulation of plant-type cell wall cellulose biosynthetic process *_name: negative regulation of plant-type cell wall cellulose biosynthetic process **name: positive regulation of plant-type cell wall cellulose biosynthetic process

NONE through I/P/R name: flavonoid transport from endoplasmic reticulum to plant-type vacuole NONE name: plant seed peroxidase activity NONE name: plant-type cell wall organization or biogenesis NONE name: regulation of plant-type cell wall organization or biogenesis NONE (needs link to PO term) name: plant cell papilla NONE name: cysteine-type endopeptidase activity involved in plant-type hypersensitive response NONE name: regulation of plant-type hypersensitive response NONE name: negative regulation of plant-type hypersensitive response NONE name: positive regulation of plant-type hypersensitive response NONE name: plant-type hypersensitive response

punt to PO:

name: plant epidermis development name: plant epidermis morphogenesis name: plant epidermal cell differentiation name: plant epidermal cell fate specification name: plant-type ovary development name: plant parenchymal cell differentiation name: regulation of plant epidermal cell differentiation name: negative regulation of plant epidermal cell differentiation name: positive regulation of plant epidermal cell differentiation

cmungall commented 8 years ago

TCs propagate over most relations (across ontologies too, but we need to fix the import chains). This includes has_part. Helps to think in terms of OWL existential restrictions. X SubClassOf R some Y.

If you accidentally introduce redundancy it's not a big deal. Ideally we'd like a reference for each TC (can't be done in OE). So if there are two separate statements, and one subsumes the other, it can still be useful to have the redundant one, as the evidence for the second may be retracted.

It looks like you only have a handful you need to worry about in the above: vacuoles, cell walls.

You can punt even more to PO: e.g.

[Term]
id: GO:0090558
name: plant epidermis development
namespace: biological_process
def: "The process whose specific outcome is the progression of the plant epidermis over time, from its formation to the mature structure." [GOC:tb]
is_a: GO:0009888 ! tissue development
intersection_of: GO:0048856 ! anatomical structure development
intersection_of: results_in_development_of PO:0005679 ! epidermis
relationship: only_in_taxon NCBITaxon:33090 ! Viridiplantae
created_by: tanyaberardini
creation_date: 2014-02-27T15:17:37Z

Let's say we didn't have the TC on that. We can assume that we'd get that from PO (maybe with a more specific taxon - I'm guessing the first viridiplantae didn't have an epidermis). But let's leave all existing ones in until we sort out import chains, and get TCs into PO

paolaroncaglia commented 8 years ago

Thanks Tanya and Chris. Tanya, in reply to your questions

"Note that there are various GOTAX:ids for both Viridiplantae (95 ids) and Magnoliophyta (32 ids), all with the same NCBITaxon:id. Which one is correct or are they all valid? Why are there so many?"

They are all valid. They used to be created by the 'old' system - one for each TC added.

Cheers, Paola

tberardini commented 8 years ago

Plant ones remaining:

name: flavonoid transport from endoplasmic reticulum to plant-type vacuole name: plant seed peroxidase activity name: plant cell papilla

ADDED name: plant-type cell wall organization or biogenesis (through regulates relationship) name: regulation of plant-type cell wall organization or biogenesis

ADDED name: plant-type hypersensitive response (through regulates relationship) name: regulation of plant-type hypersensitive response (through regulates relationship) name: negative regulation of plant-type hypersensitive response (through regulates relationship) name: positive regulation of plant-type hypersensitive response (through regulates relationship) name: cysteine-type endopeptidase activity involved in plant-type hypersensitive response

tberardini commented 8 years ago

Can't commit changes due to the UBERON synonym problem which has caused OE to come to a screeching halt. Will try again tomorrow.

tberardini commented 8 years ago

Added TCs. Back to holiday. :+1:

paolaroncaglia commented 8 years ago

Added:

archaeal or bacterial-type flagellum-dependent cell motility

archaeal-type flagellum-dependent cell motility archaeal-specific GTP cyclohydrolase activity archaeal-type flagellum

Next up: look at non-prokaryotic and nematode-related terms; possibly more.

paolaroncaglia commented 8 years ago

Note for self: will restrict the following to be only in eukaryotes:

eukaryotic 43S preinitiation complex eukaryotic 48S preinitiation complex eukaryotic 80S initiation complex eukaryotic translation elongation factor 1 complex eukaryotic translation initiation factor 2 complex eukaryotic translation initiation factor 2B complex eukaryotic translation initiation factor 3 complex eukaryotic translation initiation factor 4F complex

eukaryotic elongation factor-2 kinase regulator activity eukaryotic initiation factor 4E binding eukaryotic initiation factor 4G binding eukaryotic initiation factor eIF2 binding eukaryotic translation initiation factor 2alpha kinase activity eukaryotic translation initiation factor 3 complex assembly eukaryotic translation initiation factor 4F complex assembly sulfurated eukaryotic molybdenum cofactor(2-) metabolic process

paolaroncaglia commented 8 years ago

Note for self: term names containing 'nematode' are already all taxon-constrained.

paolaroncaglia commented 8 years ago

Added rules to last set of terms above. Closing now.

paolaroncaglia commented 8 years ago

Re-opening because it looks like a few plant-related terms may be missing taxon restrictions. I ran across these:

Suggestions for ‘rules’ to catch them all: Search for ‘plant’ not only in term labels, but also in term definitions; in term comments too? Search for ‘PO:’ (presumably only in def comments?) Search for ‘pollen’/‘pollin’ in term labels and definitions Others?

paolaroncaglia commented 8 years ago

(Will ask Tanya when she's back from leave)

tberardini commented 8 years ago

I'm pretty sure I skipped all the ones that had PO xps because I thought that taxon-restrictions would be imposed at the source ontology (PO) and then inherited.

paolaroncaglia commented 7 years ago

Thanks @tberardini (and sorry for the delay).

@cmungall : Tanya writes "I thought that taxon-restrictions [for plant terms such as pollination etc, see above] would be imposed at the source ontology (PO) and then inherited.". Is this (still) the case? Is this filed as a ticket somewhere? Many thanks,

Paola

cmungall commented 7 years ago

From @cooperl09

The taxon restraint is incorrect for microspore- see https://www.britannica.com/science/microspore

I reverse inferred the PO one from GO:

[Term]
id: GO:0009556
name: microsporogenesis
namespace: biological_process
def: "The process in which the microsporocyte undergoes meiosis, giving rise to four haploid microspores." [GOC:mtg_plant, GOC:tb]
synonym: "microspore development" EXACT systematic_synonym []
is_a: GO:0048236 ! plant-type spore development
intersection_of: GO:0048856 ! anatomical structure development
intersection_of: results_in_development_of PO:0020048 ! microspore
relationship: only_in_taxon NCBITaxon:3398 {id="GOTAX:0000141"} ! Magnoliophyta
relationship: part_of GO:0009555 ! pollen development

The text definition is suspiciously unlike the OWL definition. cc @tberardini

tberardini commented 7 years ago

This is going to require more thought. What's giving me the most trouble is the 'from its formation to the mature structure part'. Even applying this def to the parent, 'plant-type spore development' doesn't seem quite right. I'll consult with Leonore on Monday, while looking at the parentage.

tberardini commented 7 years ago

After discussion with @lreiser, we will move this term and its children out from the 'anatomical structure development' branch into the 'sexual sporulation' branch. The taxon restriction is fine. Will take care of the xps too.

tberardini commented 7 years ago

Ok. Cleaned up.

paolaroncaglia commented 7 years ago

@tberardini thanks for taking care of ’microsporogenesis’.

@cmungall: wrapping up, I think we still need to resolve the following (or have I missed some communication?): The following terms refer to plants but don’t have taxon rules (yet): plant cell papilla pollination pollen wall There may be more (see my comment here for ideas to search them https://github.com/geneontology/go-ontology/issues/11313#issuecomment-237842225). Tanya writes "I thought that taxon-restrictions [for plant terms such as pollination etc, see above] would be imposed at the source ontology (PO) and then inherited.". Is this (still) the case? Is this filed as a ticket somewhere? Many thanks.

cmungall commented 7 years ago

On 14 Dec 2016, at 2:59, paolaroncaglia wrote:

@tberardini thanks for taking care of ’microsporogenesis’.

@cmungall: wrapping up, I think we still need to resolve the following (or have I missed some communication?): The following terms refer to plants but don’t have taxon rules (yet): plant cell papilla

we should axiomatize the comment:

comment: Part of papilla cell (PO:0025166), which is a shoot epidermal 
cell (PO:0025165) in plants. Replaces the obsolete term papillae 
(PO:0002001).

and inherit

pollination

what would the desired TC be here? We know the species that are pollinated. Do we have an exhaustive list of all species that pollinate? I read last week that some marine arthropods and worms pollinate seagrass. Though there was some controversy as to whether this was true pollination.

pollen wall

and part_of to PO

There may be more (see my comment here for ideas to search them https://github.com/geneontology/go-ontology/issues/11313#issuecomment-237842225). Tanya writes "I thought that taxon-restrictions [for plant terms such as pollination etc, see above] would be imposed at the source ontology (PO) and then inherited.". Is this (still) the case? Is this filed as a ticket somewhere? Many thanks.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/11313#issuecomment-267005722

lreiser commented 7 years ago

Chris, It looks like the GO definition excludes the pollinator aspect of pollination and restricts to the activities that occur exclusively in plants including Gymnosperms and Angiosperms.

"The cascade of biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm-central cell fusion."

Pollination,by most folks definitions, includes the act of transferring pollen to the female reproductive structure (by wind, biological transfer or other method) but I think here in GO it is more restrictive as a means to capture the events that lead up towards fertilization once the pollen lands on the lady parts.

The way this definition is written it would limit to flowering plants (that have stigma). So maybe Angiosperms.

cmungall commented 7 years ago

@lreiser - good point.

it's classified under these:

is_a: GO:0044703 ! multi-organism reproductive process
is_a: GO:0044706 ! multi-multicellular organism process

I think "pollination" as defined in GO is actually single-organism, based on this. This will make the angiosperm valid. We can still make it part-of a multi-organism process.

You are right about normal usage as well:

https://en.wikipedia.org/wiki/Pollination "Pollination is the process by which pollen is transferred to the female reproductive organs of a plant, thereby enabling fertilization to take place"

GO is right to focus on the part occurring in the plant though. I wonder if the GO term should have a more restrictive label.

mcourtot commented 7 years ago

@tberardini: is it correct to say pollen wall part_of some pollen sac ( http://purl.obolibrary.org/obo/PO_0025277)? Or can you suggest the most appropriate PO term?

mcourtot commented 7 years ago

Requested papilla cell (PO:0025166).

Re pollination: should the label be updated to "plant pollination"? Other suggestion? I can make it into a single organism reproductive process (GO:0044702) and add the following TX: relationship: only_in_taxon NCBITaxon:33090 {id="GOTAX:0000422"} ! Viridiplantae (green plants) relationship: only_in_taxon NCBITaxon:3398 {id="GOTAX:0000418"} ! Magnoliophyta (flowering plants)

cooperl09 commented 7 years ago

@mcourtot The pollen wall (GO:0043667) should have a part_of relationship to pollen (PO:0025281), not to pollen sac (PO:0025277).

tberardini commented 7 years ago

@cooperl09 : Thanks for answering for me! I can check that off my list now. :)

cooperl09 commented 7 years ago

@mcourtot Re: def'n of pollination needs to be expanded to include gymnosperms, or should create another class to encompass that process. Suggest going with the more generic definition from above- Then it would be applicable to all seed plants. The idea to rename "plant pollination" although, is somewhat redundant.

cooperl09 commented 7 years ago

Was there a question or request about papilla cell (PO:0025166)?

lreiser commented 7 years ago

@mcourtot this definition could be made inclusive by eliminating the flowering plant specific term stigma. Also I would think we would want to define fertilization as sperm- egg cell fusion, no?

"The cascade of biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm-central cell fusion."

The cascade of biological processes occurring in plants beginning when the pollen makes contact with the female reproductive structure and continues up, to but not including, fertilization, as defined by sperm-egg fusion.

The need to have gymosperm/angio differentiation would depend on children right- because there are no pollen-pistil interactions there - might be worth a new instance with different children for gymnosperms

mcourtot commented 7 years ago

(no question about papilla cell, just made a note that it was requested to be imported into GO. I also now requested to import pollen (PO:0025281) - this should take 1-2 days to show up in the GO file after which I can make the changes)

TODO:

tberardini commented 7 years ago

Experimental evidence of pollination in marine flowers by invertebrate fauna http://www.nature.com/articles/ncomms12980

freaky!

The organism being pollinated is still a plant though (marine angiosperm Thalassia testudinum). I still think it's redundant (and a little odd) to call it 'plant pollination' given the very clear definition.

mcourtot commented 7 years ago

Happy to defer to the expert :) thanks for the feedback @tberardini!

mcourtot commented 7 years ago

All done (but as discussed I did not update the label of the pollination class). Committed revision 38920.