spore-bearing organs should not be classified as animal organs

[cmungall]

howler here spotted by @selewis:

[Term]
id: GO:0075259
name: spore-bearing organ development
namespace: biological_process
def: "The process whose specific outcome is the progression of a spore-bearing organ over time, from its formation to the mature structure. A spore-bearing organ is an anatomical structure that produces new spores." [GOC:mah, GOC:mcc, GOC:pamgo_curators]
synonym: "fruiting structure development" EXACT []
***is_a: GO:0048513 ! animal organ development
is_a: GO:0048608 ! reproductive structure development
***relationship: never_in_taxon NCBITaxon:33208 {id="GOTAX:0000457"} ! Metazoa

Although this looks like a taxon error, it's actually a naming error.

GO:0048513 ! animal organ development is defined: Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions

nothing there says anything about animal-specificity. The original intent was for plant, animal and even "fungal organs"

the name was changed early this year: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0048513#term=history

I assume this was to reflect the fact we were using the metazoan-specific uberon organ to axiomatize this:

intersection_of: results_in_development_of UBERON:0000062 ! organ

we're still in limbo here - undecided as to whether to generalize the upper levels of uberon (making them equivalent with CARO classes of the same name) which would require some changes in uberon, or to use a mix of uberon and caro

ultimately I don't think 'organ' is a particularly useful term in anatomy, and especially unuseful as a developmental grouping in GO

[paolaroncaglia]

Hi @cmungall and all,

Not sure who among us changed the label of GO:0048513 ’organ development’ to ‘animal organ development’ back in January; he/she may wish to comment here. @dosumis @mcourtot @ukemi @tberardini

If there are still uncertainties on the ultimate naming/generalization of that class, the safest quick fix at the moment may simply be to change the label back to ‘organ development’, as many descendants of GO:0048513 are indeed plant terms (e.g. ‘leaf senescence’). If that sounds ok, I’ll implement. We could then set this ticket to pending while we wait for a resolution on ‘organ’.

[tberardini]

From the commit log:

r30527 | davidos | 2015-12-22 08:25:21 -0800 (Tue, 22 Dec 2015) | 1 line

fixed some of the problems arising from bringing over uberon taxon constraints + making regulates transitive. Fixed include spliting organ dev into plant and animal organ dev terms. Fixing remaining inconsistencies will require work on Uberon and possibly CL too.

svn diff -r 30526:30527 gene_ontology_write.obo

id: GO:0048513 -name: organ development +name: animal organ development

---

From the rest of that diff (above), it looks like @dosumis moved a bunch of stuff around to tidy up plant vs. animal organ development. The term 'spore-bearing organ development' may have not been moved during this update.

[cmungall]

It may be simpler to keep this is animal organ development for now, and remove the fungal terms from underneath.

The final strategy will need to wait until FAO is in place. We may end up getting rid of generic organs

[tberardini]

There's definitely cleaning up that needs doing beneath the initial children of this term. I spotted 'maintenance of floral organ identity' here:

animal organ development --[p] maintenance of organ identity ----[i] maintenance of floral organ identity

also

animal organ development --[p] multicellular structure septum development (slated for obsoletion, #12496, waiting for mouse annotation transfer) ----[i] bunch of plant terms

Probably need to step down the graph at each node to make sure that all children are sorted out.

[dianeoinglis]

Fungal structures have been described as models for multicellular development by researchers that want to pursue that angle and not because it is an established fact. There are many more articles, definitions and descriptions of fungi that refer to spore-bearing "structures" than those that use the term "spore-bearing organ."

I think the term "spore-bearing structure" should be created for fungal anatomical structures. It is technically more accurate than "spore-bearing organ" for fungi. Conidiophores would then become a spore-bearing structure.

[selewis]

Another +1

Thanks Diane

On Tue, Aug 16, 2016 at 12:04 AM, Diane O Inglis notifications@github.com wrote:

Fungal structures have been described as models for multicellular development by researchers that want to pursue that angle and not because it is an established fact. There are many more articles, definitions and descriptions of fungi that refer to spore-bearing "structures" than those that use the term "spore-bearing organ."

I think the term "spore-bearing structure" should be created for fungal anatomical structures. It is technically more accurate than "spore-bearing organ" for fungi. Conidiophores would then become a spore-bearing structure.

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[paolaroncaglia]

Ok, thanks @tberardini and @cmungall for your feedback.

I reviewed all descendants of ‘animal organ development’. Unless anyone has objections, I will remove the links:

‘spore-bearing organ development’ is_a ‘animal organ development’ ‘maintenance of floral organ identity’ is_a ‘maintenance of organ identity’ ‘bract morphogenesis’ is_a ‘organ morphogenesis’ ‘establishment of floral organ orientation’ is_a ‘establishment of organ orientation’ ‘leaf morphogenesis’ is_a ‘organ morphogenesis’ ‘floral organ morphogenesis’ is_a ‘post-embryonic organ morphogenesis’ ‘floral organ senescence’ is_a ‘organ senescence’ ‘post-embryonic root development’ is_a ‘post-embryonic organ development’

Links to ‘animal organ development’ also need to be removed from the following terms, but I’d need @tberardini to suggest an appropriate parent please (either an existing one, or a new one to be created):

‘cotyledon boundary formation’ ‘organ boundary specification between lateral organs and the meristem’ ‘shoot organ boundary specification’ ‘leaf senescence’

As for the plant-related children of ‘multicellular structure septum development’, I presume @tberardini will take care of them as part of https://github.com/geneontology/go-ontology/issues/12496, but let me know if not.

Hopefully I haven’t missed any descendant of ‘animal organ development’ that should be housed elsewhere, but if so, they can be taken care of as they arise.

Sounds like @dianeoinglis ' suggestion to create a term for ’spore-bearing structure’ should be addressed by FAO. @cmungall , is there a tracker?

Thanks,

Paola

[tberardini]

After reviewing the descendants of 'animal organ development', I think we need to create the following new terms with taxon constraints. I can do some of this through templates when TG is back up. The rest needs to be done manually.

• [x] plant organ morphogenesis
• [x] plant organ formation
• [x] formation of plant organ boundary
• [x] plant organ senescence
• [x] specification of plant organ position
• [x] specification of plant organ axis polarity
• [x] establishment of plant organ orientation
• [x] regulation of timing of plant organ formation
• [x] maintenance of plant organ identity

I suggest renaming the apparently generic versions of 'organ %' to be 'animal organ %' to avoid future confusion when selecting terms for annotation or as new parents for new terms.

I'll need to move some Arabidopsis annotations from the animal versions to the new plant terms (when they exist) but that should further clean up things.

@paolaroncaglia: after you sort out the NTR for FAO for 'spore-bearing structure', you can assign this to me.

[cmungall]

What do we think of a more radical suggestion and ditch all organs as a grouping and just use a pan-species pan-scale 'anatomical structure'?

[tberardini]

You mean, for example, getting rid of 'animal organ development' (or merging it into 'anatomical structure development') and pushing all the is_a kids up a level to be direct children of 'anatomical structure development'?

Interesting. Then put/inherit the appropriate taxon restraints on the actual terms like 'adipose tissue development' and 'floral organ development'. Yes?

[cmungall]

On 17 Aug 2016, at 12:40, Tanya Berardini wrote:

Interesting. Then put/inherit the appropriate taxon restraints on the actual terms like 'adipose tissue development' and 'floral organ development'. Yes?

Correct

Maybe best discussed on a call

[tberardini]

I'm going to hold off on addition of any new terms until after we've discussed this possible approach as a group.

[paolaroncaglia]

I added the topic to today's agenda (GO editors call). I won't be able to make the call, but happy to refer to minutes if there is a resolution. Thanks!

[cmungall]

On 17 Aug 2016, at 6:55, paolaroncaglia wrote:

Sounds like @dianeoinglis ' suggestion to create a term for ’spore-bearing structure’ should be addressed by FAO. @cmungall , is there a tracker?

I thought Maria Costanza and I set up a GitHub repo, but I can't find it. If we were to do this would there be interest in an informal consortia of us (GO, Val, Diane) keeping it up to date? It's one more moving piece but will make it easier in the long run.

[tberardini]

After this morning's GO eds meeting, we decided that the new 'xxx plant organ xxx' terms should be created as proposed. I'll do that and move the necessary plant terms out of '(animal) organ xxx' parentage.

[dianeoinglis]

I don't think Maria Costanzo set up a GitHub repo. I see that I was the last person to make changes to FAO obo to add terms for Cryptococcus...although Maria held my hand with the OBO-editor. I am certainly interested in keeping it up-to-date and it is in need of an update soon. There are a few questionable placements, some term defs that need improvement and some new terms that should be added.

All the links from the main FAO page are to SGD and are defunct. But, the Biomodels Ontology has 28 mappings to FAO out of 89 total FAO terms, Uberon has 21. Is it preferable for one of us to edit and update the obo ourselves or would it be reasonable to talk Biomodels into incorporating the complete set and updating with them? How are the terms in the GO being tied into FAO? Is it strict such that a term better be in the FAO or no-go?

What are the suggestions for how to handle the FAO and what are possible options? Diane

[tberardini]

@dianeoinglis - I'm checking with Stacia at SGD to see what's up with FAO editing. Will report back. @cmungall , @ValWood - additional thoughts on what to do with FAO maintenance?

[tberardini]

Response from Stacia:

We haven’t done anything with it since Maria left last November. The documentation she left for us (last updated Feb 2014) states that "Other editors can be added by asking Suzi Lewis and Chris Mungall.”

big sigh. i guess we need to update the contact info on it.

http://www.ontobee.org/ontology/FAO

hope this helps.

[dianeoinglis]

Well, there is an issue that perhaps Stacia and other SGD'ers don't realize. The phenotype curation at SGD, CGD, and formerly AspGD rely on the FAO for autoreplacement of the APO term "formation of anatomical structure" where the "anatomical structure" is called upon from the FAO. That should not be an issue for updating the FAO. The Stanford databases check the file into cvs and only the FAO terms in that file are available in the phenotype curation interface. They are unlikely to care about new terms beyond those already available in the Stanford DBs. I thought this might be worth mentioning.

[tberardini]

Added

[Term] id: GO:1905392 name: plant organ morphogenesis namespace: biological_process def: "The developmental process by which a plant organ is generated and organized." [GO_REF:0000083, GOC:tb, GOC:TermGenie] intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of PO:0009008 ! plant organ created_by: tb creation_date: 2016-08-24T00:21:19Z

[Term] id: GO:1905393 name: plant organ formation namespace: biological_process def: "The process that gives rise to the plant organ. This process pertains to the initial formation of a structure from unspecified parts." [GO_REF:0000081, GOC:tb, GOC:TermGenie] intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of PO:0009008 ! plant organ created_by: tb creation_date: 2016-08-24T00:21:27Z

[cmungall]

For FAO, I suggest I create a github repo, seed it with the latest version of FAO (in sourceforge?). I can show @dianeoinglis how edit this - or if edits are infrequent I can check files in. I will change the OBO metadata - would you be the new contact @dianeoinglis ?

External users should largely be unaffected. If people have mappings they should still work. SGD should be unaffected.

Thanks for the info on how FAO is used in SGD. It's always useful to know how an ontology is being used (I'd like to improve the OBO site to better show this, perhaps via bioSharing). This is also useful from an AGR integration POV.

[tberardini]

Added: +id: GO:0090691 +name: formation of plant organ boundary +namespace: biological_process +def: "The regionalization process that specifies plant organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues." [GOC:tb] +is_a: GO:0048859 ! formation of anatomical boundary +intersection_of: GO:0048859 ! formation of anatomical boundary +intersection_of: occurs_in PO:0009008 ! plant organ

Moved out plant terms under 'formation of organ boundary' to this new term. Changed term name of 'formation of organ boundary' to 'formation of animal organ boundary' and added xp to UBERON:organ for that term.

[tberardini]

Added: +id: GO:0090693 +name: plant organ senescence +namespace: biological_process +def: "The process that occurs in a plant organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism." [GOC:tb] +is_a: GO:0007568 ! aging +relationship: part_of GO:0099402 ! plant organ development

Moved out plant terms under 'organ senescence' to this new term. Changed term name of 'organ senescence' to 'animal organ senescence'. Fixed Arabidopsis annotations that were directly to the now-animal term to child terms that were plant specific.

[dianeoinglis]

Yes, I can be the FAO contact. Both OBOfoundry and SourceForge have the most current files. Awesome!

http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo

[cmungall]

@dianeoinglis - you should have full admin rights here:

https://github.com/obophenotype/fungal-anatomy-ontology

Here is the updated OBO page:

http://obofoundry.org/ontology/fao.html

I took the cute space-alien mushroom image from the FAO site, but this can easily be replaced

[cmungall]

since we're on a fungal role here I'm going ahead and axiomatizing the fungal development terms in GO, and adding an fao_imports

[dianeoinglis]

Great! I may have to send you questions about OBO-editor. I recall the namespace is important. Are there GO editors in addition to Val that can follow the issue tracker? If so, I will create a ticket for terms that I think should be added with defs and proposed placement. I think it would be ideal for a few additional opinions and comments on terms before I add or change. A sanity check from an experienced GO editor is what I'm hoping for.

[cmungall]

Good questions! Let's take this here: https://github.com/obophenotype/fungal-anatomy-ontology/issues/1

Maybe some of the others can follow us over there

[ValWood]

I'm not a GO editor ;) But I'll pitch in on the tracker if I notice anything ....we don't use anatomy terms much for fission yeast so I haven't had much input although I am following and it all sounds good.

[ValWood]

On 25/08/2016 02:53, Chris Mungall wrote:

Good questions! Let's take this here: obophenotype/fungal-anatomy-ontology#1 https://github.com/obophenotype/fungal-anatomy-ontology/issues/1

Maybe some of the others can follow us over there

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I notified SGD too...

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[tberardini]

I removed the link between 'spore-bearing organ development' and 'animal organ development'. There was another existing is_a parent, 'reproductive structure development'.

[tberardini]

added post-embryonic plant morphogenesis post-embryonic plant organ morphogenesis post-embryonic plant organ development

Then a whole bunch of renaming the 'organ' terms to 'animal organ', moving plant terms out under the new terms, looking at parentage of plant terms and checking. More still to do but the egregious misplacements should be gone.

[tberardini]

Will recheck for terms that still need to be addressed next week after ontology structure has been updated in AmiGO so that I can look at annotations of plant terms to child terms of 'animal organ development'.

[tberardini]

Added:

+id: GO:0090701 +name: specification of plant organ identity

+id: GO:0090700 +name: maintenance of plant organ identity

More incremental clean up of term names to distinguish animal organs from plant organs. Added xp to UBERON:organ and PO:plant organ when possible.

[tberardini]

Still left to sort out as they all now still fall under animal organ development but either have plant genes annotated directly to them or have plant specific terms as children terms.

• [x] specification of organ axis polarity
• [x] specification or organ position
• [x] specification of organ number
• [x] regulation of timing of organ formation
• [x] establishment of organ orientation

[tberardini]

Added the remaining terms necessary, split out plant and animal and links to plant/animal organ morphogenesis/development terms. Still need to clean up the annotations. Will transfer these tomorrow when the new terms are in our curation database.

[tberardini]

+id: GO:0090706 +name: specification of plant organ position

+id: GO:0090707 +name: establishment of plant organ orientation

+id: GO:0090708 +name: specification of plant organ axis polarity

+id: GO:0090709 +name: regulation of timing of plant organ formation

[tberardini]

5 annotations to A. thaliana left. 3 IMP (UniProtKB), 2 IEA (InterPro). Two of them were disputed by myself and have been corrected by UniProt just today. The other IMP annotation I disputed today and I'm sure it will be corrected shortly.

I've opened Interpro helpdesk tickets to address the mappings leading to the two IEA annotations.

[Support #99763] AutoReply: Please update mapping: IPR031135 [Support #99764] AutoReply: Please update mapping: IPR029961

Should all be cleaned up by December 2016. I hope.

[tberardini]

Last IMP annotation has been cleaned up by UniProt (thanks, Emmanuel). The Interpro mappings have been updated and will be released in January.

Thanks for pointing this out Tanya. I have corrected the mapping, but it won't be publicly visible until our next release which will be in January.

cheers, Lorna.