This ticket should document the things we need to do to get up and running with the new FAO github repo.

OBO-Edit setup

I'll put some instructions in README-editors.md -- at the moment these are a bit Protege-centric, but it makes sense to keep using OE for now

The main thing to remember is to set up ID ranges - I'll add something on this soon

GitHub

Tickets are easy in github, but getting set up with checkin/checkout can be harder

Some people like the command line, others prefer graphical clients - @dianeoinglis are you on a mac or PC?

Are there GO editors in addition to Val that can follow the issue tracker

There are a variety of options you can tag people like this: @ValWood, @mah11 and they'll see the message. They can also choose whether to follow individual tickets, or the whole repo. I also gave @mah11 rights to edit files directly, do we have representatives for other fungal clades?

If so, I will create a ticket for terms that I think should be added with defs and proposed placement

I think that's a great idea. It doesn't hurt to be too granular (unless we're adding 100s of terms at a time, in which case obviously batch the tickets)

In FoodOn we've needed to define common language references to mushrooms which include a "fruitbody and 'derives from' some [NCBITaxon]" axioms, e.g. trumpet chanterelle. Is FAO interested in housing/managing such terms? Here's our branch labelled mushroom fruitbody. The subclasses could perhaps have the term "fruitbody" appended to them for clarity.

Hi,

How would you advise to reference FAO in a manuscript?
Also, the homepage link is broken in the README.

Thanks!

make text definitions follow genus-differentia(e) pattern more closely, and generally flow better

Fruitbody or fruiting body is the term used for the spore-bearing structure that are formed during sexual development following mating between two compatible mating-types, typically 'a' and 'alpha' strains. Cryptococcus and several other Basidiomycetes can self-mate (same-sex mating) under starvation conditions. As the nuclei are identical, this same-sex mating process is interchangeably referred to as haploid fruiting or monokaryotic fruiting. The process is similar to sexual fruiting however the resulting basidiospores are genetically identical.

I propose to add the term 'monokaryotic fruitbody' with the synonym 'haploid fruitbody.'

[term]
id (will be): FAO:0001023
name: 'monokaryotic fruit body'
Def: "a specialized structure that produces or bears asexually derived spores from same-sex mating." [FAO:curators, FAO:doi]
synonym: "monokaryotic fruiting body" EXACT [ ]
synonym: "haploid fruiting body" EXACT [ ]
is_a: FAO:0000001 ! fungal structure

Please review and comment on whether the information for this proposed term is accurate and acceptable.

Thanks,
Diane

@mah11
@tberardini

This term is being created for defining the GO term 'aerial mycelium formation'

[term]
id (will be) : FAO:0001030 FAO:0001031
name: 'aerial mycelium'
def: a type of pre-sporulating mycelium that extends aerially, or perpendicular, to its substrate.
is_a: FAO: 0000011 ! 'mycelium'

I can't see any difference between "fruitbody" and "sporophore", either from the FAO text definitions or from searching google & PubMed. In #2
wasn't sure about the scopes for some of the synonyms added to "sporophore"; I made them all EXACT based on what I found (or didn't find) online.

If they are different, what should I put in the definitions to distinguish them? (I'd also remove "fruitbody" synonyms from sporophore in that case.) If they're not different I'll merge them.

@dianeoinglis @Achchuthan Any objections, comments, questions?

[Term]
id: FAO:0000007
name: fruitbody
def: "Any specialized structure which bears or contains sexually or asexually derived spores." [FAO:curators, SGD:clt]
synonym: "fruiting body" EXACT []
xref: BTO:0000487
is_a: FAO:0002004 ! multicellular fungal structure, multicellular organism

[Term]
id: FAO:0000010
name: sporophore
def: "A multicellular anatomical structure that functions in the production of spores, which are directly borne upon or within sporogenous cells that form part of the sporophore." [FAO:curators]
synonym: "fruit body" EXACT [FAO:doi]
synonym: "fruitbody" EXACT [FAO:doi]
synonym: "fruiting body" EXACT [FAO:doi]
synonym: "spore-bearing structure" EXACT [FAO:doi]
synonym: "spore-producing structure" EXACT [FAO:doi]
synonym: "sporocarp" EXACT [FAO:doi]
xref: GO:0075259
is_a: FAO:0002004 ! multicellular fungal structure, multicellular organism

FAO:0000012 and FAO:0001024 both have name 'basidiocarp'. Looks like the latter was in the bulk addition from #23, and means the same thing as the older term. Keep older ID; manually craft definition based on both.

Greetings FAO,

We'd like to import some of your classes into ENVO, but they dangle uncomfortably off the top level.
Could fungal structure be placed under UBERON's anatomical structure?

Also, would it be possible to define that term? Based on composite structure, this could read:
"A multicellular formation composed of cells from one or more species of fungus."

(will be) id: FAO:0001027
name: spherule
def: "a large, round, thick-walled structure that contains endospores such as those produced by Coccidioides species within a host."
is_a: FAO:0000001 ! fungal structure
is_a: FAO:0000052 ! sporangium
created_by: dinglis

Please review and comment on whether the information for this proposed term is accurate and acceptable.

@mah11
@tberardini

The term 'hyphal tip' is a cell part. It's the apex of a growing hypha where hyphal tip cell growth occurs. Cell parts are not currently included in the FAO. Either the 'hyphal tip' terms should be obsoleted and the new term 'hyphal tip cell' be created or all 'hyphal tip' terms be converted to 'hyphal tip cell.'

The following terms are affected:
FAO:0001011
FAO:0001012
FAO:0001015
FAO:0001016
FAO:0001017
FAO:0001019
FAO:0001020
FAO:0001021

Grouping term

(will be) id: FAO:0001029
name: sexual structure
def: "any structure that develops during the mating process for the purpose of sexual reproduction."
is_a: FAO:0000001 ! fungal structure
created_by: dinglis

@mah11
@tberardini

• Hulle cell
• clamp cell
• conidiophore foot cell

should be is-a unicellular structure

See #37 - I don't fully understand the report, but it doesn't look like something I can fix in the ontology. @cjm, any advice?

added sexual structure ! FAO:0002010 for #8
figure out which terms should go under it, and assert links (unless FAO gets logical definitions first ... ha ha)

The synonym 'spore-bearing organ' should be modified to 'spore-bearing structure.'

Reciprocal: obophenotype/cell-ontology#447

We could keep the cell types in CL, but IMO it's cleaner if CL is pan-metazoan, and FAO becomes analogous to PO, which gross anat and cell types in one integrated ontology for a clade.

If FAO developers agree I can make a PR

See also geneontology/go-ontology#11313 (comment)

cc @thomaspd

Structure formed by filamentous fungi through which nuclei pass from one conidium to the other.

(will be) id: FAO:0001025
def: " a short, thin, unbranched tubular structure (bridge) formed when two conidia or conidial germlings fuse."
is_a: FAO:0000001 ! fungal structure
created_by: dinglis

Please review and comment on whether the information for this proposed term is accurate and acceptable.

@mah11
@tberardini

GO:0048646 "conidium formation" has is_a "anatomical structure formation involved in morphogenesis," but "morphogenesis" (change in cell shape) is not the goal of this process. Additionally, there are no cells that change shape rather this is an organismal process where a population of cells form new cells with a different shape. The new term "anatomical structure formation involved in asexual reproduction" should be created and replace the "anatomical structure formation involved in morphogenesis" term that is currently an "is_a" term for conidium formation. "Anatomical structure formation involved in sexual reproduction" should also be created as well as a parent term "anatomical structure formation involved in reproduction."

Terms requested:
"anatomical structure formation involved in reproduction" (parent)
"anatomical structure formation involved in asexual reproduction"
"anatomical structure formation involved in sexual reproduction"

New term request:

(will be) id: FAO:0001026
name: germ tube
def: "the outgrowth that emerges from a spore following release from dormancy. Note that for historical reasons, the term "germ tube" is inappropriately used for the hypha that emerges from a Candida albicans yeast cell that produces new cells in a filamentous form."
synonym: "spore germination tube" EXACT [ ]
xref: GO:0009847
is_a: FAO:0000001 ! fungal structure
develops_from: FAO:0000023 asexual spore
develops_from: FAO:0000017 sexual spore
created_by: dinglis

Please review and comment on whether the information for this proposed term is accurate and acceptable.

@mah11
@tberardini

!

NTR for the first cell upon which a conidiophore develops.

id (will be): FAO:0001024
name: conidiophore foot cell
def: "a specialized cell with an enlarged cell wall that develops in series of vegetative hyphae in a mycelium upon which a conidiophore develops."
develops_from: FAO:0001003 | hypha in mycelium
created_by: dinglis

Please review and comment on whether the information for this proposed term is accurate and acceptable.

@mah11
@tberardini

There are about a dozen terms with no is_a parent either asserted or inferred (well, not much is inferred because FAO doesn't have logical defs yet). Looks like all can at least be is_a FAO:0000001 ! fungal structure.

@dianeoinglis is this ontology still being developed? I don't see any commits since my initial creation.

For definitions, see: geneontology/go-ontology#15616 (comment)

There is a term for unicellular structures and for composite (more than one organism) but the terms that Iack either term are the multicellular structures, such as sporophore, conidiophore, etc. As time permits, let's add this missing term.

NTR: 000xxxx multicellular structure, unicellular organism.
Def: a fungal structure composed of two or more cells of a single unicellular organism.
is_a FAO:0000001 fungal structure

NTR: 000xxxx multicellular structure, multicellular organism
Def: a fungal structure composed of two or more cells of a single multicellular organism.

New GO term to add to FAO:

spore-bearing structure

geneontology/go-ontology#12605

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

To distinguish between other types of hyphae.

(will be) id: FAO:0001028
name: mating filament
def: "the hypha that emerges from a yeast-form cell upon stimulation by the pheromone of a compatible mating partner."
is_a: FAO:0000001 ! fungal structure
created_by: dinglis

@mah11
@tberardini

In #33, @dianeoinglis asked for "FAO:0000061 fused clamp" to become is_a multicellular fungal structure, multicellular organism (now FAO:0002004), but the ontology structure is:

septate hypha
[is_a] clamp cell
-- [part_of] fused clamp
-- [part_of] unfused clamp

It doesn't make sense to have a multicellular structure be part_of a cell, which is what would be implied by adding the fused clamp is_a multicellular structure link.

So I wonder if the structure should be this instead?

septate hypha
[part_of] clamp cell
[is_a] fused clamp
[is_a] unfused clamp

i.e. fused and unfused are types of hyphal clamp, and a clamp cell is part of a hypha. Then the multicellular parent could be added to fused clamp with no nasty consequences.

If this sounds nuts, please bear with me - I'm very much still a beginner at learning fungal anatomy! I can make the changes if they do look OK.

Hi @mah11,
Can I request a new term for appressorium in FAO please? This term is present in BTO.

id: FAO:xxxxxxx
name: appressorium
def: "The flattened thickened tip of a hyphal branch by which some parasitic fungi are attached to their host."
is_a: FAO:0001001 ! hypha
xref: BTO:0000085

Thanks & best wishes,
Achchuthan

Hi!

The ISBN:0879693798 used as a cross-reference for the definition of FAO:0001023 is invalid. If that helps, the closest valid one is ISBN:0879693797 which links to Power of Bacterial Genetics: A Literature-Based Course but I don't know if that the expected reference.

This term does not refer to a fungal structure, it is a class of organism and does not need to be in the current FAO. Please obsolete with the next release.

This term is being created as the source of the logical definition of a new GO term, GO:0097738 'substrate mycelium formation.'

[term]
id (will be) : FAO:0001031 FAO:0001030
name: 'substrate mycelium'
def: an invasive mycelium that forms within a solid or semi-solid substrate such as wood, soil or agar. [FAO:doi, FAO:pamgo, PMID: 3891055]
is_a: FAO:0000011 ! mycelium
is_a: FAO:0000001 ! fungal structure
xref: GO:0097738