Apollo-sv contains many classes that should be in other ontologies

[cmungall]

apollo-sv contains many classes that are out of scope and should be in other OBO ontologies. Note that in many cases here the deficiency is in OBO, either existing vocabularies do not accept terms or we have not agreed OBO-wide where certain terms belong. This problem is perpetuated by the use of BFO shadow classes (e.g. foo + foo datum). While not necessarily apollo-sv's problem, I would recommend this team is proactive in making tickets on other ontology repos to get terms submitted and reporting back to OBO where there are problems.

In OBO we also need a better way of indicating which ontologies typically mint classes that may eventually be housed elsewhere.

Here is a random sampling:

we still don't have a good story for symbiosis types in OBO cc @diatomsRcool, but these should probably be housed elsewhere:

id	label
APOLLO_SV:00000337	ectosymbiosis
APOLLO_SV:00000338	antagonism
APOLLO_SV:00000339	amensalism
APOLLO_SV:00000340	agonism
APOLLO_SV:00000341	intimate agonism
APOLLO_SV:00000342	ectosymbiotic parasitism
APOLLO_SV:00000343	facultative ectosymbiotic parasitism
APOLLO_SV:00000344	obligatory ectosymbiotic parasitism
APOLLO_SV:00000345	ectosymbiotic parasitoidism
APOLLO_SV:00000346	facultative ectosymbiotic parasitoidism
APOLLO_SV:00000347	obligatory ectosymbiotic parasitoidism
APOLLO_SV:00000348	ectosymbiotic commensalism
APOLLO_SV:00000349	facultative ectosymbiotic commensalism
APOLLO_SV:00000350	obligatory ectosymbiotic commensalism
APOLLO_SV:00000351	ectosymbiotic mutualism
APOLLO_SV:00000352	facultative ectosymbiotic mutualism
APOLLO_SV:00000353	obligatory ectosymbiotic mutualism
APOLLO_SV:00000354	endosymbiosis
APOLLO_SV:00000355	endosymbiotic parasitism
APOLLO_SV:00000356	transient agonism
APOLLO_SV:00000357	predation
APOLLO_SV:00000358	grazing
APOLLO_SV:00000359	facultative endosymbiotic parasitism
APOLLO_SV:00000360	obligatory endosymbiotic parasitism
APOLLO_SV:00000361	endosymbiotic parasitoidism
APOLLO_SV:00000362	facultative endosymbiotic parasitoidism
APOLLO_SV:00000363	obligatory endosymbiotic parasitoidism
APOLLO_SV:00000364	endosymbiotic commensalism
APOLLO_SV:00000365	facultative endosymbiotic commensalism
APOLLO_SV:00000366	obligatory endosymbiotic commensalism
APOLLO_SV:00000367	endosymbiotic mutualism
APOLLO_SV:00000368	facultative endosymbiotic mutualism
APOLLO_SV:00000369	obligatory endosymbiotic mutualism
APOLLO_SV:00000596	symbiosis

ENVO or PCO cc @pbuttigieg @ramonawalls

id	label
APOLLO_SV:00000097	ecosystem
APOLLO_SV:00000094	community
APOLLO_SV:00000113	atmosphere of the Earth
APOLLO_SV:00000035	organism population universal

I believe that environmental variables are currently scoped for ENVO but this could be discussed

id	label
APOLLO_SV:00000513	mean rate of hydrological precipitation
APOLLO_SV:00000514	mean air temperature

STATO or IAO (or EDAM, which is not OBO):

id	label
APOLLO_SV:00000076	μ
APOLLO_SV:00000077	σ
APOLLO_SV:00000078	beta distribution
APOLLO_SV:00000079	deprecated log normal distribution
APOLLO_SV:00000080	uniform distribution
APOLLO_SV:00000081	triangular distribution
APOLLO_SV:00000082	Bayesian network
APOLLO_SV:00000434	statistical confidence

Even though it's not OBO, I would use EDAM here. Or we can raise this to an OBO level ticket:

id	label
APOLLO_SV:00000203	NCBI taxon identifier
APOLLO_SV:00000319	NLM ID
APOLLO_SV:00000320	ISSN Linking
APOLLO_SV:00000321	ISO Title Abbreviation
APOLLO_SV:00000324	NLM Title Abbreviation
APOLLO_SV:00000325	URI creation date

diseases

id	label
APOLLO_SV:00000574	acute respiratory illness

OBA cc @matentzn

id	label
APOLLO_SV:00000471	minimum eggs per oviposition site
APOLLO_SV:00000472	age-dependent fecundity reduction
APOLLO_SV:00000442	migration speed

[ramonawalls]

I don't know what a "organism population universal" is, but f you can define it, I'm happy to include it in PCO, assuming it does not already exist with another label.

[hoganwr]

Plenty of stories behind many of these terms that perhaps could inform how to prevent the problem from arising again. Would be happy to share those in whatever is an appropriate forum.

We tried working with ENVO. Sometimes when you need a term, you need it pretty quickly. Delay on the part of the host "ontology" leaves you with the idea of "well, we'll stick it here now and fix it later when the proper ontology finally adds it." I'm guilty of that as an owner of multiple ontologies.

Many of these are annotation properties, I think (NLM Title Abbreviation?)

Never heard of OBA and would guess we created those terms before it existed.

The symbiosis terms were a student project presented at ICBO and published in open access journal. Was a very systematic approach. How to handle student projects? Hold up PhDs waiting for terms?

On Mon, Jun 7, 2021 at 7:07 PM Ramona Walls @.***> wrote:

I don't know what a "organism population universal" is, but f you can define it, I'm happy to include it in PCO, assuming it does not already exist with another label.

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[hoganwr]

Also, Apollo-SV long predated STATO

On Mon, Jun 7, 2021 at 7:21 PM Bill Hogan @.***> wrote:

Plenty of stories behind many of these terms that perhaps could inform how to prevent the problem from arising again. Would be happy to share those in whatever is an appropriate forum.

We tried working with ENVO. Sometimes when you need a term, you need it pretty quickly. Delay on the part of the host "ontology" leaves you with the idea of "well, we'll stick it here now and fix it later when the proper ontology finally adds it." I'm guilty of that as an owner of multiple ontologies.

Many of these are annotation properties, I think (NLM Title Abbreviation?)

Never heard of OBA and would guess we created those terms before it existed.

The symbiosis terms were a student project presented at ICBO and published in open access journal. Was a very systematic approach. How to handle student projects? Hold up PhDs waiting for terms?

On Mon, Jun 7, 2021 at 7:07 PM Ramona Walls @.***> wrote:

I don't know what a "organism population universal" is, but f you can define it, I'm happy to include it in PCO, assuming it does not already exist with another label.

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[hoganwr]

Also, we recognize the issue and just ceded about 10 terms back to IAO, which by the way, was a pretty dead letter when we created those classes.

On Mon, Jun 7, 2021 at 7:25 PM Bill Hogan @.***> wrote:

Also, Apollo-SV long predated STATO

On Mon, Jun 7, 2021 at 7:21 PM Bill Hogan @.***> wrote:

Plenty of stories behind many of these terms that perhaps could inform how to prevent the problem from arising again. Would be happy to share those in whatever is an appropriate forum.

We tried working with ENVO. Sometimes when you need a term, you need it pretty quickly. Delay on the part of the host "ontology" leaves you with the idea of "well, we'll stick it here now and fix it later when the proper ontology finally adds it." I'm guilty of that as an owner of multiple ontologies.

Many of these are annotation properties, I think (NLM Title Abbreviation?)

Never heard of OBA and would guess we created those terms before it existed.

The symbiosis terms were a student project presented at ICBO and published in open access journal. Was a very systematic approach. How to handle student projects? Hold up PhDs waiting for terms?

On Mon, Jun 7, 2021 at 7:07 PM Ramona Walls @.***> wrote:

I don't know what a "organism population universal" is, but f you can define it, I'm happy to include it in PCO, assuming it does not already exist with another label.

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[diatomsRcool]

and I am guilty of not being fast enough and of creating out-of-scope terms :( I will add that I have several symbiosis-related terms in ecocore (which is a new ontology), so those APOLLO terms could be re-homed there.

[dillerm]

We published a paper on those symbiosis classes explaining the need to create these classes, and it basically boiled down to there not being suitable or detailed representations of these interactions (note: ECOCORE, to my knowledge, did not exist when we started working on these classes). We did have some conversations with GO about 'symbiosis' since they also have a class for it, but I think we decided that their approach of constraining it to being only about the molecular/genetic aspects of such interactions was too restricting (they originally had a definition that was really good and then changed it).

[cmungall]

Thanks all for your comments - it seems apollo-sv has been diligent in trying to get the appropriate terms in different ontologies (including the exemplary practice of filing tickets in github repos rather than emails). It seems that something is not working right at the OBO level, it should not be this hard to get terms in. There are some genuinely hard problems such as how best to modularize a complex domain like ecology / symbiotic interactions. Maybe some kind of dedicated meeting (virtual) around this is required perhaps around ICBO time?

[cmungall]

Do you happen to have the ENVO tickets handy?

On Mon, Jun 7, 2021 at 4:21 PM Bill Hogan @.***> wrote:

Plenty of stories behind many of these terms that perhaps could inform how to prevent the problem from arising again. Would be happy to share those in whatever is an appropriate forum.

We tried working with ENVO. Sometimes when you need a term, you need it pretty quickly. Delay on the part of the host "ontology" leaves you with the idea of "well, we'll stick it here now and fix it later when the proper ontology finally adds it." I'm guilty of that as an owner of multiple ontologies.

Many of these are annotation properties, I think (NLM Title Abbreviation?)

Never heard of OBA and would guess we created those terms before it existed.

The symbiosis terms were a student project presented at ICBO and published in open access journal. Was a very systematic approach. How to handle student projects? Hold up PhDs waiting for terms?

On Mon, Jun 7, 2021 at 7:07 PM Ramona Walls @.***> wrote:

I don't know what a "organism population universal" is, but f you can define it, I'm happy to include it in PCO, assuming it does not already exist with another label.

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.

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[dillerm]

Here is the ENVO ticket for the terms you listed: https://github.com/EnvironmentOntology/envo/issues/387.

[zhengj2007]

'ORCID identifier' was add in IAO with ID, IAO_0000708.

APOLLO_SV_00000496 (ORCID) should be deprecated and add annotation 'term replaced by': http://purl.obolibrary.org/obo/IAO_0000708

[hoganwr]

The IAO purl still points to a 2020 version, so how to update Apollo-SV before getting my class back?

[zhengj2007]

I am preparing the new release of IAO now and will let you know when it's out. @hoganwr

[hoganwr]

Great - thanks!

On Thu, Oct 27, 2022 at 11:30 AM jie zheng @.***> wrote:

I am preparing the new release of IAO now and will let you know when it's out. @hoganwr https://github.com/hoganwr

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[StroemPhi]

@hoganwr the IAO PURL now points to the new release, so APOLLO-SV:ORCID can be obsoleted.

[hoganwr]

Thanks! I've done that, made a new release of the ontology (w/a slight reorganization), and updated the PURL to always point to the latest. Once the PURL redirects, hopefully ontobee picks it up and pulls in the new version, and then all will be well.