Apollo-sv contains many classes that should be in other ontologies #207
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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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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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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.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#207 (comment)>,
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> .
>
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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.
>>
>> —
>> You are receiving this because you are subscribed to this thread.
>> Reply to this email directly, view it on GitHub
>> <#207 (comment)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/AAJR55S6GMQFDZHBNCEM3Z3TRVGJ5ANCNFSM46IHTLGQ>
>> .
>>
>
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and I am guilty of not being fast enough and of creating out-of-scope terms :( |
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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). |
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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?
… |
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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.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
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#207 (comment)>,
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Here is the ENVO ticket for the terms you listed: EnvironmentOntology/envo#387. |
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'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 |
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The IAO purl still points to a 2020 version, so how to update Apollo-SV before getting my class back? |
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I am preparing the new release of IAO now and will let you know when it's out. @hoganwr |
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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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@hoganwr the IAO PURL now points to the new release, so APOLLO-SV:ORCID can be obsoleted. |
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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. |
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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:
ENVO or PCO cc @pbuttigieg @ramonawalls
I believe that environmental variables are currently scoped for ENVO but this could be discussed
STATO or IAO (or EDAM, which is not OBO):
Even though it's not OBO, I would use EDAM here. Or we can raise this to an OBO level ticket:
diseases
OBA cc @matentzn
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