Add VO:0005503 to group vaccines for diseases
#620
Conversation
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CC @zhengj2007 |
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@cthoyt Thanks for adding the term for grouping the vaccines for diseases. It looks good to me. We are working on improving VO, including building the modules and fixing the issues (e.g. duplicated labels). We may postpone merging the changes you made and include it in the template. |
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@zhengj2007 is there a timeline on that? I have several contributions I would like to make that would be useful for an ongoing project, but I don't want to work towards contributing it if merging isn't timely |
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@zhengj2007 I don't understand. Does my proposed change conflict with other upcoming changes? If it's a matter of the ID ranges, you can assign me a certain range and I will update it to that. Otherwise, waiting months would be a big problem for my project |
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Hey All,
I will speak with Oliver about this today on when we're pushing the next
merge update. I will get a clearer timeline for you later today and would
be pushing for inclusion.
My current understanding is that the primary case is that the creation of
the template file would use those new terms to update and fix all the
issues of the ontology would be responsible for the delay. I don't see an
issue at this point for doing a minor update patch to include those terms;
only for updating the appropriate vaccines into the correct categories.
…On Sat, Sep 23, 2023 at 2:31 AM Charles Tapley Hoyt < ***@***.***> wrote:
@zhengj2007 <https://github.com/zhengj2007> I don't understand. Does my
proposed change conflict with other upcoming changes?
If it's a matter of the ID ranges, you can assign me a certain range and I
will update it to that. Otherwise, waiting months would be a big problem
for my project
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--
Anthony Huffman,
DCMB Student,
He Lab
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Quick update:
After speaking with Oliver, the primary concern with this method is
potential effects the intermediate structure from these new terms will have
to be settled. Otherwise, he is in favor of the general idea. It currently
will appear that we will schedule a meeting to resolve this situation
sometime next week; you are welcome to join along with generation of
further terms. I will let @yongqunh schedule the meeting. I hope this
works; if everything can be resolved before then we will probably push a
merged version within the next two weeks.
…On Sat, Sep 23, 2023 at 7:52 AM Anthony Huffman ***@***.***> wrote:
Hey All,
I will speak with Oliver about this today on when we're pushing the next
merge update. I will get a clearer timeline for you later today and would
be pushing for inclusion.
My current understanding is that the primary case is that the creation of
the template file would use those new terms to update and fix all the
issues of the ontology would be responsible for the delay. I don't see an
issue at this point for doing a minor update patch to include those terms;
only for updating the appropriate vaccines into the correct categories.
On Sat, Sep 23, 2023 at 2:31 AM Charles Tapley Hoyt <
***@***.***> wrote:
> @zhengj2007 <https://github.com/zhengj2007> I don't understand. Does my
> proposed change conflict with other upcoming changes?
>
> If it's a matter of the ID ranges, you can assign me a certain range and
> I will update it to that. Otherwise, waiting months would be a big problem
> for my project
>
> —
> Reply to this email directly, view it on GitHub
> <#620 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ANDAISGOJTRH6KL3T7WXF6DX3Z65FANCNFSM6AAAAAA5DBMKUU>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: ***@***.***>
>
--
Anthony Huffman,
DCMB Student,
He Lab
--
Anthony Huffman,
DCMB Student,
He Lab
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Yes. I talked to Anthony today. I was in traveling yesterday so did not check emails. Sorry for that. It appears to be good to have a term "vaccine for disease". I do have a question here: is there any vaccine that is not for a disease? If there is none, than vaccine = "vaccine for disease". In this case, it may not be necessary to generate such a term. Then, we can put the axiom |
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In general, not all vaccines immunize against disease. For example, there are several vaccines that work as contraceptives (see VO:0000759 hierarchy), as profertility agents (see VO:0000372) However, the purpose I have here is to note that there are many ways of describing a vaccine:
Because there are many senses in which you might talk about a vaccine, I think it makes sense to have multiple sub-hierarchies corresponding to each. A given vaccine can be part of multiple of these, as it's obviously the case that a given vaccine typically has all of these properties. How it is, these annotations are actually very sparse, and some specific vaccines are only annotated based on one of them (when it would be ideal to have all) Many terms can't be annotated with a disease, for example, DNA Vaccines (VO:0000032) are a totally different subhierarchy for vaccines that describe the platform. This is why we should not add any annotations to the top-level vaccine term, since when you talk about DNA Vaccine, you don't imply that it has a certain activity, just that it works in a given way. As a follow-up to the change in this PR, I will also propose a "vaccine by platform" grouping term |
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Thanks for clarification. I think it makes sense. I will next merge pull request. |
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Luckily the curation of the material basis of a disease is within the domain of the Disease Ontology / MONDO, and this can be imported. |
Similarly to vaccineontology#620, this pull request adds a mid-level grouping term between VO:0000001 (vaccine) and four child terms: 1. fungal vaccine 2. bacterial vaccine 3. protozoan vaccine 4. virus vaccine This is added in the term "vaccine for pathogen" (VO:0005504). It has the axiom `immunizes against microbe` some 'organism'` as a reminder that all subclasses of this term should include a statement saying specifically which taxa they immunize against Finally, this PR adds a domain (vaccine) and range (organism) annotation to `immunizes against microbe`
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@yongqunh thank you for looking this over. I hope we can add a few other similar PRs in quick succession! |
Similarly to vaccineontology#620, this adds a mid-level grouping term between VO:0000001 (vaccine) and several children representing vaccine platforms: 1. conjugate vaccine 2. DNA vaccine 3. inactivated vaccine 4. live virulent vaccine 5. live attenuated vaccine 6. passive vaccine 7. toxoid vaccine 8. whole organism vaccine 9. virus-like particle vaccine 10. recombinant vector vaccine 11. RNA vaccine 12. subunit vaccine This is added in the term "vaccine for platform" (VO:0005505). This doesn't add any axiomization regarding this grouping at the moment, since it's not yet clear if there's a shared way of ontologizing "what is a platform". Looking forward, platforms are typically defined as a combination of the one or more of the components/antigens/adjuvants/other ingredient types
cthoyt
changed the title
VO:0005503 to group vaccines for diseases
Part of #619
This PR does the following:
'immunizes against disease' *some* 'disease'This makes it easier to group vaccine terms that are specifically about the disease for which they immunize.
Further, this simple demonstration shows that it will be possible to make slightly larger changes in subsequent contributions to group the other vaccine sub-hierarchies such as target-based terms and platform-based terms.