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An ontology for MIDAS data types
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Serology and monoclonal antibody data #55

Closed LucieContamin closed 7 months ago

LucieContamin commented 8 months ago

I am currently adding data about:

Is it correct to note these entries with the topic: "immunogen" (An antigen capable, on its own, of inducing an immune response.) or should I pick (or add) another topic?

Thanks

hoganwr commented 8 months ago

We could add:

https://ontobee.org/ontology/CIDO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCIDO_0000018 which is "COVID-19 diagnostic process by serological assay". I couldn't find anything more general w.r.t. serology that would work.

For monoclonal antibodies,maybe we can create a drug ontology term 'monoclonal antibody therapeutic agent' that defines it along the lines as a product with monoclonal antibody as part, and that monoclonal antibody has a clinical drug role (or perhaps we need to be careful to follow FDA drug vs. biologic distinction, but we could do it)

Fo

On Mon, Jan 29, 2024 at 2:28 PM Lucie Contamin @.***> wrote:

I am currently adding data about:

Is it correct to note these entries with the topic: "immunogen" (An antigen capable, on its own, of inducing an immune response.) or should I pick (or add) another topic?

Thanks

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harryhoch commented 8 months ago

"COVID-19 diagnostic process by serological assay" is a process not a count. consider adding new term.

harryhoch commented 8 months ago

Is the monoclonal antibody a count? a rate? what is the nature of the data

LucieContamin commented 8 months ago

To be precise for the " monoclonal antibody" topic, it's about the estimate number that have, intent or intent not to receive Nirsevimab (monoclonal antibody treatment) Among Females Aged 18-49 Years Who Have a Baby <8 Months, Are Currently Pregnant, or Are Trying to Get Pregnant (results from a telephone survey)

LucieContamin commented 7 months ago

To add more information, the data represent an estimated percentage of persons with the intent or not to receive Nirsevimab from a survey.

hoganwr commented 7 months ago

For seroprevalence import the following term into the MIDAS data OWL file: http://purl.obolibrary.org/obo/IDOMAL_0000344

harryhoch commented 7 months ago

Suggest measurement of intent to vaccinate as a new term.

@LucieContamin, isn't Nirsivemab a vaccine? Where do monoclonal antibodies come in?

LucieContamin commented 7 months ago

For seroprevalence import the following term into the MIDAS data OWL file: http://purl.obolibrary.org/obo/IDOMAL_0000344

Thanks for the seroprevalence term, just a quick questions, is it of any importance that the parent of the term seems to be "Malaria specific"?

isn't Nirsivemab a vaccine? Where do monoclonal antibodies come in?

That's a good question, I am not sure it is correct to call it a vaccine as the mechanism is slightly different. That's why I was not sure which topic to select. It is reported with Vaccine and it seems that a RSV vaccine exists for the mother but Nirsevimab is different.

According to CDC: https://www.cdc.gov/vaccines/vpd/rsv/public/child.html

Nirsevimab contains monoclonal antibodies, which are man-made proteins that protect against RSV. Though it does not activate the immune system the way an infection or vaccine would, a nirsevimab shot provides protection similar to that of a vaccine.

I am not sure the FDA call it vaccine neither: https://www.fda.gov/news-events/press-announcements/fda-approves-new-drug-prevent-rsv-babies-and-toddlers

[..] U.S. Food and Drug Administration approved Beyfortus (nirsevimab-alip) for the prevention of Respiratory Syncytial Virus (RSV) [...] Beyfortus is a monoclonal antibody with activity against RSV. Monoclonal antibodies are laboratory-made proteins that mimic the immune system’s ability to fight off harmful pathogens such as viruses. One dose of Beyfortus, administered as a single intramuscular injection prior to or during RSV season, may provide protection during the RSV season.

harryhoch commented 7 months ago

For seroprevalence import the following term into the MIDAS data OWL file: http://purl.obolibrary.org/obo/IDOMAL_0000344

Thanks for the seroprevalence term, just a quick questions, is it of any importance that the parent of the term seems to be "Malaria specific"?

@hoganwr , this is a good question. What do you think?

isn't Nirsivemab a vaccine? Where do monoclonal antibodies come in?

That's a good question, I am not sure it is correct to call it a vaccine as the mechanism is slightly different. That's why I was not sure which topic to select. It is reported with Vaccine and it seems that a RSV vaccine exists for the mother but Nirsevimab is different.

Good points, @LucieContamin. It looks like Nirvisemab has at least some use as a vaccine. See, for example:

https://www.cdc.gov/vaccines/vpd/rsv/public/child.html

@hoganwr , how should we represent this in the ontology?

harryhoch commented 7 months ago
  1. @hoganwr to add something in Apollo-SV for seroprevlance

  2. Nirvisemab raises several points:

    1. monoclonal antibody is a structural aspect, vaccine is an application. these are orthogonal
    2. intent to vaccinate - not represented. Might need a new term?
    3. rates of vaccination or raw counts?

    @hoganwr to look into points about Nirvisemab

harryhoch commented 7 months ago

estimated rate of vaccination - differs from rate of vaccination

hoganwr commented 7 months ago

Yes there is a big problem with the term being malaria specific, and in a non transparent way. Another problem is that IDOMAL is an inactive ontology, so we cannot expect to ask someone to change it or add a non-malaria-specific term. Therefore, I will create the term in Apollo-SV, basing it off the IDOMAL definition.

With respect to nivisemab, I will work on creating terms for "intention to vaccinate" and "nirvisemab immunization" in Apollo-SV, then import those terms back here, and create new releases of both.