NTRs: antibody assay kits & their manufacturers

[johnwjudkins]

Label: Scrub Typhus DetectTM IgM ELISA kit Definition: A protein microarray manufactured by InBios International that uses a 96-well plate and the 56-kDa type-specific antigen to test for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716. Parent: protein microarray Source: doi: 10.1186/s12879-020-4861-y Subclass axiom: 'has manufacturer' value InBios

Label: InBios Type: manufacturer Definition: A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases.

Label: Panbio Dengue IgM capture ELISA kit Parent: protein microarray Definition: A protein microarray, manufactured by Abbott for detection of Dengue virus, that consists of two plates, one containing stabilized Dengue viruses 1 through 4 and the other containing anti-human IgM antibody. Source: doi: 10.1016/s1386-6532(99)00076-1. subclass axiom: 'has manufacturer' value Abbott

Label: Panbio Dengue Early ELISA kit Parent: protein microarray Definition: A protein microarray manufactured by Abbott that uses an anti-NS1 monoclonal antibody to detect the NS1 Dengue viral protein. Ed. note: "Early" refers to the fact that the kit can be used for an assay in the first day of symptom onset, due to the high levels of NS1 in blood at that time. Source: https://www.globalpointofcare.abbott/en/product-details/panbio-dengue-early-elisa.html | doi: 10.1371/journal.pntd.0000738 Subclass axiom: 'has manufacturer' value Abbott

Label: Abbott Definition: A manufacturer of rapid point-of-care assay devices. Type: manufacturer Source: https://www.globalpointofcare.abbott/en/about.html

Label: SD Bioline Chikungunya IgM RDT kit Definition: A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus using analytical chromatography. Source: https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html Parent: device Subclass axiom: 'has manufacturer' value Abbott

Label: SD Bioline Chikungunya IgM capture ELISA Definition: A protein microarray manufactured by Abbott for detection of human IgM antibodies for Chikungunya virus using ELISA. Parent: protein microarray Subclass axiom: 'has manufacturer' value Abbott

Label: Advantage Chikungunya IgM Card Definition: A protein microarray manufactured by J. Mitra for detection of human IgM antibodies for Chikungunya virus, using double-antigen sandwich ELISA. Source: https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html Parent: protein microarray Subclass axiom: 'has manufacturer' value 'J. Mitra'

Label: J. Mitra Definition: A manufacturer of in vitro diagnostic assay kits in India. Type: manufacturer Source: https://jmitra.co.in/about-us/

[johnwjudkins]

Discussed 2021-11-15. Will provide definition for assay kit as device having everything needed to run some assay (to include RDTs and kits including protein microarray. Kits are combinations of devices. Definitions of individual manufacturers do not need to be this specific. Will defer to COB/workshop about device/reagent placement.

[johnwjudkins]

Proposed definition for 'assay kit':

"A device that is designed for a type of assay and contains necessary devices and reagents to complete an assay of that type, but may not contain devices and reagents common to a laboratory or large equipment ."

I word it this way to include general cases like this one where the kit includes necessary reagents, but a separate source of water and a UV spec is also needed. I was also going to mention that the evaluant is not included, but I think that is implied in the 'reagent' definition. "Include" might be better than "contain".

[johnwjudkins]

Bjoern et al: A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit.

Discussed 2022-04-04. Agree to add term with above definition & example/comment to clarify meaning. Will make PR.

[johnwjudkins]

Also discussed 2022-04-04 how to define individual manufacturers: definitions, if included, must be equivalent. Many want to include National Manufacturers Directories / Wikipedia URLs, https://www.mni.net/info/national etc. Many be a COB discussion. Manufacturer terms (for now) can be added with a descriptive rdfs:comment and no definition. Wikipedia link encouraged.

[johnwjudkins]

Here are definitions for the assay kit terms updated to reflect the addition of the 'assay kit' term, the proposed parent of these terms. These can also have 'has manufacturer' axioms to identify the manufacturer.

Label: Scrub Typhus Detect IgM ELISA kit Definition: An assay kit that is manufactured by InBios International to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716 with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen. 'capable of' some 'ELISA measuring Orientia tsutsugamushi IgM antibody'


Label: Panbio Dengue IgM capture ELISA kit Definition: An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody. Source: doi: 10.1016/s1386-6532(99)00076-1. 'capable of' some 'microarray assay measuring Dengue IgM antibody'

Label: Panbio Dengue Early ELISA kit Definition: An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody. 'capable of' some 'microarray assay measuring NS1'

Label: SD Bioline Chikungunya IgM RDT kit Definition: An assay kit that is manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus using analytical chromatography. 'capable of' some 'chromatography assay measuring Chikungunya IgM antibody' Source: https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html


Label: SD Bioline Chikungunya IgM capture ELISA kit Definition: An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA.
 'capable of' some 'ELISA measuring Chikungunya IgM antibody'

Label: Advantage Chikungunya IgM Card kit Definition: An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA. 'capable of' some 'microarray ELISA measuring Chikungunya IgM antibody' Source: https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html

[johnwjudkins]

As discussed just now (2022-08-01), 'assay kit' will be moved to 'device'. I will make a pull request.

[johnwjudkins]

Defining axioms: relation between kit and assay. Data terms from these can be connected through 'is about' relation to the material entity detected. Axioms connect kit to manufacturer. Will come back with specific design pattern.

[johnwjudkins]

For the following images, the example term to be defined is in bold/shadow, and assay terms are yellow.

The first image represents the design pattern to add terms for assay kits.

The second image represents the design pattern for the assays that the kits are designed to perform. I used "ELISA measuring..." in the label for the example term, following children of enzyme-linked immunosorbent assay. Axioms follow the same pattern as children of antigen specific antibodies assay.

[johnwjudkins]

2022-10-10: Clear up whether analyte is antigen or antibody and include relation of assay to specimen; otherwise design pattern OK.

[bpeters42]

Hi John,

For the lower graph for the ELISA assay, I think we should discuss more. There are 2 types of ELISAs, those (like in your case) that measure the presence of antibodies specific to a virus, and others (which is most of what we currently have) that measure the presence of e.g. a virus using antibodies as a reagent. It looks like we don't have this upper level distinction well done in OBI right now; in one case the antibody is the analyte, in the other, an antibody is a reagent. We need to fix that. Hector, can you please look into this?

• Bjoern

On Thu, Sep 22, 2022 at 1:14 PM John Judkins @.***> wrote:

For the following images, the example term to be defined is in bold/shadow, and assay terms are yellow.

The first image represents the design pattern to add terms for assay kits.

[image: obi-assay-kit] https://user-images.githubusercontent.com/12487421/191836450-be85758f-8145-4444-9b37-ac816ee7c690.png

The second image represents the design pattern for the assays that the kits are designed to perform. I used "ELISA measuring..." in the label for the example term, following children of enzyme-linked immunosorbent assay http://purl.obolibrary.org/obo/OBI_0000661. Axioms follow the same pattern as children of antigen specific antibodies assay http://purl.obolibrary.org/obo/OBI_0002145.

[image: obi-antibody-assays] https://user-images.githubusercontent.com/12487421/191842261-0f1f98e4-642a-49a6-92fc-7d799b9d2416.png

— Reply to this email directly, view it on GitHub https://github.com/obi-ontology/obi/issues/1456#issuecomment-1255501917, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IXY5265GEO2QT24XPTV7S44DANCNFSM5H5UPULA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[johnwjudkins]

Here's an example of the design pattern for the assays in bold above:

[johnwjudkins]

Discussed 2022-12-05. Design pattern OK. Will define assays & update.