[Obi-protocol-application-branch] Propose some vaccine related terms to be added to OBI

[Yongqun He]

Dear Bjoern and all in the OBI Protocol application branch,

 

I have just registered for an account in OBI protocol application branch. I am glad to meet you all here.

 

I propose to add three terms that are related to biomedical protocol application. These terms have been used in the Vaccine Ontology (VO, http://www.violinet.org/vaccineontology/):

 

Term 1: ‘vaccination’:

Definition: an ‘administering substance in vivo’ that involves in adding vaccine into a host (e.g., human, mouse) in vivo.

-- Realize some ‘material to be added role’ borne by some ‘material entity’ and has_role some ‘vaccine’

-- Realize some ‘target of material role’ borne by some ‘organism’ and has_role some ‘host’

Note: I have discussed with Bjoern on this term definition.

 

Term 2: ‘vaccine protection assay’

Definition: an assay that determines if a vaccine, after vaccination, protects against challenge infection with virulent pathogen. This is an assay to determine vaccine efficacy. 

To define it:

assay

and has_input some 'vaccine' and some ‘pathogen’

and has_output some 'pathogen survival count'

and utilizes_device some instrument

Note: some potential problems exist for this term. For this assay, we need to vaccinate an animal or human (has_role host) first with vaccine, then we need to change this host with pathogen. I don't know if the current OBI 'assay' handles this two-step case. To make this assay work, we also need to add the other terms: vaccine, pathogen, and 'pathogen survival count' (or something similar). 

 

Term 3: “immune response assay”

Definition: an assay that measures immune response induced by a material entity, for example, vaccine.

assay

and has_input some 'material entity'

and has_output some 'immune response'

and utilizes_device some instrument

Note: We don't have the term 'immune response' yet in OBI.

 

It is noted that the first two terms are vaccine specific and the third term covers broader areas. As we discussed in the OBI Vancouver Workshop, since vaccine research is an important part of biomedical investigation, we have agreed to at least add a few top-level terms from the Vaccine Ontology (VO) to OBI in order to link VO to OBI.

 

Please let me know if I need to provide more information. I have some other VO terms that can be potentially added to OBI protocol application branch. I would like to see the above three terms work out first.

 

Thanks!

 

Oliver

 

Yongqun "Oliver" He, DVM, PhD
Assistant Professor
Unit for Laboratory Animal Medicine
Department of Microbiology and Immunology
and Center for Computational Medicine and Biology

University of Michigan Medical School
Office: Room 105, Animal Research Facility (ARF)

Mailing: 018 ARF, 1150 W. Medical Center Dr.
Ann Arbor, MI 48109
Email: yong...@umich.edu
Tel: 734-615-8231 (O); 734-615-2455 (L)
Fax: 734-936-3235
http://www.ulam.umich.edu/academic/he.htm 
http://www.med.umich.edu/microbio/bio/he.htm

http://www.hegroup.org/  

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