Re: [Obo-discuss] Namespace and PURL requests for "OVAE" for "Ontology of Vaccine Adverse Events"

[He, Y. <yon...@me...>]

Hi Chris,

Thanks for asking. Here are my answers to your questions:

The top level ontologies of OVAE are the Vaccine Ontology (VO) and the Ontology of Adverse Events (OAE). Both VO and OAE are members of the OBO Foundry library now. 

Current OVAE imports 105 OAE classes and 307 VO classes. OVAE contains 652 terms with "OVAE_" prefix, which are mostly generated by using terms imported from OAE and VO. For example, an OVAE term called 'Afluria-associated injection-site pain AE' is a class that uses the OAE term 'injection-site pain AE' and refers to the influenza vaccine Afluria represented in VO.  

It is difficult to have OVAE simply be a subset of either/both of OAE/VO. Here are the reasons:
1.  OAE is not appropriate or responsible for representing various AEs specific for any particular medical intervention including vaccination due to the following reasons. 
    First, OAE emphasizes the representation of various AEs general for most medical interventions and related topics (e.g., methods for analysis of the causal relation between AEs and medical interventions, and factors affecting the causality analysis). Currently OAE is already large and contains over 3,000 terms. It is expected that many more AE terms will be added to OAE. Therefore, it is ideal to make OAE focused and as concise as possible. 
    Second, AE researchers related to specific medical intervention domains may have more domain-specific demands and requests. For example, vaccine AE (VAE) researchers would like to link AEs to different vaccines. The vaccine (or drug) researchers may not be interested in drug (or vaccine)-specific AEs. 
    

2. The Vaccine Ontology (VO) is not suitable for representing complex VAE data. 
     VO has been focused on classification of various vaccines, including licensed vaccines, vaccines in clinical trials, and vaccines only verified in laboratory animal models. VO also represents various types of vaccine components (e.g., vaccine antigens, adjuvants, and vectors), vaccine attributes (e.g., vaccine organism viability and virulence), vaccination methods, and other concise and closely related vaccine information. 
    The inclusion of complex VAE information (over 600 VAE terms now and expected to be thousands in the future) to VO would make VO imbalanced and lack of focus. 

Furthermore, as a relatively independent domain, VAEs have been focuses of many vaccine researchers and groups. Independent from drug AEs, clinical VAEs are reported to vaccine-specific VAERS system in the USA.

Due to these reasons, we generated the VAE-specific OVAE. Since both OAE and VO use the Basic Formal Ontology (BFO) (http://www.ifomis.org/bfo) as the top level class, the alignments between OVAE, OAE, and VO are easy and straightforward. 

The goal of current OVAE development is to generate an ontology-based VAE knowledgebase that represents known adverse events (AEs) associated with licensed vaccines. Please see the paper I provided in my early email for more information.

More comments and suggestions are welcome. Thank you!

Oliver



-----Original Message-----
From: Chris Mungall [mailto:cjm...@lb...]
Sent: Monday, July 15, 2013 2:13 PM
To: obo...@li...
Cc: He, Yongqun
Subject: Re: [Obo-discuss] Namespace and PURL requests for "OVAE" for "Ontology of Vaccine Adverse Events"

Hi Oliver

Why is a new top level ontology required here?

Does this ontology contain the intersection of classes in OAE and VO?

Or does it contain unique classes, with both OAE and VO importing this?

Is it not possible to have this simply be a subset of either/both of OAE/VO?

On Jul 15, 2013, at 7:10 AM, He, Yongqun wrote:

> Dear OBO,
> 
> I would like to request the use of the "OVAE" namespace within the OBO domain for the Ontology of Vaccine Adverse Events.
> 
> The OVAE has been developed to extend the Vaccine Ontology (VO) and the Ontology of Adverse Events (OAE) to study the domain of vaccine adverse events. I have presented the work on OVAE in the Vaccine and Drug Ontology Studies (VDOS-2013) workshop last week in Montreal, Canada. 
> 
> The OVAE source code is available in a Google Code website: http://code.google.com/p/ovae . 
> The OVAE pro-ject website is: http://www.violinet.org/ovae .
> OVAE has been deposited to the BioPortal project of the National Center of Biomedical Ontology (NCBO): 
> http://bioportal.bioontology.org/ontologies/3227
> OVAE is also deposited in Ontobee: 
> http://www.ontobee.org/browser/index.php?o=OVAE
> 
> Any suggestions and comments are welcome. Thank you!
> 
> Oliver
> 
> Yongqun "Oliver" He, DVM, PhD
> Associate Professor
> Unit for Laboratory Animal Medicine
> Department of Microbiology and Immunology Center for Computational 
> Medicine and Bioinformatics and Comprehensive Cancer Center University 
> of Michigan Medical School
> Mail: 018 ARF, 1150 W. Medical Center Dr.
> Ann Arbor, MI 48109
> Email: yon...@me...
> Tel: 734-615-8231 (O)
> http://www.hegroup.org/   
> 
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