Re: [Obi-role-branch] role branch notes april 6

[Fostel, J. (NIH/N. [C] <fo...@ni...>]

thanks for your note.
to address some of your comments....
a pathogen disposition is related to host-range, the host(s) it can infect.  eg, "Ebola virus is human pathogen" reflects this.  as does "Ebola virus causes Ebola disease in humans and non-human primates."
alternatively, "humans and non-human primates have a disposition to develop hemorrhagic fever after being infected by Ebola virus" should also be reflected in OBI.

if the pathogen infects you and you don't get the full disease, it is not realizing its role as pathogen.  it still has disposition pathogen, however, which is why we need both
if the pathogen infects you without experimental intervention, i don;t think it realizes the pathogen role either; i think it is disposition here as well.
BTW we need a better name for disease process than _disease course.

indeed, the pathogen role should be restricted to virus, bacteria, fungi, protozoa, etc.  it is currently impossible to do this in OBI as all we have under eukaryota is homo sapiens.

Oliver and would like to discuss many things under disposition; is it possible to set up a call sometime?  we would prefer not to start many long e-mail threads, but are open to this if necessary
you do have to promise to summarize comments at the top of each rather than interweaving comments, since i have trouble reading interwoven comments after a second person has added to them.  :-)

..jennifer

________________________________
From: Melanie Courtot [mailto:mco...@gm...]
Sent: Monday, April 06, 2009 3:38 PM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: obi...@li...
Subject: Re: [Obi-role-branch] role branch notes april 6

Hi Jennifer,

Sorry I couldn't make it this morning (next Monday is a holiday here as well)

On 6-Apr-09, at 9:20 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote:

Oliver and I met today
we added host role:  pathogen role is a role which inheres in an organislm and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role

So you are thinking having a pathogen disposition (e.g. for the ebola virus in a tube somewhere in a fridge) and a pathogen role which is realized when the ebola virus infects an organism.

I have a few questions:
- isn't a pathogen always pathogen for a specific organism? E.g. the Cowpox virus is pathogen only for cows. So the pathogenic disposition would be some kind of relational disposition between a pathogen and an organism?
- if I am infected by a pathogen, and it doesn't cause the disease (because I am immune, vaccinated or else), it wouldn't realize its pathogen role, right?
- should the pathogen role/disposition be restricted to more than just organism as bearers? I don't think a human can be a pathogen. Maybe virus, bacteria, fungi?


we are working on virulence factor and toxin
we would like to meet with the disposition branch for dispositions such as toxin, pathogen, host, host-range, virulence factor, allergen, immune response, disease.

There is no real disposition branch. Several people have been taking care of it when additions were needed. Lately I think it was mostly Alan and I.
Maybe if we can work on definitions as a starting point?



we also need to discuss with PPA branch as to how to represent objective of causing disease course and immune / allergic response

at our next call we will add an agent role / disposition; examples of agent = an active and efficient cause; capable of producing a certain effect; One that acts or has the power or authority to act cfwww.answers.com/topic/intelligent-agents ; wordnet.princeton.edu/perl/webwn

Could you give me more details on the use case for that one?

Thanks,
Melanie



...jennifer


Jennifer Fostel, Ph.D.
CEBS Scientific Administrator
Global Health Sector, SRA International, Inc

Laboratory of Respiratory Biology
NIEHS, NIH
PO Box 12233 Mail Drop F1-05
111 Alexander Drive
Research Triangle Park NC 27709-2233

phone 919 541 5055
fax 919 541 1460


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