The term attenuated is a disposition but not a quality

4 views
Skip to first unread message

Asiyah Yu Lin

unread,
Apr 4, 2014, 1:43:21 PM4/4/14
to infectious-disease-ontology
Dear IDO developers,

On our recent work on IDOBRU, we found out that the attenuated is a status that depends on the context.

In the vaccine domain: an attenuated pathogen is altered so that it becomes harmless or less virulent towards its host. (http://en.wikipedia.org/wiki/Attenuated_vaccine)
Many methods can make a virulent pathogen to become attenuated, for example, chemical or heat.
Genetic modification is another dedicated way to modify the pathogen. In our lab, we are looking for those genes when mutated in the Brucella, and the mutant Brucella strains will become attenuated.
We found out that, the mutant Brucella strains may attenuated in a certain host cell, (i.e. macrophage), but not in others, (i.e. Hela cell).
related text: "Moreover, the cysI mutant is only attenuated in macrophages and not in HeLa cells that do not produce an oxidative burst."]

Currently,  there are terms of attenuate in Ontobee:

Both of them are considered as a quality. 

We think the term attenuate/attenuated should be a child of disposition, such that the attenuate is realized in the process of pathogen-host interaction, i.e. the Brucella mutant macrophage interaction.

We want to hear people's opinion or agreement on this issue. 
If there is no objections, we will update the definition in VO, and suggest PATO to obsolete this term.

Thanks,
Asiyah Yu Lin 

 

****************************************************************

Asiyah Yu LIN

M.D.,M.Sc.,Ph.D.

Postdoctoral Fellow,

Oliver He Lab,

Unit for Laboratory Animal Medicine,

Department of Microbiology and Immunology,

and Center for Computational Medicine and Bioinformatics,

University of Michigan Medical School

 

Email: yu...@med.umich.edu

Tel: 734-764-0705

Fax: 734-936-3235

 

1031 MBNI,205 Zina Pitcher Place

Ann Arbor, MI 48109-2200

****************************************************************

 

Melanie Courtot

unread,
Apr 4, 2014, 2:37:58 PM4/4/14
to ido-d...@googlegroups.com
Hi Asiyah, all,

Would "attenuated" be one of those "historical qualities" as we have been calling them in OBI? That is something similar to a quality, but which is the output of a specific process (in OBI we had 'amputated' for example)
IIRC, we decided in OBI to create the independent continuant output of the process, as the single term was (as you note) did not match  bfo:quality.
So you would create an attenuation process, and the attenuated pathogen would be the specified output of the process.

Would that work?

Cheers,
Melanie


--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.



--
Mélanie Courtot
Ph.D. Candidate,
BCCRC - Terry Fox Laboratory - 12th floor
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

Asiyah Yu Lin

unread,
Apr 4, 2014, 2:54:47 PM4/4/14
to infectious-disease-ontology
Hi Melanie,

Thank you very much for your response.
The attenuated pathogen as an output is fine.

We will need a dependent continuant term 'attenuated' for linking the pathogen to an interaction with its host.
That's why we propose to update the 'attenuated' to be a disposition but not a quality.

Thanks,
Asiyah



################################################
Jedi Order:
There is no emotion, there is peace.
There is no ignorance, there is knowledge.
There is no passion, there is serenity.
There is no chaos, there is harmony.
There is no death, there is Force.

Our Jedi Code: May peace and force be with you.

Lindsay Cowell

unread,
Apr 4, 2014, 2:56:17 PM4/4/14
to <ido-discuss@googlegroups.com>
I think that's a great idea.
-------------------------------------------------------------------
Lindsay G. Cowell, PhD
Division of Biomedical Informatics
Department of Clinical Sciences
University of Texas Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX  75390-9066
 
F4.212b, MC9066

phone: 214-648-2289
fax: 214-648-2064
Lindsay...@utsouthwestern.edu




UT Southwestern Medical Center
The future of medicine, today.

Scheuermann, Richard

unread,
Apr 5, 2014, 3:45:37 AM4/5/14
to ido-d...@googlegroups.com, <ido-discuss@googlegroups.com>
Yep, sounds like a disposition to me. 

Richard

Sent from my iPhone

Barry Smith

unread,
Apr 5, 2014, 11:36:05 AM4/5/14
to ido-discuss
I think there are different senses of 'attenuated' -- in one sense, certainly, it is an OBI historical quality. (Something's signal intensity may be attenuated, because it is less than it used to be, but it is still higher than the norm for a thing of that type.)

In the sense Asiyah 'attenuated' has in mind would seem to be best represented as an abbreviation for 'attenuated disposition', which refers, of course, to a disposition. 
BS

Asiyah Yu Lin

unread,
Apr 5, 2014, 11:53:07 AM4/5/14
to infectious-disease-ontology

Thank you all for your input.
So we will change accordingly, and label it 'attenuated disposition'.

Best,
Asiyah

He, Yongqun

unread,
Apr 5, 2014, 12:01:07 PM4/5/14
to ido-d...@googlegroups.com

I also like the label 'attenuated disposition'.

 

For our own purposes, we may also add some subclasses, such as

-          microbe attenuated inside host

o   mutant microbe attenuated inside host cell

o   mutant microbe attenuated inside host organism (that is: in vivo)

§  mutant Brucella attenuated in vivo

 

General terms may go to IDO-core. Brucella-specific terms can stay in IDOBRU.

 

Thanks,

 

Oliver He

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Asiyah Yu Lin

unread,
Apr 8, 2014, 5:55:04 PM4/8/14
to infectious-disease-ontology
Another thoughts:
Similarly, if the 'attenuated disposition' is a disposition, the 'virulent' should be a disposition too.

Thanks,
Asiyah



################################################
Jedi Order:
There is no emotion, there is peace.
There is no ignorance, there is knowledge.
There is no passion, there is serenity.
There is no chaos, there is harmony.
There is no death, there is Force.

Our Jedi Code: May peace and force be with you.



Barry Smith

unread,
Apr 8, 2014, 7:52:04 PM4/8/14
to ido-discuss
Avoid using adjectives (such as 'attenuated' and 'virulent') and use instead nouns ('attenuated disposition', 'virulent disposition') when building ontologies, and you will be in good shape
BS

Asiyah Yu Lin

unread,
Apr 9, 2014, 12:29:17 PM4/9/14
to infectious-disease-ontology
Thanks for reminding, Barry.




################################################
Jedi Order:
There is no emotion, there is peace.
There is no ignorance, there is knowledge.
There is no passion, there is serenity.
There is no chaos, there is harmony.
There is no death, there is Force.

Our Jedi Code: May peace and force be with you.



Reply all
Reply to author
Forward
0 new messages