[Obi-protocol-application-branch] inconsistency when adding organism to study specinem role

[Fostel, Jennifer (NIH/NIEHS) [C]]

biomaterials:
transgenic organism
cell lysate

processes:
electrocuted
enrolled
cervical dislocation
killing
genetic trasnformation
decapitation
DNA transformation
cell lysis
electroporation
asphyxiation
intentional overdosing
DNA transduction

i need to allow all organisms with the exception of humans to play the role of a study specimen
what should i do?

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

[Richard H. Scheuermann, Ph.D.]

Why is it that a human participant can't be a study specimen?

Richard

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Richard H. Scheuermann, Ph.D.

Chief, Division of Biomedical Informatics

Director, Division of Translational Pathology

John H. Childers Professorship in Pathology

Department of Pathology

U.T. Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX  75390-9072

phone: 214-648-4115

FAX: 214-648-4070

email: richard.s...@utsouthwestern.edu

http://pathcuric1.swmed.edu/Research/scheuermann.html

[Fostel, Jennifer (NIH/NIEHS) [C]]

a human can be a study subject, and tissue from a human can be a specimen but i cannot imagine a study in which a human is entirely converted into a specimen

---

From: Richard H. Scheuermann, Ph.D. [mailto:richard.s...@utsouthwestern.edu]
Sent: Thursday, January 15, 2009 11:08 AM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: obi-rol...@lists.sourceforge.net; obi-bio...@googlegroups.com; obi-protocol-ap...@lists.sourceforge.net
Subject: Re: [Obi-role-branch] inconsistency when adding organism to study specinem role

[Bjoern Peters]

- I don't understand what the terms on the top of the email have to do
with the question at the end.

- For the question: You need to create a defined organism class:
'organism and not homo sapiens'. For that to infer correctly, disjoints
would have to be set througout the entire organism hierarchy.

- I understand that you want to keep the separation between study
subject and specimen, but this will be difficult to maintain. I still
think we need a parent role 'study object(?)' with children 'human study
subject' and 'study specimen'.

Bjoern

Fostel, Jennifer (NIH/NIEHS) [C] wrote:
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--
Bjoern Peters
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La Jolla Institute for Allergy and Immunology
9420 Athena Circle
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[Richard H. Scheuermann, Ph.D.]

behavioral research, imaging analysis, height measurement

[Richard H. Scheuermann, Ph.D.]

I guess I would like to hear the argument for why humans should be considered as a special case.  If the argument is based on the special recording requirements associated with human studies research, the same argument could be made for research involving vertebrate animals, which also have a whole series of special approval and reporting requirements.  Apparently no one cares about microbes or plants; we can do as we like to them.

But the point is, why should humans be treated differently from a theoretical perspective?

Richard

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[Fostel, Jennifer (NIH/NIEHS) [C]]

these are not specimens.....

---

From: Richard H. Scheuermann, Ph.D. [mailto:richard.s...@utsouthwestern.edu]

Sent: Thursday, January 15, 2009 1:27 PM

To: Fostel, Jennifer (NIH/NIEHS) [C]

Cc: obi-protocol-ap...@lists.sourceforge.net; obi-rol...@lists.sourceforge.net; obi-bio...@googlegroups.com

[Fostel, Jennifer (NIH/NIEHS) [C]]

i cannot think of a case where an entire human is dropped into a blender or put into a freezer for long-term storage for later assay.

these are what we do with specimens.

 

we can observe humans, as you have exemplified, but these humans do not bear the specimen role.

they do bear specified_input_role

---

From: Richard H. Scheuermann, Ph.D. [mailto:richard.s...@utsouthwestern.edu]

Sent: Thursday, January 15, 2009 1:37 PM
To: Bjoern Peters
Cc: obi-protocol-ap...@lists.sourceforge.net; obi-rol...@lists.sourceforge.net; obi-bio...@googlegroups.com
Subject: Re: [Obi-protocol-application-branch] [Obi-role-branch][obi-biomaterial] inconsistency when adding organism to studyspecinem role

[Frank Gibson]

On Thu, Jan 15, 2009 at 6:36 PM, Richard H. Scheuermann, Ph.D.
<richard.s...@utsouthwestern.edu> wrote:
> I guess I would like to hear the argument for why humans should be
> considered as a special case.

Agreed, I don't believe it is a special case. I still think the use of
the prefix study_ is confusion the issue. The Ontology of Biomedical
Investigation deals with investigations. Investigations can have
subjects and specimens, they are not a special case for the process of
study (or realisation of study design). We use the words subject and
specimen with no reference to a "study".

I would suggest that subjects are only roles played by whole organisms
and specimens are only roles played by entites_of_organism_origin.
However, the definition of what a specimen is still conflated with
sample, which is an outstanding issue that still has not been
addressed.

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

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