Re: ontology specs for self-publishing experiment

AJ,

This is a great start, and thanks for taking this on! I would like to  
see this task force propose a conceptual framework within the two  
months. It does not have to be final, but I think we need to have  
others on the list review the ontologies (http://esw.w3.org/topic/ 
HCLS/ScientificPublishingTaskForce? 
action=AttachFile&do=get&target=SPE_Specs.html) and requirements  
(http://esw.w3.org/topic/HCLS/SciPubSPERequirements) you have  
proposed, ask questions about them, and adjust/expand as needed.

I think there has been good discussions on this topic in the past,  
and I would also refer folks to the SWAN paper by Gao et al.  http:// 
www.websemanticsjournal.org/ps/pub/2006-17 . This work is inline with  
with what Tim Clark has been proposing to the group, and I think it  
is a useful model to consider. Perhaps we can combine these efforts  
and propose a workable (demo anyone?) by the end of summer...

In terms of gathering more Scientific Publishing of Experiments (SPE)  
requirements, I wanted to list some items that appear to be inter- 
related and relevant:

1. By Publishing experiments, one must also consider (i.e., include  
in the ontology):
	a. Publishing Protocols
	b. Publishing Regants and Products
	c. Stating the Hypothesis (and model using RDF) that is being tested  
by the experiment; this includes which citations are supportive or  
alternative to ones hypothesis
	d. Publishing Experimental Data (possibly as RDF-OWL aggregates and  
tables)
	e. Articulating the Results and Conclusions; specifically, whether  
the experiment refutes or supports the central Hypothesis (most of us  
agree we cannot 'prove' a hypothesis, only disprove it)

2. Hypotheses should be defined in terms of authorship (ala DC), what  
the proposed new concepts is, and what (experimental) fact (or claim)  
is required to support it. It should also refer to earlier hypotheses  
either by:
	a. extension of an earlier tested and supported hypothesis: refinement
	b. similarity or congruence with another untested hypothesis:  
supportive
	c. being an alternative to another hypothesis, that will qualify  
itself through the refutation of the earlier one: refutation
This would allow one to define rules and queries that can traverse  
the lineage of hypotheses (forwards and backwards, similar to  
citations), and how one papers work can be related to ongoing work on  
different fronts that have branched.

3. "Publication" should be a specific concept in SPE, that would  
serve to be the hub of DC metadata as well as the above experimental  
data and hypotheses. Different non-disjoint Publication "Roles" could  
be defined, such as  Peer-Reviewed, Electronically-Published, Topic  
Review, and Follow-up Data. I would also invite the folks interested  
in Clinical Publications to specify what requirements they feel  
should be included, (e.g. regulatory applications, Common Technical  
Document).

I also think it would be useful if we could add a Concept Map graphic  
for the proposed SPE ontology (class relations mainly). Sometime  
ideas can get expressed faster to the larger community using images.

cheers,
Eric




> From: AJ Chen <canovaj@gmail.com>
> Date: Sun, 25 Jun 2006 16:00:23 -0700
> Message-ID:  
> <70055a110606251600m469b7d63t405579e7a61e7ef8@mail.gmail.com>
> To: public-semweb-lifesci@w3.org
> I added the first draft of specs for the ontology being developed for
> self-publishing experiment. see the link on the task wiki page -
> http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
>
> This specs document and the requiremnets document are meant to be  
> only the
> starting point for discussion.  I truly hope more people in this  
> group will
> participate in this open development process, making comments or  
> providing
> changes to the documents.
>
> While the ontology is being developed by this community, I am going to
> develop a self-publishing tool that implements the ontology, which  
> allows
> you to try this new way of sharing research information. With easy- 
> to-use
> tools to demonstrate the benefits of sharing and searching experiment
> information in semantic data format, it will help attract more  
> people to
> contribute to the development of the ontology as well as the tools.
>
> Best,
> AJ



Eric Neumann, PhD
co-chair, W3C Healthcare and Life Sciences,
and Senior Director Product Strategy
Teranode Corporation
83 South King Street, Suite 800
Seattle, WA 98104
+1 (781)856-9132
www.teranode.com