I believe AJ has a valid point. As somewhat of an outsider to the biomedical field, but a practioner in other scientific informatics fields, I am aware of numerous other efforts to develop ontologies, or their equivalent, for describing an experiemtn and its results. For example, in the area of laboratory information management systems, there are a variety of standards that deal with recording individual experiments. Materials informatics has similar standards. They are not necessarily using an ontology construction, but they have equivalent information content.
 
What has struck me as most curious in the wealth of e-mails on this subject is the emphasis on reporting the intent of the experiment. I say this is curious because because research has an inherent component that is almost undefinable. I do this experiement ostensibly to disprove that "aspirin can cause stomach cancer in rats," but I hope to discover what effect aspirin might have on stomachs in general.
 
The ultimate point is that what we report in an archival publication (peer-reviewed, etc.) is a refinement of what we were thinking when we started.
 
Consequently, I think that AJ's suggestion of multi-tasking of a prototype ontology that can be exercised and learned from. The diversity of approaches across science is just too large to get it right the first time.
 
John Rumble
 
p.s. Several weeks ago I mentioned some work on nomenclature and linguistic barriers to scientific data standards. The link to that article is http://www.infointl.com/pdf/developing_using_standards.pdf, in the sections at the end .


-----Original Message-----
From: AJ Chen
Sent: Jul 7, 2006 3:42 AM
To: public-semweb-lifesci@w3.org
Subject: how to deal with different requirements for experiment self-publishing

All,
>From the discussions so far, I see a whole spectrum of needs for publishing experiment information.  On one end, some researchers want a quick and easy way to share an experiment, e.g. simply decompose an experiment to hypothesis, data, results, procedure, protocols used, who did it, what project it belongs to, etc. On the other end of the spectrum, some researchers want to describe it with domain-specific terms as detailed as possible, e.g using FuGO or BioPAX terms.  In the middle of the spectrum,  one may want to describe an experiment in general terms but with great details, e.g. using the terms Bill Bug provided from BIRN.

Because of this diversity of requirements, I think it is not realistic to expect one huge ontology will fit all. I would suggest we think of this task in terms of multiple phases so that incremental progress can be made within short time frame. In the first phase (current phase), we focus on a small ontology that can be used to develop quick and easy tools for self-publishing.  In the next phase, we can add more granularity to it. In the third phase, we may figure out how to bridge this general-purpose ontology to domain-specific ontologies that are developed by other groups.  An alternative approach is to have separate tasks to meet different requirements at the same time. 

What do you think? If we take the multi-phase approach, I would suggest further discussions to be focused on the objective of the current phase, i.e. a small and simple ontology.  If anyone likes the multi-task approach, please consider to propose a new task.


AJ