W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > July 2006

how to deal with different requirements for experiment self-publishing

From: AJ Chen <canovaj@gmail.com>
Date: Fri, 7 Jul 2006 00:42:45 -0700
Message-ID: <70055a110607070042q5e8b8b35r1f61cc12fbf8d170@mail.gmail.com>
To: public-semweb-lifesci@w3.org
>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.

Received on Friday, 7 July 2006 07:42:52 UTC

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