METADATA MANAGEMENT AND SEMANTICS
IN MICROARRAY REPOSITORIES
Kocabaş F1,2,*, Can T3, Baykal N1
*Corresponding Author: Fahri Kocabaş, NATO HQ C3S, Blvd Leopold III B, 1110 Brussels, Belgium;
Tel.: +32-2-707-5533; Fax: +32-2-707-5834; E-mail: FK:fahri@ii.metu.edu.tr; f.kocabas@hq.nato.int
page: 49
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CONCLUSIONS
Microarray informatics has been an active research
direction, especially in architectural and computational
aspects. The conduct of microarray experimentation
is only the first part of the process. The second
part, which is often poorly handled, is to organize,
present, exchange, understand and use the interpreted
experimental evidence. Thus, gaps and inconsistencies
as well as ambiguities in the microarray knowledge
base such as candidate theories, scientific disagreements,
and open questions can be managed and
resolved. To obtain new insights and knowledge, the
data generated by high throughput experiments need to
be transformed into meaningful executive summaries.
We propose metadata card and semantic net to represent
such summaries. Testing the hypotheses based on
these summaries may become an interesting task for
computational biology.
This study covers the improvement in the structure,
syntax, and semantics of the metadata of microarray
experiment result data sets. We demonstrate that the
introduction of metadata cards can support discovery
and exchange operations. SemNets could be a vehicle
to represent the meaning in the microarray domain.
Since domain experts created the SemNets, previously
unknown details can be revealed. The proposed framework,
MAdmf, does not replace but complements the
existing products in the microarray domain. MAdmf
can be used in microarray repositories, other high
throughput repositories, and third-party platforms. The
driving philosophy behind MAdmf comes from data
management, knowledge engineering, semantic web
and structured messaging paradigms.
We believe that once such standardization efforts
become adopted, the required tools and detailed guidance
will follow. The following topics need further
investigation. The set up of a metadata registry and
guidance for how to submit a package to the metadata
registry; the life cycle management of records; structured
data entry; configuration model to include states
(retired, incomplete, or complete) and status in each
state (conflicting, derived, or verified); the synchronization
mechanism among various repositories over
metadata information elements.
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