Biomedical Engineering Reference
In-Depth Information
Furthermore, the Human Proteome Organization Proteomics Standards
Initiative (HPO-SI) has helped enable the development of unifi ed standards
for proteomics. Through a collaborative model, HPO-SI has had an integral
role in the development, publication, and adoption of several new interchange
formats, commonly accepted terminologies, and data standardization, and
presents a view on developments and policy. Additionally, repositories to
support the HPO-SI formats are readily being established, while minimum
reporting requirements have been developed and submitted for journal pub-
lication after prolonged exposure to community input via the PSI website [11].
Building off the standards developed by the PSI-MI, several public interac-
tion databases came together to establish the International Molecular
Interaction Exchange (IMEx) consortium (http://imex.sf.net). The IMEx con-
sortium is an international collaboration among several public interaction data
providers all agreeing to share curation efforts and to:
Develop and work to a single set of curation rules when capturing data
from both directly deposited interaction data and publications in peer-
reviewed journals
Capture full details of an interaction in a “ deep ” curation model
Perform a complete curation of all protein - protein interactions experi-
mentally demonstrated within a publication
Make interaction available in a single search interface on a common
website
Provide the data in standards compliant download formats
Make all IMEx records freely accessible under the Creative Commons
Attribution License
One additional example of the standardization efforts is the Minimum
Information About a Proteomics Experiment (MIAPE) guidelines, which are
aimed at the establishment of “ MIAPE - compliant ” reporting [12] .
3.6 CHALLENGES AND OPPORTUNITIES IN
COMPUTATIONAL BIOLOGY
3.6.1
Open - Access Repositories
Due to the large amount of genomic data accumulated, the need for publicly
available data repositories arose for collecting the data generated by the
various research groups. This need, for example, is fi lled in North America by
the Gene Expression Omnibus (GEO), developed by the National Center for
Biotechnology Information (NCBI) [13]; in Europe by ArrayExpress, devel-
oped by the European Bioinformatics Institute (EBI) (http://www.ebi.ac.uk/
microarray-as/ae); and in Japan by the Center for Information Biology Gene
Expression database (CIBEX), developed by the DNA Data Bank of Japan
(DDBJ) (http://cibex.nig.ac.jp). These repositories were established to store
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