Biology Reference
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without a lot of preliminary manual work. The first contribution of the
PIG to the expansion of the pool of proteomics data available as usable
electronic resources was the development of the Make2D-DB package, 71
an open source software that helps build a federated 2-DE database on
one's own website (http://world-2dpage.expasy.org/make2ddb/).
Such a SWISS-2DPAGE-like database maker provides various text search
mechanisms (protein/gene name, protein description, author name,
species, etc.), search by experimental data (pI/Mw range or identifica-
tion methods), as well as an interactive graphical query interface.
Moreover, all search tools can be used to query any number of local data-
base(s) and/or similar remote interface(s). The output result clearly
states the origin of the resulting hits. In such a case, results are produced
as human-readable lists in HTML. These comprehensible lists are partic-
ularly adapted for end-users who can navigate through related informa-
tion (spot data, gel image, protocols, etc.); for instance, it is possible to
retrieve the complete list of identified spots for a given gel, species, or
identification method. Additionally, advanced users can easily retrieve
data as computer-readable lists through logical URLs. Make2D-DB is
not only an environment to create query interfaces; it also ensures data
reliability and consistency, is compliant with current proteomics stan-
dards (http://www.psidev.info/), and includes automated updates from
external resources (UniProt Knowledgebase, NCBI taxonomy, etc.). It is
also designed to take in much experimental information as possible in
order to improve the quality assessment of the database content (link to
protocols in MIAPE format or in separate plain text file, links to MS data,
Spectra Viewer which highlights identified peaks, etc.).
As a continuation to this project, the PIG launched the World-
2DPAGE Portal (http://world-2dpage.expasy.org/portal/) in 2006.
This complement is more than just a useful list of existing databases. It
currently involves eight SWISS-2DPAGE-like databases that can be
simultaneously queried, even though they are running in many European
and Asian countries. Globally, it can be seen as a virtual unique database
with up to 91 reference maps for 10 species, totalizing nearly 10 300
identified spots, enabling the biggest gel-based proteomics datasets to be
accessible from a single interface.
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