Biology Reference
In-Depth Information
•
the SWISS-MODEL Repository, a database of automatically gen-
erated 3-D protein structural models.
All databases available on ExPASy are explicitly cross-referenced to
other molecular biology databases or resources available on the Internet.
Approximately 30 implicit links to other additional resources are created
on demand when certain views of UniProtKB are generated. This con-
cept is targeted at data collections that do not have their own system of
unique identifiers, but can be referenced via identifiers such as accession
numbers or gene names. GeneCards is an example of a database implic-
itly linked to UniProtKB; it only shares an identifier with UniProtKB
(the HUGO-approved gene name). Implicit links are a specific feature
of ExPASy and are not available on other Web servers or in the
UniProtKB data files downloadable by File Transfer Protocol (FTP).
They significantly enhance database interoperability and strengthen the
role of UniProtKB as a central hub for the interconnection of molecu-
lar biology resources.
ExPASy has an extensive collection of software tools. Some of them
are targeted toward access and display of the databases listed above.
Others can be used for data analysis, such as the prediction of protein
sequence features or the processing of proteomics data originating from
2-D PAGE and MS experiments. ExPASy tools that are specifically
designed for MS data analysis perform computations and predictions
while using annotations documented in the UniProtKB feature tables
(e.g. the input form of PMF engine Aldente includes the optional selec-
tion of a range of protein features). This assists the detection of possible
splice variants, PTMs, or protein processing.
The European Bioinformatics Institute (EBI) also develops and main-
tains a number of proteomics databases and federates a very wide spectrum
of protein-related databases; however, software tools available at the EBI are
not specifically targeted at MS data analysis. Conversely, the Institute for
Systems Biology (ISB) offers a wide panel of software tools for proteomics
studies, but does not develop or maintain a wide variety of protein-related
databases with the exception of PeptideAtlas. ExPASy thus remains the server
that best covers the diversity of requirements for proteomics researchers as
well as the window into PIG and SIB developments and databases.
