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The SIGMOID project is
intended to produce a database of
cellular signaling pathways and models thereof, to marshall the
major forms of data and knowledge required as input to cellular
modeling software and also to organize the outputs. Such
cellular signaling and regulatory pathways are commonly hand-drawn
in biological literature as an aid to intuitive understanding.
Pathway databases can provide the same assistance in
the context of attempts to achieve a quantitative understanding
of cellular processes by numerical simulation. They can also serve
as an aid to capturing and querying both expert knowledge and
heterogeneous data sets pertaining to pathways. Cell model
databases are a subject of current research. SIGMOID works
at the interface of these two areas.
To this end an object schema has been designed which incorporates
reactions, reactants and models. Reactions are further divided into
elementary and composite biological processes, and reactants are
divided into elementary and composite biological objects such as
proteins (elementary in many but not all situations) and protein
complexes. This coarse ontology is refined into a number of more
detailed categories whose representation in common modeling software
can be expected to be different.
Some tools for the SIGMOID project are currently implemented in Python
and initially targeting the Linux platform, though there are plans
also
to provide an API in Java. SIGMOID is initially being developed in a
collaboration between the Institute for Bioinformatics and Genomics
(IGB, www.igb.uci.edu) at the University of California Irvine, the
Beckman Institute (BI, www.bi.caltech.edu) of the California Institute
of Technology, and the Bioengineering Department at Johns Hopkins
University. Most components are being made available under the
MIT open source license.
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