What is MDdb
MDdb provides a Science Gateway
as an effort to address the lack of a global standard, metadata definitions,
tools, and platforms that implement and enforce them,
to share, find, access, operate, reuse, or reproduce numerical simulation
digital research objects (e.g., Molecular Dynamics)
-from methodological and analytical pipelines to raw trajectory data-
based on the Findability, Accessibility, Interoperability, and Reusability
What is the benefit
MDdb allows for registration and retrieval of records, citation, and
(see an example).
Each entry is assigned a unique identifier (F, A, for humans and machines).
The ID resolves to a Study Infopage with tools
to interpret the work’s rich metadata (I, R, for humans and machines) and
numerical simulation results by interactive 3D visualization through
Where does the data come from
Research groups that produce scientific numerical simulations around the world are
the main data source. All fields with a molecular interest, experts or not,
are the direct users. Furthermore, education institutions at all
levels also benefit from this initiative.
How does it work
MDdb organizes and hosts detailed information about
computational simulations. All MDdb
entries are managed on a web server (F, A), represented in human
and machine-readable formats (e.g., text and HTML). The latter are
machine-actionable using the metadata and API provided by MDdb.
The metadata contains detailed information about provenance, protocols, relevant links for
rich citation, and cross-references to well-known
identifiers (e.g., wwPDB or UniProt) that conform to
data standards in the chemical and structural biology domains (I, R).
MDdb metadata is kept in the Resource
Description Framework (RDF) representation, which explicitly types
all records, leaving no ambiguity about what the data represents (R).