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OraCIF
is being developed by MSD as part of the TEMBLOR project work package WP9.7 is a set of
database facilities and services to extract data from source database(s)
containing macromolecular structure information. Its initial aim is to produce
mmCIF format files from MSD Archive and
Search
databases for exchange with RCSB.
Export to XML is also supported.
OraCIF
contains a highly generic core that can be specifically configured. The
code
takes information about the source database(s), the dictionary defining the
structure of the resulting mmCIF/XML file(s) and the mapping between them, held
in a separate mapping "metadatabase". These three sources of
information are used to build a set of specific export routines that extract
information from the source database(s) and write it into mmCIF/XML format
files.
In order to do this,
OraCIF requires five separate components:
Together these form a
complex system that uses the knowledge from the mapping metadatabase
and the mmCIF
dictionary to produce mmCIF/XML files. Firstly, the
Generator takes the mapping information from the metadatabase along the mmCIF
dictionary and the known structure of source database(s) to build a
set of database stored procedures for extracting information.
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The Selector provides an interface for defining which of the data -in
terms of PDB identifiers- in the source database(s) should be extracted. The
Exporter then takes the list of target data provided by Selector and uses the
procedures created by the Generator to extract the required data. The
Transformer takes these data and restructures them into the correct mmCIF or
XML format. A final component, termed the Comparer, uses the
procedures created by the Generator to compare the contents of an mmCIF
file with the corresponding information in the source database(s). |
OraCIF is currently moving from late alpha into early beta phase
of development.
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Introduction
Generator
Exporter
Transformer 
Comparer