PDB, ligands and sequences and the CSD molecular, packing and interaction
similarity. The Internet has also become a vehicle for educational resources based
on crystallographic data, e.g. of particular note are the symmetry resources produced
by Professor Dean Johnston at Otterbein University [131]; the International Union of
Crystallography (IUCr) managed list of numerous online educational resources
[132]; other society resources such as the BCA [133] and ECA [134]; and resources
linked to the crystallographic databases [135–137].
As mentioned previously, a key development that aided the storage and analysis
of crystallographic data was the innovation of the Crystallographic Information File
(CIF) [56, 57]. This standardised computer and human readable format was
implemented by the IUCr for their journals and rapidly taken up by the community.
Less than 10 years after its launch, over 90% of the structures added to the CSD in
2000 were deposited in CIF format. Newly refined data can now be emailed directly
from Olex2 to request CCDC numbers ready for inclusion in a publication manuscript. The use of CIF has enabled automation of some processes by computers
including a web deposition service [138], introduced in 2010, for sending the
finalised file to CCDC. This was an improvement on the mailing of paper copies
previously used and has enabled automated checking of the data as it is deposited.
Following further enhancements, the service is now fully interactive providing
feedback to users through the process and is designed to help increase the quality
of data and incentivise depositions. Today the service links up to ORCID so users
can associate their researcher ID to their datasets; it checks the syntax of submitted
files and allows the author to add extra information including a link to raw diffraction
data. The eight-step process also enables the researcher to check the unit cell against
existing structures, add crystallographer details to ensure the crystallographer and
send the file through the IUCr’s CheckCIF [61, 139] service to check the integrity of
the data.
3.3 The Transition to Informatics: Methods and Tools
to Leverage Databases
3.3.1 Knowledgebases
Information on individual crystal structures is useful, although much more can be
learnt from the trends revealed by combining the data together. Extracting this
information and compiling it into a form that can be used to compare a given
structure to many others that have similar chemistry leads to the formation of derived
libraries of ‘knowledge’. The CSD has collated two knowledgebases, for molecular
geometry and intermolecular interactions.
114
S. J. Coles et al.
similarity. The Internet has also become a vehicle for educational resources based
on crystallographic data, e.g. of particular note are the symmetry resources produced
by Professor Dean Johnston at Otterbein University [131]; the International Union of
Crystallography (IUCr) managed list of numerous online educational resources
[132]; other society resources such as the BCA [133] and ECA [134]; and resources
linked to the crystallographic databases [135–137].
As mentioned previously, a key development that aided the storage and analysis
of crystallographic data was the innovation of the Crystallographic Information File
(CIF) [56, 57]. This standardised computer and human readable format was
implemented by the IUCr for their journals and rapidly taken up by the community.
Less than 10 years after its launch, over 90% of the structures added to the CSD in
2000 were deposited in CIF format. Newly refined data can now be emailed directly
from Olex2 to request CCDC numbers ready for inclusion in a publication manuscript. The use of CIF has enabled automation of some processes by computers
including a web deposition service [138], introduced in 2010, for sending the
finalised file to CCDC. This was an improvement on the mailing of paper copies
previously used and has enabled automated checking of the data as it is deposited.
Following further enhancements, the service is now fully interactive providing
feedback to users through the process and is designed to help increase the quality
of data and incentivise depositions. Today the service links up to ORCID so users
can associate their researcher ID to their datasets; it checks the syntax of submitted
files and allows the author to add extra information including a link to raw diffraction
data. The eight-step process also enables the researcher to check the unit cell against
existing structures, add crystallographer details to ensure the crystallographer and
send the file through the IUCr’s CheckCIF [61, 139] service to check the integrity of
the data.
3.3 The Transition to Informatics: Methods and Tools
to Leverage Databases
3.3.1 Knowledgebases
Information on individual crystal structures is useful, although much more can be
learnt from the trends revealed by combining the data together. Extracting this
information and compiling it into a form that can be used to compare a given
structure to many others that have similar chemistry leads to the formation of derived
libraries of ‘knowledge’. The CSD has collated two knowledgebases, for molecular
geometry and intermolecular interactions.
114
S. J. Coles et al.