Standards-based curation of a decade-old digital repository dataset of molecular information

Journal of Cheminformatics
Matthew J HarveyJames J P Stewart

Abstract

The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.

References

Mar 1, 1990·Journal of Computer-aided Molecular Design·J J Stewart
Jun 21, 2001·Journal of Chemical Information and Computer Sciences·J H VoigtM C Nicklaus
Aug 9, 2005·Journal of Molecular Modeling·Peter Murray-RustYong Zhang
Mar 31, 2006·The Journal of Physical Chemistry. a·Partha P BeraPaul v R Schleyer
May 2, 2008·Nucleic Acids Research·Daeui ParkSunghoon Lee
Jul 30, 2008·Journal of Chemical Information and Modeling·Jim DowningMatt J Harvey
Oct 1, 2009·Nature Chemistry·Henry S Rzepa
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Aug 15, 2012·Journal of Cheminformatics·Marcus D HanwellGeoffrey R Hutchison
Oct 20, 2012·Public Health Nutrition·Philip C Calder, Agneta Yngve
Jan 25, 2013·Journal of Cheminformatics·Henry S Rzepa
Jan 25, 2013·Journal of Cheminformatics·Stephen HellerIgor Pletnev
Aug 13, 2014·Journal of Computer-aided Molecular Design·Jeremy G Frey, Colin L Bird
Aug 30, 2014·Journal of Chemical Information and Modeling·Matthew J HarveyHenry S Rzepa
Jan 1, 2014·Scientific Data·Raghunathan RamakrishnanO Anatole von Lilienfeld
Mar 1, 2015·Chemical Science·Katrina A BadiolaPaul M Ylioja

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Citations

Jan 17, 2017·Journal of Cheminformatics·Muthukumarasamy Karthikeyan, Renu Vyas
Feb 12, 2017·Journal of Cheminformatics·Matthew J HarveyHenry S Rzepa

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Software Mentioned

JSmol
DataCite Search API
InChIkey
OAI
SWORD
CNRI
RegisterDOI
OpenData
SPECTRa SWORD
Dspace

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