Literature DB >> 25086851

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community.

Antony Williams1, Valery Tkachenko.   

Abstract

Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the semantic web, has motivated RSC to rearchitect and create a more generic data repository utilizing these new technologies. This article will provide an overview of our activities in delivering data sharing platforms for the chemistry community including the development of the new data repository expanding into more extensive domains of chemistry data.

Mesh:

Year:  2014        PMID: 25086851     DOI: 10.1007/s10822-014-9784-5

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  3 in total

Review 1.  Open PHACTS: semantic interoperability for drug discovery.

Authors:  Antony J Williams; Lee Harland; Paul Groth; Stephen Pettifer; Christine Chichester; Egon L Willighagen; Chris T Evelo; Niklas Blomberg; Gerhard Ecker; Carole Goble; Barend Mons
Journal:  Drug Discov Today       Date:  2012-06-07       Impact factor: 7.851

2.  The Innovative Medicines Initiative: a pre-competitive initiative to enhance the biomedical science base of Europe to expedite the development of new medicines for patients.

Authors:  A Jackie Hunter
Journal:  Drug Discov Today       Date:  2008-04-24       Impact factor: 7.851

3.  The Spectral Game: leveraging Open Data and crowdsourcing for education.

Authors:  Jean-Claude Bradley; Robert J Lancashire; Andrew Sid Lang; Antony J Williams
Journal:  J Cheminform       Date:  2009-06-26       Impact factor: 5.514

  3 in total
  19 in total

1.  Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

Authors:  Kai Dührkop; Huibin Shen; Marvin Meusel; Juho Rousu; Sebastian Böcker
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-21       Impact factor: 11.205

2.  Tales from the war on error: the art and science of curating QSAR data.

Authors:  Marvin Waldman; Robert Fraczkiewicz; Robert D Clark
Journal:  J Comput Aided Mol Des       Date:  2015-08-20       Impact factor: 3.686

3.  biochem4j: Integrated and extensible biochemical knowledge through graph databases.

Authors:  Neil Swainston; Riza Batista-Navarro; Pablo Carbonell; Paul D Dobson; Mark Dunstan; Adrian J Jervis; Maria Vinaixa; Alan R Williams; Sophia Ananiadou; Jean-Loup Faulon; Pedro Mendes; Douglas B Kell; Nigel S Scrutton; Rainer Breitling
Journal:  PLoS One       Date:  2017-07-14       Impact factor: 3.240

4.  Many InChIs and quite some feat.

Authors:  Wendy A Warr
Journal:  J Comput Aided Mol Des       Date:  2015-06-17       Impact factor: 3.686

Review 5.  Promises and pitfalls of untargeted metabolomics.

Authors:  Ilya Gertsman; Bruce A Barshop
Journal:  J Inherit Metab Dis       Date:  2018-03-13       Impact factor: 4.982

6.  ChemProt-3.0: a global chemical biology diseases mapping.

Authors:  Jens Kringelum; Sonny Kim Kjaerulff; Søren Brunak; Ole Lund; Tudor I Oprea; Olivier Taboureau
Journal:  Database (Oxford)       Date:  2016-02-13       Impact factor: 3.451

7.  Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

Authors:  Manish Sud; Eoin Fahy; Dawn Cotter; Kenan Azam; Ilango Vadivelu; Charles Burant; Arthur Edison; Oliver Fiehn; Richard Higashi; K Sreekumaran Nair; Susan Sumner; Shankar Subramaniam
Journal:  Nucleic Acids Res       Date:  2015-10-13       Impact factor: 16.971

Review 8.  Towards operando computational modeling in heterogeneous catalysis.

Authors:  Lukáš Grajciar; Christopher J Heard; Anton A Bondarenko; Mikhail V Polynski; Jittima Meeprasert; Evgeny A Pidko; Petr Nachtigall
Journal:  Chem Soc Rev       Date:  2018-11-12       Impact factor: 54.564

Review 9.  Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.

Authors:  Ahmet Sureyya Rifaioglu; Heval Atas; Maria Jesus Martin; Rengul Cetin-Atalay; Volkan Atalay; Tunca Doğan
Journal:  Brief Bioinform       Date:  2019-09-27       Impact factor: 11.622

10.  UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.

Authors:  Jon Chambers; Mark Davies; Anna Gaulton; George Papadatos; Anne Hersey; John P Overington
Journal:  J Cheminform       Date:  2014-09-04       Impact factor: 5.514

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.