Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform

被引:466
作者
Alvarez-Moreno, M. [1 ,2 ]
de Graaf, C. [2 ,4 ]
Lopez, N. [1 ]
Maseras, F. [1 ,3 ]
Poblet, J. M. [2 ]
Bo, C. [1 ,2 ]
机构
[1] ICIQ, Inst Chem Res Catalonia, Tarragona 43007, Catalonia, Spain
[2] Univ Rovira & Virgili, Dept Phys & Inorgan Chem, Tarragona 43007, Catalonia, Spain
[3] Univ Autonoma Barcelona, Dept Chem, Bellaterra 08193, Catalonia, Spain
[4] ICREA, Catalan Inst Res & Adv Studies, Barcelona 08010, Catalonia, Spain
关键词
MARKUP LANGUAGE CML; SEMANTICS;
D O I
10.1021/ci500593j
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
We present the ioChem-BD platform (www.iochem-bd.org) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers needs in the form of HTML5 reports, supporting information, and other research media.
引用
收藏
页码:95 / 103
页数:9
相关论文
共 22 条
[1]  
Adams N., 2009, NATURE PRECEDINGS, DOI DOI 10.1038/NPRE.2009.3714.1
[2]   The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age [J].
Adams, Sam ;
de Castro, Pablo ;
Echenique, Pablo ;
Estrada, Jorge ;
Hanwell, Marcus D. ;
Murray-Rust, Peter ;
Sherwood, Paul ;
Thomas, Jens ;
Townsend, Joe .
JOURNAL OF CHEMINFORMATICS, 2011, 3
[3]  
Addison M. S., JASIG CAS DOCUMENTAT
[4]  
Allinson J., 2008, ARIADNE
[5]  
[Anonymous], 2004, EXTENSIBLE MARKUP LA
[6]  
Apache Lucene, HIGH PERF FULL FEAT
[7]  
Berners-Lee T., TED C
[8]   Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: The Collaborative Chemistry Database Tool (CCDBT) [J].
Chen, Mingyang ;
Stott, Amanda C. ;
Li, Shenggang ;
Dixon, David A. .
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2012, 34 :67-75
[9]   Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance [J].
Frey, Jeremy G. ;
Bird, Colin L. .
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2013, 3 (05) :465-481
[10]  
Gartner R., 2002, METS METADATA ENCODI