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The Open Spectral Database: an open platform for sharing and searching spectral data
BACKGROUND: A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data i...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Springer International Publishing
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065085/ https://www.ncbi.nlm.nih.gov/pubmed/27795739 http://dx.doi.org/10.1186/s13321-016-0170-2 |
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author | Chalk, Stuart J. |
author_facet | Chalk, Stuart J. |
author_sort | Chalk, Stuart J. |
collection | PubMed |
description | BACKGROUND: A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. RESULTS: The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. CONCLUSION: The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers. |
format | Online Article Text |
id | pubmed-5065085 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-50650852016-10-28 The Open Spectral Database: an open platform for sharing and searching spectral data Chalk, Stuart J. J Cheminform Database BACKGROUND: A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. RESULTS: The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. CONCLUSION: The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers. Springer International Publishing 2016-10-14 /pmc/articles/PMC5065085/ /pubmed/27795739 http://dx.doi.org/10.1186/s13321-016-0170-2 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Database Chalk, Stuart J. The Open Spectral Database: an open platform for sharing and searching spectral data |
title | The Open Spectral Database: an open platform for sharing and searching spectral data |
title_full | The Open Spectral Database: an open platform for sharing and searching spectral data |
title_fullStr | The Open Spectral Database: an open platform for sharing and searching spectral data |
title_full_unstemmed | The Open Spectral Database: an open platform for sharing and searching spectral data |
title_short | The Open Spectral Database: an open platform for sharing and searching spectral data |
title_sort | open spectral database: an open platform for sharing and searching spectral data |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065085/ https://www.ncbi.nlm.nih.gov/pubmed/27795739 http://dx.doi.org/10.1186/s13321-016-0170-2 |
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