Abstract
BackgroundA 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.ResultsThe 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.ConclusionThe 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.
Highlights
IntroductionA number of websites make available spectral data for download (typically as JCAMP-Data eXchange format (DX) text files) and one (ChemSpider) that allows users to contribute spectral files
A number of websites make available spectral data for download and one (ChemSpider) that allows users to contribute spectral files
The usefulness of spectral data in JCAMP-Data eXchange format (DX) format is somewhat limited due to the specification being over 30 years old, and if saved using compression, difficult to transfer to other software
Summary
A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that allows users to contribute spectral files. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is available. Tools to make research data freely available are vitally important to the open science movement. Providing a mechanism to allow conversion of legacy data in JCAMP-DX format is an important activity in-of-itself, as the community needs spectral data for comparison/ standardization in many different applications
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