In honor of JC Bradley, and the spirit of openness that he inspired, a new online resource called the Open Spectral Database (http://www.osdb.info) was announced in August of this year (aplha version). Built using open source tools, using open code, and open to community input about design and functionality, the OSD is available for anyone to submit spectral data and make it available to the scientific community. This paper will detail the reaction to the website, look at how the site has evolved since August (beta version), and offer a glimpse of what the future may bring for the site.

1. Reactions to
The Open Spectral Database
http://osdb.info
Stuart J. Chalk, Department of Chemistry
University of North Florida
schalk@unf.edu
Instigator: Tony Williams
SCTY 28 – Pacifichem 2015

2.  What would Jean-Claude Bradley have wanted?
 Share and Reuse Research Data!
 How Do You Make Everything Open?
 JCAMP Implementation
 The Open Spectral Database
 Data Model
 Live Demo (fingers crossed)
 Future Plans
 Conclusion
Outline

3. What Would JCB Have Wanted?
 Simple: Openness as the norm not the exception
 Data made available, without restriction, so its useful
 Mechanisms/tools to make data available
 Formats to allow others to get the data…
 …but also so its easy to use
 Annotated data to make it easy to find
 Community driven promotion of and action on these issues

4.  Ryan P. Womack (2015) Research Data in Core Journals in Biology, Chemistry, Mathematics,
and Physics. PLoS ONE 10(12): e0143460. doi:10.1371/journal.pone.0143460
Share and Reuse Research Data!

5.  You have to know/define what “everything” means
 Open Data
 Open Data Model
 Open and useable data structures
 Open Code
 Open to input from the community on all aspects
 Open to add, extend, change, and rethink all of this
How Do You Make Everything Open?

6.  Spectral data – There are many formats but only one
open and generally accepted standard – JCAMP
 Its not perfect…
 …but its an output format people can share
 Lets export the data, metadata, and inference as
much as possible from JCAMP files
 Not as easy as it seems…
First Attempt

8.  Great data exchange format, however…
 …not meant to be computer input…
 …more a way to get data out so a human can process
 Missing parameters (metadata)
 Missing data
 Incorrect values
 Extra data
 Incorrectly compressed
Challenges with JCAMP

9.  Upload JCAMP spectra
 Data and metadata extracted
 Organize metadata so it can be used to find data
 Use REST based website and API to make data available
and allow searching – document API
 Make the website available as a project on GitHub and
invite the community to get involved
The Open Spectral Database

10.  Apache 2.4 (http://httpd.apache.org)
 PHP 5.6 (http://www.php.org)
 CakePHP 2.7 PHP Framework (http://cakephp.org)
 MySQL 5.5 (http://www.mysql.com)
 jQuery (JavaScript) (http://jquery.com)
 Flot for jQuery (http://www.flotcharts.org)
 Jsmol (http://jmol.org)
 Bootstrap CSS (http://getbootstrap)
 eXtensible Markup Language (http://www.w3.org/TR/xml/)
 JavaScript Object Notation (JSON) (http://json.org)
 JSON for Linked Data (JSON-LD) (http://www.w3.org/TR/json-ld/)
Technology

11.  JCAMP file is imported into PHP as an array, then
 Clean
 Uncomment ($$)
 Separate
 Labeled Data Records (LDRs)
 Parameters (##.)
 User Defined Labels (##$)
 Validate
 Standardize
 Decompress
 Convert to output format or store in database
Ingestion Process

12.  In order to organize the data and metadata it is
distributed across a number of tables in the database
 This is a generic science data model that is being used
for multiple projects
 Not limited to spectra or even just Chemistry data
Data Model

13. Data Model

14.  File upload
 Export formats
 Search API
Live Demo

15. Semantic
Annotation

16.  Enthusiastic Feedback with constructive comments…
 Spectral list is boring needs molecules linked to spectra
 Less metadata on the spectral page with option to see more
 Revise homepage to make it more inviting
Reactions to Alpha Version

17.  Again Enthusiastic…
 ”Love the layout! Very clean…”
 “Nice Work!” (Twitter comment)
 … with constructive comments
 Needs a zoom spectra feature
 Clicking on spectrum provides data that is not useful
 Maybe you could use JSpecView rather than Flot?
Reactions to Beta Version

18.  Handle more complicated JCAMP files
 Handle file formats other than JCAMP
 Export in AnIML format
 Expand the API
 Improve Flot viewer functionality (e.g. zoom)
 Add JSpecView spectral viewer
 Endpoint summary page
 Document the website (GitHub)
 Document how to contribute to the website (GitHub)
 Solicit feature requests and encourage contributions
Things To Do

19. Take Home
 The OSD is open for the community to develop and
implement ideas about open spectral data re:
 Data Model
 API features
 Export Formats
 Services
 Community Involvement!
 Use as a data source for other applications
 Submission of feature requests
 Participation as code contributor

20.  schalk@unf.edu
 Phone: 904-620-5311
 Skype: stuartchalk
 Twitter: @StuChalk
 LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
 ResearcherID: http://www.researcherid.com/rid/D-8577-2013
Questions?