As a mechanism to improve the sharing of data in Flow Injection Analysis, the Flow Analysis Database (http://www.fia.unf.edu) has been re-imagined to improve communication of the research on FIA, SIA, and related technologies across the vibrant communities in Europe, Asia, and the Americas. This talk will present the new version of the Flow Analysis Database by highlighting - The REST interface for each access to citation, analyte, matrix, technique, and keyword based resources - Documented API for automated data integration - Integration of the ChAMP specification - Ontological support for FA concepts - Individual user accounts with author bibliography Future additions will include - Language translation support using Google Translate - ORCID integration - Personal FIA library, and update notification

1. Bringing Flow Injection Analysis
to the Semantic Web
http://www.fia.unf.edu
Stuart J. Chalk, Department of Chemistry
University of North Florida
schalk@unf.edu
ANYL 430 – Pacifichem 2015

2.  History
 Original Website
 New Website Philosophy
 Semantic Annotation – What Does it Mean?
 REST Style Website and API
 The Chemical Analysis Metadata Platform
 The Flow Analysis Ontology
 User Capabilities
 Technology
 Demo of New Website
 Future Plans
 Take Home
Outline

3. A History of the
Flow Analysis Database (FAD)
 Citations original came from the Tecator bibliographies and the
bibilographies published in “Flow Injection Analysis” 1st and 2nd
Editions (Ruzicka and Hansen)
 First Online January 1997 (Apache, Lasso)
 Revised in 2003 (Apache, PHP, MySQL)
 Continually upgraded through 2007
 Contributions from some FIA researchers
 Pioneering work by Jarda Ruzicka, Elo Hansen, Gary Christian
 Graham Marshall, Koos van Staden, Bo Karlberg, Victor Cerda
 Still used but technology limited
 Supported by one person

4. The Current FAD Website

5. The Current FAD Website

6.  Engage the community
 Significantly enhance the functionality
 Bring the site up to date with current web technologies
 Add user accounts
 Provide data for integration into other websites
 Integrate data from other websites
 Supported, updated, developed by the community
New Website Philosophy

7.  Representational State Transfer (REST)
 URL written with an indication of the content returned
 The response to requested the REST URL contains a
snapshot of data as it currently stands (always true)
 REST style URLs typical do not have GET variables
appended to the end
 Application Programming Interface
 http://chalk.coas.unf.edu/fad/citations/view/[id]/[format]
 http://chalk.coas.unf.edu/fad/citations/view/7112/XML
REST Website and API

8.  Providing computer interpretable meanings to concepts
 Uses the Resource Description Framework (RDF)
Semantic Annotation Means?
<?xml version="1.0"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:fao="https://chalk.coas.unf.edu/fad/files/ontology/fao.owl
<rdf:Description rdf:about="https://www.fia.unf.edu/ANCH1994V0066P00660">
<rdfs:label>ANCH1994V0066P00660</rdfs:label>
<fao:Interference/>
<fao:Reverse/>
<fao:Sensitivity/>
<fao:Dispersion/>
</rdf:Description>
</rdf:RDF>

11. Chemical Analysis
Ontology (CAO)

12. Chemical Analysis
Ontology (CAO)

13.  Use the existing keywords that characterize the citations
 Categorize (group) the keywords into different types
 Create an ontology document in the Web Ontology
Language (OWL)
 Add ontological term entries to the ontology file using
Protégé
 Add definitions of terms in the ontology (ongoing)
 Each term has a unique entity definition
 Make the ontology available online and users can
reference the ontological terms in their work
The Flow Analysis Ontology

14. The Flow
Analysis
Ontology
(Alpha version)

15.  User account
 Personal citation database (in development)
 “My Publications”
 Primary Author metadata
 User preferences
 ORCID Integration (in development)
 Language Support (in development)
User Capabilities

16.  CakePHP 2.7 PHP Framework (http://cakephp.org)
 Apache 2.4 webserver (http://httpd.apache.org)
 PHP 5.6 (http://www.php.org)
 MySQL 5.5 (http://www.mysql.com)
 jQuery (JavaScript) (http://jquery.com)
 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/)
Technologies

17. Live Demo
Alpha Version Development Site @
https://chalk.coas.unf.edu/fad/

18.  Phase I
 Beta version of new website by April 2016
 Phase II
 Add citations from 2007-present
 Metadata and abstracts
 User annotation of these new articles
 Integration of CrossRef for improvement of metadata
 Fedora-Commons integration
 Text extraction training and optimization
 Phase III
 Text extraction from all PDFs
 Text cleanup based on training set
 Full-text search implementation
Future Plans

19. Take Home
 The new version of the FAD website:
 Builds capabilities based on the existing citation metadata
 Encourages community involvement
 Brings flow injection methodologies to the semantic web
 Integrates with external websites

20.  schalk@unf.edu
 Phone: 904-620-1938
 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?