Bringing Flow Injection Analysisto the Semantic Webhttp://www.fia.unf.edu

Stuart J. Chalk, Department of ChemistryUniversity of North Florida

schalk@unf.edu

ANYL 430 – Pacifichem 2015

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

A History of theFlow 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

The Current FAD Website

The Current FAD Website

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

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

Providing computer interpretable meanings to concepts

Uses the Resource Description Framework (RDF)

Semantic Annotation Means?

<?xml version="1.0"?><rdf:RDFxmlns: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>

Chemical Analysis Ontology

(CAO)

Chemical Analysis Ontology

(CAO)

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

The Flow Analysis Ontology

(Alpha version)

User account Personal citation database (in

development) “My Publications” Primary Author metadata User preferences

ORCID Integration (in development) Language Support (in development)

User Capabilities

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

Live Demo

Alpha Version Development Site @

https://chalk.coas.unf.edu/fad/

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

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

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?