1. Faculty Profiling and Searching in
the Eureka Research Workbench
using VIVO and ScientistsDB
Matthew Morse, Israel Hurst, and Stuart J. Chalk
Department of Chemistry
University of North Florida
schalk@unf.edu
2014 Fall ACS Meeting

2. Outline
 Motivation
 What is Eureka?
 What is VIVO?
 VIVO API
 What is ScientistDB?
 MediaWiki API
 Search Approaches
 ElasticSearch
 Usage
 Future Plans
 Conclusion

3. Motivation
 Eureka Research Workbench is an Electronic
Laboratory Notebook (ELN) …
 …plus representation of resources
 …and needs to be social
 Find colleagues that you can collaborate with
 There are many places to get this information

4. Electronic Notebooks
 Scientists need to move to
digital notebooks…
 ...and record not just the data
but the flow and context
 How science is done
is important for searching,
aggregation, meta-analysis
 We need more than an electronic version of a notebook
 We need a science version of “Second Life” (SciLife?)

5. Eureka Research Workbench (ERW)
 Started in 2006 after getting involved in the
Analytical Information Markup Language (AnIML) project
 Store all research notes/data in a digital format
 Capture the workflow of scientists
 Writing in a lab notebook is equivalent to
“multi-type” blogging in the digital world
 How to capture information? Many data types! (ExptML)
 How to store files “online”? (Fedora-Commons)
 How to access files in the browser? (CakePHP)
 How to represent laboratory resources? (ExptML)
 How to link data together? RDF (in Fedora-Commons)

6. Experiment Markup Language (ExptML)
 A specification (written in XML) that describes different
types of information recorded during the scientific process
(http://exptml.sourceforge.net)
 Sample
 Solution
 Space
 Specimen
 Substance
 Task
 Template
 Timeline
 User
 Vendor
 Annotation
 Api
 Calculation
 Chemical
 Citation
 Customer
 Data
 Dataset
 Definition
 Element
 Equipment
 Event
 Experiment
 Group
 Message
 Project
 Protocol
 Quote
 Report
 Result

7. What is VIVO?
 An interdisciplinary network: Enabling collaboration and discovery
among scientists across all disciplines.
 Open source software out of Cornell University
 Now part of Duraspace (Dspace, Fedora-Commons, and VIVO)
 Often integrated with other academic services
 Semantic representation -> Vivo Ontology
 (https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology)
 http://vivoweb.org/

8. VIVO API
 Interface to search for different types of ‘individuals’
 Faculty members
 Subjects
 Departments
 …
 Available in multiple download formats
 N-Triples, RDF, N3, Turtle, JSON-LD
 https://wiki.duraspace.org/display/VIVO/The+ListRDF+API

9. What is ScientistsDB?
 Mediawiki site containing nearly 50,000 scientists
 Wikipedia entries
 …plus manual additions
 Tony Williams, RSC
 Sean Atkins, CDD Vault
 http://www.scientistsdb.com/

10. MediaWiki API
 Mediawiki is the software that runs Wikipedia
 Available for download (http://www.mediawiki.org)
 Access to all data in a mediawiki MySQL database
 Components
 Authentication
 Search
 CRUD
 http://www.mediawiki.org/wiki/API:Main_page

11. Search Approaches
 VIVO
 listRDF API for faculty
(http://<instance>/listrdf?vclass=http://vivoweb.org/ontology/core#
FacultyMember)
 Faculty member information (as JSON)
(http://<instance>/individual/a52486491431389?format=json)
 ScientistsDB
 Retrieve infobox
(http://www.scientistsdb.com/api.php?action=query&format=json
&list=categorymembers&cmtitle=Category:Scientist
 Extract records with ‘fields’ field

12. ElasticSearch
 Data is stored on a cluster of computers running
Elasticsearch NoSQL software
 All data is ingested as JSON
 Uses Apache Lucene to index data
 http://www.elasticsearch.org/overview/elasticsearch

13. Implementation
 Development of CakePHP plugins for
 VIVO (multiple locations)
 ScientistDB
 Elasticsearch
 CakePHP can access each of these anywhere in its
Model-View-Controller (MVC) code

14. Future Plans
 Ingest more installations of VIVO
 Work with technical staff at VIVO to make multi-site
search available to all VIVO users
 Improve code to clean up infobox data
 Work with Tony and Sean to evaluate if there are
better ways to retrieve subject fields

15. Conclusion
 ScientistDB plugin works
 VIVO plugin very close…
 Eureka needs to be collaborative software and
therefore being able to find other researchers in your
field is an important part of the system
 Development of many more plugins to access online
datasources within Eureka

16. Questions?
 schalk@unf.edu
 Phone: 904-620-5311
 Skype: stuartchalk
 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