This document discusses integrating faculty and scientist profiling data from external sources like VIVO and ScientistsDB into the Eureka Research Workbench system. It presents the motivations for enhancing collaboration features in Eureka. Details are provided on accessing data through the APIs of VIVO, ScientistsDB, and Elasticsearch to profile and search for researchers. The implementation involves developing CakePHP plugins to ingest data from these sources. Future plans include expanding the number of integrated sources to better enable finding collaborators.

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