Science is rapidly being brought into the electronic realm and electronic laboratory notebooks (ELN) are a big part of this activity. The representation of the scientific process in the context of an ELN is an important component to making the data recorded in ELNs semantically integrated. This presentation outlined initial developments of an Electronic Notebook Ontology (ENO) that will help tie together the ExptML ontology, HCLS Community Profile data descriptions, and the VIVO-ISF ontology.

1. The Electronic
Notebook Ontology
Stuart J. Chalk
Department of Chemistry, University of North Florida
schalk@unf.edu
VIVO 2015 – August 2015

2.  Motivation
 Inspiration
 Electronic Scientific Notebooks
 The Experiment Markup Language
 VIVO-ISF Ontology
 HCLS Community Profiles
 Analysis
 Important Questions
 Ontology
 Conclusion
Outline

3.  There’s something
missing from the big data landscape in science…
 VIVO captures data about scientists (faculty)…
 …but not about the data they produce
 HCLS Community Profile outlines metadata for describing
datasets but does not mention laboratory notebooks
 Electronic laboratory notebooks are set to become the
standard way scientists capture data
 How do we link these together?
Motivation

5.  Scientists need to move to
digital notebooks…
 ...and record not just the data
but the flow and context
Traditional Laboratory Notebooks
 How science is done
is important for searching,
aggregation, meta-analysis

6.  Developed out of Laboratory Information
Management Systems (LIMS)
 Content Management System for Scientists
 Storage of
 Research data
 Research resources (instruments, samples, scientists)
 The story of the scientific endeavor
 Link to external resources
 Display chemical structures
 Allow aggregation, processing of data
 Be compliant with industry standard record keeping
Electronic Laboratory Notebooks

7. Electronic Laboratory Notebooks

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

9. ExptML Ontology

10. VIVO-ISF Ontology
https://wiki.duraspace.org/download/attachments/51052811/PeopleOrgsRolesGrants.2014-03-14.png

11.  The Healthcare and Life Science (HCLS) Community Profile
is a Note from the Semantic Web HCLS Interest Group
 Access to consistent, high-quality metadata is critical to finding,
understanding, and reusing scientific data. This document
describes a consensus among participating stakeholders in the
Health Care and the Life Sciences domain on the description of
datasets using the Resource Description Framework (RDF). This
specification meets key functional requirements, reuses existing
vocabularies to the extent that it is possible, and addresses
elements of data description, versioning, provenance,
discovery, exchange, query, and retrieval.
Data Descriptions:
HCLS Community Profile
http://www.w3.org/TR/hcls-dataset/

12.  Describes three levels for
description of datasets
 Summary Level
 Type declaration (rdf:type =
dctypes:Dataset)
 Title (dct:title = rdf:langString)
 Description (dct:description =
rdf:langString)
 Publisher (dct:publisher = IRI)
 Version Level
 Type declaration (rdf:type =
dctypes:Dataset)
 Title (dct:title = rdf:langString)
 Description (dct:description =
rdf:langString)
 Creator (dct:creator = IRI)
 Publisher (dct:publisher = IRI)
 Version identifier (pav:version =
xsd:string)
 Version linking (dct:isVersionOf = IRI)
 Distribution Level
 Type declaration (rdf:type =
void:Dataset OR dcat:Distribution)
 Title (dct:title = rdf:langString)
 Description (dct:description =
rdf:langString)
 Creator (dct:creator = IRI)
 Publisher (dct:publisher = IRI)
 License (rdf:type = IRI)
Data Descriptions:
HCLS Community Profile
http://www.w3.org/TR/hcls-dataset/#datasetdescriptionlevels

13.  Goal: Automated identification of datasets that could
be made searchable and/or distributable
 When an ELN functions what does it do?
 Orchestrates access to the system (authentication)
 Supplies GUI to allow information to be
 Displayed
 Entered
 Processed
 Processes files to bring them into the system
 Sends requests to internal/external servers to get data
Analysis

14.  Is this information a dataset?
 Does dataset belong to this author?
 Is the dataset available?
 Is there appropriate metadata?
 At what HCLS levels can this dataset be made available?
 What mechanism is used to make the dataset available?
Important Questions

15.  Actions that deal with datasets
 Software actions
 User actions
 Clues that something is research data
(not metadata or someone else’s data)
 Collection of metadata for annotation of datasets
 Inference that a HCLS dataset has been created
Dataset Identification

16. Electronic Notebook Ontology (ENO)

17. ENO

18. ENO

19.  Providing a mechanism to link research data to VIVO
profiles would
 Add value to VIVO
 Provides faculty with a resource for their
data management plans
 Creates opportunities for automatic aggregation
of research data into institutional repositories
 Needs to be implemented in a test ELN…
Take Home

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