1.
Facilitating Data Curation:
a Solution Developed in the Toxicology Domain
Christophe Debruyne1,3, Jonathan Riggio1, Emma Gustafson2, Declan
O'Sullivan3, Mathieu Vinken2, Tamara Vanhaecke2, and Olga De Troyer1
1 WISE – Vrije Universiteit Brussel, Belgium
2 IVTD – Vrije Universiteit Brussel, Belgium
3 ADAPT – Trinity College Dublin, Ireland
2020-02-05 @ ICSC

2.
Context
• The goal of toxicology is to understand the adverse effects of
chemical compounds or physical agents on living organisms.
• The IVTD Group in the VUB aims to collect safety testing data of
cosmetic ingredients available in publicly available safety evaluation
reports with the goal of creating a knowledge base.
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3.
Problem
• Subject matter experts currently rely on spreadsheets, which the
experts consider a “computational database”
– a term that experts in this domain use for any technology and representation
allowing for some data manipulation and analysis, ranging from spreadsheets
to more complex (domain-specific) database technologies.
• Spreadsheets, however, causes problems for: data curation, data
analysis, and data exploration.
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4.
Problem
• Semantic Technologies can overcome the challenges that come with
spreadsheets, and furthermore allows data to be linked with
external datasets.
• But these technologies are not easily accessible to these subject
matter experts [1]
• How can we facilitate subject matter experts in the domain of
toxicology in the creation of a knowledge base for the available
safety evaluation reports?
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5.
Structure of a Spreadsheet
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6.
Structure of a Spreadsheet
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7.
Proposed Solution: Using the Jigsaw Metaphor to Guide
Experts in Creating Resources
• An interface metaphor [2] is drawing upon the knowledge of
familiar concepts to facilitate learning and using a system.
• The Jigsaw Metaphor is drawing upon one’s familiarity with jigsaw
puzzle pieces, and has been successful for other tasks:
programming, querying, data integration,…
• In our proposed solution, the Jigsaw puzzle pieces guide subject
matter experts in creating valid data entries.
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8.
The Prototype
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The prototype is
built on top of
Google Blockly for
the metaphor and
Apache Jena for the
knowledge base.

9.
The Prototype
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10.
Knowledge Organization
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ns:Test
a owl:Class .
ns:SkinAbsorptionInVitroNonOECD
a owl:Class .
ns:year
a owl:DatatypeProperty ;
owl:range xsd:string .
...
Ontology
Stored as an OWL file on the Web with
the namespace as the location (URL)

11.
Knowledge Organization
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...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECDns:Test
a owl:Class .
ns:SkinAbsorptionInVitroNonOECD
a owl:Class .
ns:year
a owl:DatatypeProperty ;
owl:range xsd:string .
...
Ontology
Representation: attributes and
attribute groups
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD
Stored as an OWL file on the Web with
the namespace as the location (URL)
Each graph stored as a named graph in
triplestore 1

12.
Knowledge Organization
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<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECDns:Test
a owl:Class .
ns:SkinAbsorptionInVitroNonOECD
a owl:Class .
ns:year
a owl:DatatypeProperty ;
owl:range xsd:string .
...
Ontology
Representation: attributes and
attribute groups
Instances of reports and studies
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD
Stored as an OWL file on the Web with
the namespace as the location (URL)
Each graph stored as a named graph in
triplestore 1
Each graph stored as a named graph in triplestore 2

13.
Knowledge Organization
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<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECDns:Test
a owl:Class .
ns:SkinAbsorptionInVitroNonOECD
a owl:Class .
ns:year
a owl:DatatypeProperty ;
owl:range xsd:string .
...
Ontology
Representation: attributes and
attribute groups
Instances of reports and studies
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD
Stored as an OWL file on the Web with
the namespace as the location (URL)
Each graph stored as a named graph in
triplestore 1
Each graph stored as a named graph in triplestore 2

14.
Knowledge Organization
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<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
<http://.../dossier/7>
a ns:Report ;
ns:contains [
a ns:SkinAbsorptionInVitroNonOECD ;
ns:year "ND"^^xsd:string ;
...
] ;
...
.
Graph <http://.../dossier/7>
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECDns:Test
a owl:Class .
ns:SkinAbsorptionInVitroNonOECD
a owl:Class .
ns:year
a owl:DatatypeProperty ;
owl:range xsd:string .
...
Ontology
Representation: attributes and
attribute groups
Instances of reports and studies
...
ns:attribute [
ns:predicate ns:year ;
ns:order "C"
] ;
...
Graph
ns:SkinAbsorptionInVitroNonOECD
Stored as an OWL file on the Web with
the namespace as the location (URL)
Each graph stored as a named graph in
triplestore 1
Used for
generating jigsaw
pieces
Composed
reports used for
generating RDF
Experts
”assemble”
reports
Each graph stored as a named graph in triplestore 2

15.
Representing the Structure of Puzzle Pieces
• ns:attributeGroup relating instances
of ns:Study or ns:AttributeGroup to
instances of ns:AttributeGroup;
• ns:attribute relating instances of
ns:Study and ns:AttributeGroup to
instances of ns:Attribute;
• ns:predicate relates an ns:Attribute to
a predicate from the ontology;
• ns:order and ns:color.
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16.
Generating RDF
Blockly.Blocks['...#SkinAbsorptionInVitroNonOECD-Endpoints'] = {
init: function() {
this.jsonInit({
"type": "...#SkinAbsorptionInVitroNonOECD-Endpoints",
"message0": 'Endpoints',
"message1": 'methodOfAnalysis %1',
"args1": [{
"type": "field_input",
"name": "http://ontologies.vub.be/oecd#methodOfAnalysis" }],
// OMMITTED FOR BREVITY
"output": "...#SkinAbsorptionInVitroNonOECD-Endpoints",
"colour": 202 });
}
};
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IRIs of the ontology are encoded
in the block definitions. Blockly
XML is then transformed into RDF

17.
Conclusions and Future Work
• We proposed the adoption of a jigsaw metaphor to facilitate data
curation by subject matter experts.
• Future work is twofold:
– Use of the tool by subject matter experts for foreseen in 2020
– Adoption of the jigsaw metaphor defining and maintaining the various
blocks
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18.
References
1. L. McKenna, C. Debruyne, and D. O'Sullivan, "Understanding the position of
information professionals with regards to linked data: A survey of libraries,
archives and museums,'' in Proceedings of the 18th ACM/IEEE on Joint
Conference on Digital Libraries, JCDL 2018, Fort Worth, TX, USA, June 03-07,
2018, J. Chen et al., Eds. ACM, 2018, pp. 7—16.
2. T. D. Erickson, "Working with interface metaphors,'' in Readings in Human-
Computer Interaction. Elsevier, 1995, pp. 147—151.
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