To integrate science into the semantic web it is important to capture the context of research as it is done. ExptML is designed to store information and workflows from the scientific process.

1. Experiment Markup Language:
A Combined Markup Language and
Ontology to Represent Science
Stuart J. Chalk
Department of Chemistry
University of North Florida
schalk@unf.edu
2014 Spring ACS Meeting – CINF Paper 19

2.  Digital Representation of Science
 Electronic Notebooks
 The Eureka Research Workbench
 Experiment Markup Language
 ExptML Schema and Files
 Semantic Data and Ontologies
 File Storage
 Eureka Interface
 Web Interface
 Conclusion
Outline

3.  Most research on digital science is focused on the data
 Standards exist for the digital representation of
 Data -> individual measurements, time series, spectra
 Molecules
 Chemical Reactions
 Context is important!
 Context can be added ad-hoc
 Needs to be added systematically - to be searchable
 We need a digital representation of the scientific process
Digital Representation of Science

4.  Conceptualized in 2006
 Need a way to store
 Research activities
 Laboratory resources
 Data
 Need to capture the workflow of scientists – not define it
 Writing in a lab notebook is equivalent to blogging…
 …but the context of the entries is important and varies
 Many data types, so how to capture information?
 Experiment Markup Language (ExptML)
Eureka Research Workbench

5.  A specification (written in XML) that describes different
types of information recorded during the scientific process
(http://exptml.sourceforge.net)
Experiment Markup Language (ExptML)
 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

6. ExptML Chemical Schema

7. ExptML
Chemical
Schema

8. ExptML Chemical (Instance)

9.  To allow ExptML to capture a scientific workflow, an ontology
is needed to represent the structure
 Needs to be
 Flexible – able to be used in a wide variety of areas
 Logical – the links make sense in the context of science
 Searchable – so we can find research done in a similar way
 Comprehensive! This is the BIG problem
 Many existing ontologies
Linking ExptML Files

10.  In computer science and ontology
“formally represents knowledge as a set of concepts within
a domain, and the relationships between those concepts. It
can be used to model a domain and support reasoning about
concepts.”*
 In essence, an ontology allows us to define the
relationships and assertions about concepts
 For samples represented in ExptML we define
 isSample (assertion)
 hasSample (relationship)
 isSampleOf (relationship)
ExptML Ontology
*https://en.wikipedia.org/wiki/Ontology_(information_science)

11. ExptML Ontology

12.  XML is nice for storage, archiving and transmitting
information…
 …but it is not so easy to use in software
 Many XML readers but each have their own syntax
 Can be cumbersome to deal in software with
 File size (XML is verbose)
 Namespaces
 Data types (e.g. string, decimal, etc…)
 So the solution is…
Developments in ExptML

13.  JSONize it!
 Compact string representation of arrays of data
 Used in AJAX requests in web browsers
Javascript Object Notation (JSON)
{
“exptmlid”: “exptml:ann1”,
“anntype”: “comment”,
“text”: “Had to wait for the biochemistry lab
to finish using the spectrophotometer before the I
could get on it. The standards sat around for 1 hr
30 minutes before I could run them.”,
“date”: “2011-11-25T11:05:17-04:00”
}
<annotation id="exptml_ann1" xmlns="urn:exptml:schema:draft:0.4"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="urn:exptml:schema:draft:0.4
http://exptml.sourceforge.net/files/schema/exptml_annotation.xsd"
version="0.4">
<anntype>comment</anntype>
<text>Had to wait for the biochemistry lab to finish using
the spectrophotometer before the I could get on it. The standards
sat around for 1 hr 30 minutes before I could run them.</text>
<date>2011-11-25T11:05:17-04:00</date>
</annotation>

14.  JSON-based Serialization for Linked Data
 Current W3C recommendation*
 Allows us to define a specification for the JSON data
 “@content” is equivalent to an XML Schema
JSON-LD
*http://www.w3.org/TR/json-ld
{
“@context”:
{
“exptmlid”: “http://www.w3.org/2001/XMLSchema#string”,
“anntype”: “http://www.w3.org/2001/XMLSchema#string”,
“text”: “http://www.w3.org/2001/XMLSchema#string”,
“date”: “http://www.w3.org/2001/XMLSchema#dateTime”
}
}

15. JSON-LD
{
“@context”:
{
“exptmlid”: “http://www.w3.org/2001/XMLSchema#string”,
“anntype”: “http://www.w3.org/2001/XMLSchema#string”,
“text”: “http://www.w3.org/2001/XMLSchema#string”,
“date”: “http://www.w3.org/2001/XMLSchema#dateTime”
}
“exptmlid”: “exptml:ann1”,
“anntype”: “comment”,
“text”: “Had to wait for the biochemistry lab to finish
using the spectrophotometer before the I could get on it. The
standards sat around for 1 hr 30 minutes before I could run
them.”,
“date”: “2011-11-25T11:05:17-04:00”
}

16.  @id represents an Internationalized Resource Identifier (IRI)
 The IRI identifies a node and allows this data to be linked
JSON-LD
{
“@context”: “http://exptld.org/annotation.jsonld”
“@id”: “https://eureka.coas.unf.edu/exptml:ann1”,
“anntype”: “comment”,
“text”: “Had to wait for the biochemistry lab to finish
using the spectrophotometer before the I could get on it. The
standards sat around for 1 hr 30 minutes before I could run
them.”,
“date”: “2011-11-25T11:05:17-04:00”
}

17.  Current the ontology defines generic relationships
 Should be expanded to provide additional context
Developments in the Ontology
<rdf:Property rdf:ID="http://exptml.sourceforge.net/exptml_ontology.owl#hasSolution">
<rdfs:label>has solution</rdfs:label>
<rdfs:comment>Indicates that an experiment makes use of a particular
solution</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://exptml.sourceforge.net/exptml_ontology.owl#rels"/>
</rdf:Property>
<rdf:Property rdf:ID="http://exptml.sourceforge.net/exptml_ontology.owl#hasBuffer">
<rdfs:label>has buffer</rdfs:label>
<rdfs:comment>Indicates that an experiment makes use of a buffer (solution)</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://exptml.sourceforge.net/exptml_ontology.owl#hasSolution"/>
</rdf:Property>
<rdf:Property rdf:ID="http://exptml.sourceforge.net/exptml_ontology.owl#hasReagent">
<rdfs:label>has reagent</rdfs:label>
<rdfs:comment>Indicates that an experiment makes use of a reagent (solution)</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://exptml.sourceforge.net/exptml_ontology.owl#hasSolution"/>
</rdf:Property>
<rdf:Property rdf:ID="http://exptml.sourceforge.net/exptml_ontology.owl#hasCalibrationStandard">
<rdfs:label>has calibration standard</rdfs:label>
<rdfs:comment>Indicates that an experiment makes use of a calibration standard</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://exptml.sourceforge.net/exptml_ontology.owl#hasSolution”/>
</rdf:Property>

18.  BIG Problem!
 Context is specific to the science and the scientist
 How many sub-properties of “hasSolution” are needed?
 Additional context is domain specific so…
 … we need to integrate other related ontologies
 Map “hasSolution” to predicates in other ontologies
 Use VIVO to choose the ‘best’ domain specific ontology
 Aggregate science ontologies? – requires software/time
 Evaluate ElasticSearch (http://www.elasticsearch.org)
Expand the Ontology

19.  JSON-LD is a concrete RDF syntax!*
 JSON-LD can be converted to triples
Combine ML and Ontology?
*http://www.w3.org/TR/json-ld/#relationship-to-rdf
{
"@context": "http://exptld.org/annotation.jsonld",
"@id": "https://eureka.coas.unf.edu/exptml:ann1",
"anntype": "comment",
"text": "Had to wait for the biochemistry lab to finish using the
spectrophotometer before the I could get on it. The standards
sat around for 1 hr 30 minutes before I could run them.",
"date": "2011-11-25T11:05:17-04:00",
"hasUser": [
{ "@id": "https://eureka.coas.unf.edu/exptml:usr1” },
{ "@id": "https://eureka.coas.unf.edu/exptml:usr11”}
],
"hasExperiment": { "@id": "https://eureka.coas.unf.edu/exptml:exp1" }
}

20.  Nice start - allows for conceptual evaluation of the approach
 Needs work – “science cannot be described by one alone”
 TODO
 Integrate and aggregate existing ontologies
 Work with ELN developers e.g. LabTrove and elnItemManifest*
 Encourage ontology development in areas where gaps exist
e.g. Chemical Analysis
 Contribute to standards development
e.g. Research Data Alliance (RDA) – http://rd-alliance.org
Conclusion
* “First steps towards semantic descriptions of electronic laboratory notebook records“,
S J Coles, J G Frey, C L Bird, R J Whitby and A E Day, J. Cheminformatics, 2013, 5:52 http://doi.dx.org/10.1186/1758-2946-5-52

21. References
 Eureka – http://sourceforge.net/projects/eureka
 Fedora-Commons – http://fedora-commons.org
 XML – http://www.w3.org/standards/xml
 ExptML – http://exptml.sourceforge.net/
 JSON-LD – http://www.w3.org/TR/json-ld
 UnitsML – http://unitsml.nist.gov/
 RDF – http://www.w3.org/RDF/
 CIR – http://cactus.nci.nih.gov/chemical/structure
 RDA – http://rd-alliance.org
 Research Data Alliance (https://rd-alliance.org/)
 http://www.nytimes.com/2013/08/13/science/how-to-share-scientific-data.html