247th ACS Meeting: Experiment Markup Language (ExptML)

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

 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

 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

 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

 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

 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

 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)

 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

 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>

 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”
}
}

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”,
“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”
}

 @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”,
“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”
}

 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>

 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

 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" }
}

 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

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

247th ACS Meeting: Experiment Markup Language (ExptML)

More Related Content

What's hot (13)

Similar to 247th ACS Meeting: Experiment Markup Language (ExptML) (20)

More from Stuart Chalk (18)

Recently uploaded (20)

247th ACS Meeting: Experiment Markup Language (ExptML)