Toward Semantic Representation of Science in Electronic Laboratory Notebooks (ELNs)

Toward Semantic Representation of Science in Electronic

Laboratory Notebooks (ELNs)Stuart J. Chalk

Department of Chemistry, University of North Florida

schalk@unf.edu

CINF Paper 50 – 251st ACS Meeting Spring 2016

#ACSCINFDataSummit

Utopia: A Global Research Network What is an Electronic Notebook? The Semantics of Semantics What Needs to be Semantically Represented? Current lay of the land

ELN Item Manifest P-PLAN Ontology VIVO-ISF Ontology Chemical Analysis Metadata Platform HCLS Community Profiles Electronic Notebook Ontology A generic scientific data model Experimental information for LD (ExptLD)

Take Home Conclusion

Outline

“Big Data” and the “Semantic Web” are the current buzz words du jour but what do they mean for chemistry?

Lots of heterogeneous data and metadata with even more “semantic” data to represent it

Look at what we want rather that what we have… We went chemical data that is:

Easy to share, find, and compare Freely available but with provenance Globally sourced and without IP restrictions on reuse

Utopia: A Global Research Network

An electronic way to record data… ...equivalent to a laboratory notebook

But ELN’s should not be thought of so lowly...

An ELN must:* Keep track of research data Reference resources used in research and… …capture the story of research

What is anElectronic Laboratory Notebook?

* Insight from Tony Williams

The interface should mirror a laboratory notebook Behind the scenes though it should use state of the

art software, data formats, data/metadata practices, and web technologies to manage data generation, workflows, remote data access, authentication etc…

As a result it needs to speak the same language as other data sources and store data in a format that others can read and reuse

Foundational building block of a Global Research Network

What should an ELN be?

Semantics is the study of meaning-> We need to give meaning to what is created in an ELN

Described in computers using the Resource Description Framework (RDF) which: Makes statements about objects… … their relationships to other objects... ...using subject-predicate-object “triples”

RDF allows knowledge representation Meaning is represented by using one or more

ontologies

The Semantics of Semantics

RDF in JSON-LD{ "@context": { "name": "http://schema.org/name", "isAlive": "http://example.org/isAlive", "age": "http://example.org/age", "height": "http://schema.org/height", "@base": "http://www.unf.edu/chemistry/stuart_chalk.aspx" }, "@id": "", "name": "Stuart Chalk", "isAlive": true, "age": 49, "height": 188.0}

http://json-ld.org/playground/

<http://www.unf.edu/chemistry/stuart_chalk.aspx> <http://example.org/age>

"49"^^<http://www.w3.org/2001/XMLSchema#integer> .

<http://www.unf.edu/chemistry/stuart_chalk.aspx> <http://example.org/isAlive>

"true"^^<http://www.w3.org/2001/XMLSchema#boolean> .

<http://www.unf.edu/chemistry/stuart_chalk.aspx> <http://schema.org/height>

"188"^^<http://www.w3.org/2001/XMLSchema#integer> .

<http://www.unf.edu/chemistry/stuart_chalk.aspx> <http://schema.org/name>

"Stuart Chalk" .

RDF in JSON-LD

Everything!

What areas? Data, Results and Resources Models, Tools for Data Workup (Equations, Tests,

Stats) General Workflows (Protocols and Procedures) The Research Story (What, Why, How)

User discussion and annotation ELN usage timeline

The Science (Area, Hypotheses, Theories) The People (Expertise, Provenance, Integrity,

Eminence)

What Needs to beSemantically Represented?

The P-PLAN Ontologyhttp://purl.org/net/p-plan

Workflows

Implement in Kepler, Taverna, Knime?

People: The VIVO-ISF Ontology

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

The Chemical Analysis Metadata Platform (ChAMP)http://champ-project.org/

Identification of metadata related to chemical analysis and definition of an ontology to describe terms

Examples in both XML and JSON-LD with associate XML Schema and JSON-LD context Journal Article Standard Method of Analysis Reference Material

The Science: ChAMP (an example)

ChAMP

ChAMP

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/

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

Electronic Notebook Ontology (ENO)

ENO

ENO

Use a GenericScientific DataModel

Captures dataand metadataabout datasetsand links torelated data

JSON-LD isideal file format

Data andResources

A specification (written in XML) that describes different data 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 Communication Customer Data Dataset Definition

Element Equipment Event Experiment Group Project Protocol Quote Report Result

Experimental Linked Data (ExptLD)

Define data packetsthat capture themetadata of Resources Data

Integrate with otherExptLD packets to create a SciData document

Or convert to RDF and store in a triplestore

A lot exists to semantically represent the scientific process that can be leveraged as part of an ELN system

A data standard needs to be agreed upon Agreeing on implementation standards will take time

because of size of user community Integration and coverage of ontologies will be

necessary to fully implement a system that underpins a Global Research Network

Domain specific knowledge representation needed in many areas

Take Home

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?