Scientific Unitsin the Electronic Age

Stuart J. Chalk, Department of ChemistryUniversity of North Florida

schalk@unf.edu

CINF Paper 49 – 251st ACS Meeting Spring 2016

#ACSCINFDataSummit

Why Do Computers Need to Know About Units? What Do We Need? Unit Systems Implementation of

Units for Computers Text Units XML Units Semantic Units

What We Really Need Things To Do Conclusion

Outline

From: http://unitsml.nist.gov/Presentations/UnitsML_for_TC.pdf

Computers are used to represent data Data is not useful unless it has a context – meaning Part of the context of data is its unit of measure Publication of scientific data – it needs definitive units!

Why do ComputersNeed to Know About Units?

From: http://www.slideshare.net/petermurrayrust/text-and-data-mining-explained-at-ftdm

What Do We Need?

A way to uniquely identify and give meaning to units… …and dimensions, quantities, properties(?) A way to uniquely identify and give meaning to

fundamental constants and conversion factors Must describe the semantics of prefixes Must accommodate all languages (spoken and

computer) Must be usable at different levels of technology Must be unit system agnostic Must be as future-proof as possible

(extensible/adaptable)

What Do We Need?

A standards organization to host a platform providing unambiguous representations of any unit of measure

Tools/services to allow identification of units that can be used to represent the same quantity

Tools/services to allow systems to interconvert units and provide a mechanism to document the conversion

Must be compliant with the tools/services supporting big data and the semantic web

From: http://physics.nist.gov/cuu/pdf/SIDiagramColor.pdf

International System of Units (SI) Including CGS and MKS

UK Imperial System US Customary Units Burmese Indian Astronomical Units Troy (mass) Units

Historical/Obsolete Units and Unit Systemshttps://en.wikipedia.org/wiki/List_of_obsolete_units_of_measurement

Unit Systems

Implementations of Units for Computers

Text String XML (Tagged

Text) Semantically

(URI)

International Virtual Observatory Alliance (IVOA)http://www.ivoa.net/documents/VOUnits/

Standardization of string representations of unit labels (“VOUnits”) in the astronomy community

Text String Representation

From: http://www.ivoa.net/documents/VOUnits/20140523/VOUnits-REC-1.0-20140523.pdf

MathML (https://www.w3.org/TR/mathml-units) Presentation of Units Unit Symbols in Content MathML Conversion

of Units

XML Representation

<apply><divide/><csymbol definitionURL='http://.../units/meter#c>cm</csymbol><csymbol definitionURL='http://.../units/second>s</csymbol>

</apply>

<apply> <times/><csymbol definitionURL='http://.../units/meter#c>cm</csymbol><apply>

<power/><csymbol definitionURL='http://.../units/second>s</csymbol><cn type='integer'>-1</cn>

</apply></apply>

<csymbol definitionURL='http://.../units/kyne'>kyn</csymbol>

Geographic Markup Language (GML)http://www.opengeospatial.org/standards/gml

Provides Unit References (“unitOfMeasure” element) Unit Definitions (“unitDefinition” element) “BaseUnit”, “DerivedUnit”, and

“ConventionalUnit”

XML Representation

<gml:DerivedUnit gml:id="m3"><gml:identifier codeSpace=“…/?iid=79">cubic metre</gml:identifier><gml:quantityType>Volume</gml:quantityType><gml:derivationUnitTerm uom="#m" exponent="3"/>

</gml:DerivedUnit>

Scientific, Technical, andMedical Publishing (STTML)Part of the Chemical Markup Language (CML)http://cml.sourceforge.net/schema/

XML Representation

<stm:unit id="second" name="second" unitType="time"> <stm:description>The SI unit of time</stm:description></stm:unit>

<stm:unit id="newton" name="newton" unitType="force”><stm:description>The SI unit of force</stm:description>

</stm:unit>

<stm:unit id="g" name="gram" unitType="mass" parentSI="kg" multiplierToSI="0.001" abbreviation="g”>

<stm:description>0.001 kg.</stm:description></stm:unit>

<stm:unit id="inch" name="inch" parentSI="meter" abbreviation="in" multiplierToSI="0.0254" ><stm:description>An imperial measure of length</stm:description>

</stm:unit>

UnitsMLhttp://unitsml.nist.gov/

NIST Project – intended to be published as a standard under OASIS

Fundamental representation of dimensions, units, quantities

UnitsDB a symbiotic project (internal to NIST) Never formally standardized under OASIS…

…and NIST ran out of funding

XML Representation

XML Representation

From: http://www.oasis-open.org/committees/download.php/42538/UnitsML-Guide-v1.0-wd01.pdf

XML Representation

From: http://www.oasis-open.org/committees/download.php/42538/UnitsML-Guide-v1.0-wd01.pdf

XML Representation

<units xmlns="http://units.nist.gov/2003/01/units/SI"xmlns:q="http://units.nist.gov/2003/01/quantities"xmlns:usym="http://units.nist.gov/2003/01/symbols/units”>

<unit commonName="meter" unitID="unit0001" symbol="m"><system type="base">SI</system><name xml:lang="en-US">meter</name><name xml:lang="en-GB" >metre</name><name xml:lang="fr" >mètre</name><unitSymbolRef unitSymbolIDRef="usym:symbol0001">m</unitSymbolRef><quantityRef quantityIDRef="q:quantity0001" /><history href="http://…">…</history><definition href="http://…">…</definition><remarks href="http://…">…</remarks>

</unit></units>

XML Representation

<quantity quantityID="quantity0001” commonName="length” type="base"><name xml:lang="en-US">length</name><quantSymRef quantSymbolIDRef="qsym:symbol0001">l</quantSymRef><dimSymRef dimSymbolIDRef="dsym:symbol0001">L</dimSymRef><unitSIRef unitSIIDRef="SI:unit0001" />

</quantity>

<prefix prefixID="prefix0004" commonName="mega" symbol="M” power="6" system="SI" base="10">

<name xml:lang="en-US" >mega</name><prefixSymbolRef prefixSymbolIDRef="psym:symbol0004" />

</prefix>

<dimensionSymbols xmlns="http://units.nist.gov/2002/01/symbols/dimensions" ><dimensionSymbol dimensionSymbol ID="symbol0001" commonSymbol="L">

<symbolFont family="sans-serif" style="normal" weight="bold">L</symbolFont></dimensionSymbol><dimensionSymbol dimensionSymbol ID="symbol0005" commonSymbol="Θ">

<symbolFont family="sans-serif" style="normal" weight="bold">Θ</symbolFont></dimensionSymbol>

</dimensionSymbols>

“Semantics” - the branch of linguistics andlogic concerned with meaning

Rather than just identify a unit,indicate the meaning of a unit

Resource Description Framework (RDF) Subject-Predicate-Object “triples” RDF-XML (https://www.w3.org/TR/rdf-syntax-grammar/) JSON-LD (JSON for Linked Data)

Ontological Definitions

Semantic Representation

Units of Measure Ontology (UO)https://github.com/bio-ontology-research-group/unit-ontologyhttp://www.ontobee.org/ontology/UO

Semantic Representation

Semantic Web for Earthand EnvironmentalTechnology (SWEET)http://sweet.jpl.nasa.gov/

“SWEET 2.3 is highly modularwith 6000 concepts in 200separate ontologies.”

Semantic Representation

Quantities, Units, Dimensions and Data Types Ontology (QUDT) Version 1

http://www.qudt.org/ Version 2

http://www.linkedmodel.org/doc/2015/DOC_schema-qudt-v2.0 Space Time Vocabulary

http://qudt.org/vocab/unit/units-space-and-time.html Physical Chemistry and Molecular Physics Vocabulary

http://qudt.org/vocab/unit/units-physical-chemistry-and-molecular-physics.html

Semantic Representation

Semantic Representation

Semantic Representation

Semantic Representation

Semantic Units Model

From: http://www.allhands.org.uk/2006/proceedings/papers/614.pdf

Semantic Units Model

From: http://www.allhands.org.uk/2006/proceedings/papers/614.pdf

Semantic Units Model

From: http://www.allhands.org.uk/2006/proceedings/papers/614.pdf

A Metrology Ontology!

What Do We Really Need?

From: http://ontology.iupac.org/ontology.pdf

Official MetrologyDefinitions

From: http://www.bipm.org/utils/common/documents/jcgm/JCGM_200_2012.pdf

Write up a summary of current state of units Develop a proposal to implement units in computers based

on best features of existing work Development of a metrology ontology

(33 results on google – none are a general ontology for metrology)

Evaluate support technology needed to implement the ontology Identify specific use cases and implement solutions

Formalize as a standard, with use cases and example implementations Applicable for text, XML, and Semantic formats… ...databases, ELNs, instrument software,

Things To Do

schalk@unf.edu Phone: 904-620-5311 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?