115 improving interoperability by incorporating unitsml into

1. Introduction

As scientific markup languages proliferate, it is verydesirable to have a single scheme for handling scientif-ic units of measure to facilitate moving information

between different domains. Since units are independentof the software used, it is reasonable to separate unitsfrom the technical data. An incorrect description of ameasurement unit can falsify an entire experiment.Therefore, it is important that the handling of units be

Volume 115, Number 1, January-February 2010Journal of Research of the National Institute of Standards and Technology

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[J. Res. Natl. Inst. Stand. Technol. 115, 15-22 (2010)]

Improving Interoperability by IncorporatingUnitsML Into Markup Languages

Volume 115 Number 1 January-February 2010

Ismet Celebi

Physics Laboratory,National Institute of Standardsand Technology,Gaithersburg, MD, 20899

and

Wiesbaden ComputerIntegrated Laboratory (WICIL),RheinMain University of AppliedSciences,Wiesbaden, Germany

Robert A. Dragoset andKaren J. Olsen

Physics Laboratory,National Institute of Standardsand Technology,Gaithersburg, MD, 20899

Reinhold Schaefer

Wiesbaden ComputerIntegrated Laboratory (WICIL),RheinMain University of AppliedSciences,Wiesbaden, Germany

and

Gary W. Kramer

Biochemical Science Division,National Institute of Standardsand Technology,Gaithersburg, MD, 20899

[email protected]@[email protected]@[email protected]

Maintaining the integrity of analytical dataover time is a challenge. Years ago, datawere recorded on paper that was pasteddirectly into a laboratory notebook. Thedigital age has made maintaining theintegrity of data harder. Nowadays,digitized analytical data are often separatedfrom information about how the samplewas collected and prepared for analysis andhow the data were acquired. The data arestored on digital media, while the relatedinformation about the data may be writtenin a paper notebook or stored separatelyin other digital files. Sometimes theconnection between this “scientificmeta-data” and the analytical data is lost,rendering the spectrum or chromatogramuseless. We have been working withASTM Subcommittee E13.15 onAnalytical Data to create the AnalyticalInformation Markup Language orAnIML—a new way to interchange and

store spectroscopy and chromatographydata based on XML (Extensible MarkupLanguage). XML is a language fordescribing what data are by enclosingthem in computer-useable tags.Recording the units associated with theanalytical data and metadata is an essentialissue for any data representation schemethat must be addressed by all domain-specific markup languages. As scientificmarkup languages proliferate, it is verydesirable to have a single scheme forhandling units to facilitate movinginformation between different datadomains.

At NIST, we have been developing ageneral markup language just for units thatwe call UnitsML. This presentation willdescribe how UnitsML is used and how itis being incorporated into AnIML.

Key words: analytical experiments;AnIML; data storage; device integration;interoperability; Markup Language;Scientific Units of Measure; UnitsML;Web services; XML.

Accepted: December 3, 2009

Available online: http://www.nist.gov/jres

appropriately developed to allow for the unambiguousstorage, exchange, and processing of numeric data.Units of measure are not only needed by laboratoryautomation systems, but nearly all other applicationdomains. Examples include: physics, chemistry,materials, and mathematics. The field of aeronauticaland space engineering had the infamous Mars ClimateOrbiter problem. The loss of NASA’s Climate Orbiteron September 23, 1999 was traced to a measurementunit problem. The 125 million dollar space orbiter waslost as it entered the orbit of Mars. Mission managershave concluded that the cause of the mishap was con-fusion over the type of units used to measure thestrength of thruster firings. The problem was due to anerror in communication between the Mars ClimateOrbiter spacecraft team in Colorado and the missionnavigation team in California. The peer review pre-liminary findings indicate that one team used Englishunits (e.g., inches, feet, pounds) while the other usedmetric units for a key spacecraft operation [1, 2].

Developers have requested a single language forencoding units properties in XML. At the NationalInstitute of Standards and Technology (NIST), we aredeveloping a schema for encoding scientific units,quantities, and dimensions in XML, named UnitsML(Units Markup Language). The development anddeployment of a markup language for units will allowfor the unambiguous storage, exchange, and processingof numeric data, thus facilitating the collaboration andsharing of information. The usage of UnitsML in othermarkup languages will prevent duplication of effort andimprove interoperability. Today there are many markuplanguages based on XML that could incorporateUnitsML including MathML (Mathematics MarkupLanguage), AnIML (Analytical Information MarkupLanguage), and AMDML (Atomic and Molecular DataMarkup Language), etc.

2. Extensible Markup Language

XML (Extensible Markup Language) is a standardfor the production of human and machine readabledocuments. XML is a W3C (World Wide WebConsortium)-recommended general-purpose markuplanguage for creating special-purpose markup lan-guages. A markup language is a mechanism to describeboth markup and content in the same document. XMLdefines the rules for the syntax and structure of suchdocuments. For a concrete XML application, the detailsof the respective documents must be specified. Thisrequires the definition of structural components and

their arrangement within a document tree. XML istherefore a standard for the definition of arbitrarymarkup languages. A markup language like XML,which is used for the definition of other languages, iscalled a meta language. One of the main purposes ofXML is to facilitate the sharing of data across differentsystems or software modules or the sharing differenttypes of data to be exported for interoperability orarchival purposes [3-5].

3. Analytical Information MarkupLanguage

Analytical Information Markup Language (AnIML),is a markup language for analytical chemistry data that is currently under development by ASTM subcom-mittee E13.15. It is a combination of a highly flexiblecore schema, a technique schema, and a set of analyti-cal technique instance documents (ATID files). Thecore schema defines containers for result data in ageneric manner. The ATID files are XML files, whichapply tight constraints to the flexible core. EachATID file refers to a specific analytical technique.The organisation of ATID files is specified by thetechnique schema. Extensions of ATID files are possi-ble for vendor-specific, institutional-specific, anduser-specific parameters. The goal of AnIML is tointerchange and store analytical results and their metadata [6].

More information about AnIML can be found on theAnIML web site, http://www.animl.org/.

4. Units Markup Language

Units Markup Language (UnitsML) is a generalXML-based markup language for encoding scientificunits. It has a single schema for handling units, whichis desirable to facilitate moving information betweendifferent data domains. The UnitsML schema isdesigned for incorporating scientific units into otherXML documents or into any XML-based software.Various tools are under development to assist in the useof UnitsML.

“The value of a quantity is its magnitude expressedas the product of a number and a unit” [7]. The value ofa quantity Q can be written as Q = N U, where N is thenumerical value of Q when the value of Q is expressedin the unit U (Example: length = 5 m) [7]. UnitsMLdoes not describe the numerical value; it only describesthe unit.


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The main requirement for use of UnitsML is theavailability of its schema. It can be problematic foreach user to collect information on units and theassociated quantities and to define conversions toother units. Alternatively, users can refer to unit defini-tions from a third party database. Such a databasecontaining information on units, prefixes, quantities,and dimensions encoded in the UnitsML schema isunder development at NIST. This database, calledUnitsDB, contains detailed units and dimensionalityinformation for SI units and an extensive collection ofcommon, non-SI units. The database includes informa-tion on units, quantities, symbols, language-specificunit names, and representations in terms of other units,including conversion factors to reference units. In therepresentations table, the units database describes allunits in terms of the seven SI (International System ofUnits) base units [7]. In addition some units aredescribed in terms of related, appropriate units. Table 1shows the expression of farad in the database. Recallthat a farad is a unit of capacitance equal to onecoulomb per volt. Reducing the definition of farad to SIbase units gives F = C · V–1 = m–2 · kg–1 · s4 · A2.

Figure 1 presents a few tables from UnitsDB andshows how SI-derived units are stored in the database.

More information about UnitsML can be found onthe UnitsML website, http://unitsml.nist.gov/. More

information about SI units can be found athttp://www.bipm.org/ and http://physics.nist.gov/SP811/.

5. Ways to Incorporate UnitsML IntoOther Markup Languages

UnitsML has been designed to be a componentfor inclusion into other markup languages. There areseveral different ways to incorporate UnitsML intoother markup languages. These are referencing to theschema, including the schema, importing the schema,and redefining the schema elements.

5.1 Refer to the UnitsML Schema

UnitsML may be included in schema-based markuplanguages by referencing the UnitsML schema in aninstance document. The W3C’s finalization of the XMLSchema specification allows greater flexibility andspecificity in defining constraints than are availablewith DTDs (Document Type Definitions). One impor-tant part of using schemas is being able to referencethem within other XML documents. Making a refer-ence from within an XML document requires a declara-tion of the XML schema instance namespace, a prefixmapping (xsi), and associated URI (Uniform ResourceIdentifier) to give access to the attributes needed forreferencing the XML schemas. If needed, there can bedefined a default namespace to provide a home for allnon-prefixed elements in the document. Once the XMLschema instance namespace is available, one canprovide the schemaLocation attribute within it.The schemaLocation attribute consists of two values.The first value, or argument, is the namespace,


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Table 1. Storage of the unit farad in UnitsDB

Base Unit Prefix Power Numerator

meter none –2kilogram none –1second none 4ampere none 2

Fig. 1. Storage of SI derived units in UnitsDB.

which must be unique (URI), and the second is theactual resolvable schema location (URL—UniformResource Locator). In this case, the first referencedschema location is the host schema and the second theUnitsML schema. In the same way we could referencea third, fourth, or additional schemas. There are manymore options for referencing schemas, using them withand without namespaces. These options are document-ed in the W3C XML Schema specification.

One way of incorporating UnitsML into AnIMLdocuments by referencing is to create compound docu-ments that reference the AnIML core schema andUnitsML schema. An example is shown in Listing 1.

Features of UnitsML can be incorporated into XMLinstance documents by using the actual UnitsMLschema within the host schema. The problem with thisis the availability of the UnitsML schema. The follow-ing methods are dependent on having the UnitsMLschema file (.xsd). The user could download theUnitsML schema to make it available offline. In thiscase, the user is responsible for updating the UnitsMLschema, when schema updates are available on the

UnitsML server. The UnitsML tool, which is describedbelow in “Tools under development,” should be able towarn the user of this update and to update the offlineschema. To do this some changes must be made in thehost schemas. There are three ways that this can becarried out:

5.2 <include> the UnitsML Schema

This directive results in the UnitsML schema beingbrought into the host schema within the host schemanamespace. The element <include> brings in defini-tions and declarations from the UnitsML schema intothe host schema. It requires the UnitsML schema to bein the same target namespace as the host schema name-space [8].

<xs:include schemaLocation = “unitsml.xsd”/>

Listing 2 shows an example of the include method onan AnIML instance document. Compared with theimport example shown in Listing 3, we see the differ-ence in namespaces.


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Listing 2. AnIML Core with UnitsML included in the schema.

Listing 1. AnIML Core with UnitsML Schema-Referencing.

5.3 <import> the UnitsML Schema

The import function behaves similarly to the includedirective with the difference that it is possible to importelements from other namespaces. In the examplebelow, only the units element is imported from theUnitsML schema [8].

<xs:import namespace="http://unitsml.nist.gov/2009"schemaLocation="unitsml.xsd"/><xs:element ref="unitsml:units"/>

Using the import option, an AnIML data file wouldlook like the example shown in Listing 3. It showsthat the AnIML core namespace (xmlns:animlcore) isdifferent than the UnitsML namespace (xmlns:unitsml)and that the units part of the document is describedcompletely in UnitsML. The following element of the<UnitSet> element <Unit> is defined globally in theUnitsML schema. Therefore since this example doesn’tneed information on prefixes, quantities, or dimen-sions, it is possible to use the <Unit> element directlywithout using the root element <UnitsML>.

5.4 <redefine> the Elements of UnitsML

The redefine directive can be used in place of theinclude function. This directive, however, allows

elements from the UnitsML schema to be redefined tomeet current needs in the combined schema [8].

<xs:redefine schemaLocation="unitsml.xsd">

The redefined elements from the UnitsML schemaare placed here.

</xs:redefine>

The instance documents using redefined schemaelements look the same as those using the includemethod. An example is given in Listing 2.

AnIML is a little different than other markuplanguages because AnIML works with two schemas. Ithas a core and a technique schema. In this case thereare actually three schemas, including the UnitsMLschema. Figure 2 shows one possible method ofincorporating UnitsML into AnIML. This examplerequires that the AnIML client have real-time access tothe internet to get the information from the UnitsDBdatabase.

Table 2 summarizes the four options for incorporat-ing UnitsML into a host markup language.


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Listing 3. AnIML Core with UnitsML imported in the schema.


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Fig. 2. Structural overview of incorporating UnitsML into a compound data file. Theevent sequence is: 1. request; 2. response; 3. generating instance document.

Table 2. Overview of the ways to incorporate UnitsML into host markup language

Incorporation Method Reference Include Import Redefine

Different Namespace option Yes No Yes NoRedefine of elements option No No No YesChanges in host schema required No Yes Yes Yes

6. Tools Under Development

We are currently working on web services to processqueries that will return UnitsML code containinginformation from the UnitsDB. A web service providesintegration over existing internet protocols, which makesthe service compatible with most operatingsystems and programming languages. To use the webservice, clients are required to support the XML-basedWeb Service Description Language (WDSL) and theXML-based exchange protocol SOAP (formerly SimpleObject Access Protocol). Most recently developed webservices packages support these standards. Figure 3shows how the UnitsML web services will work. Theservice information could be published using the XML-based UDDI (Universal Description, Discovery, andIntegration) protocol. Applications can look up webservices information to determine options to use. Thepublic interface to the web service is described by theWSDL, an XML-based service description on how tocommunicate using the web service. After the clientreceives the information describing the services, thecommunication between client and server uses theSOAP protocol. The services in the UnitsML Server willbe written in Java and will use the JDBC (Java DatabaseConnectivity) driver to communicate with the database.The internal processing of the XML file in the UnitsMLServer will be done using XML tools such as, a data binding framework, SAX (Simple API for XML), andDOM (Document Object Model) [3-5].

We are also working on a solution to manage offline-stored units information in UnitsML for clients lacking areal-time internet connection. With this tool, users willbe able to manage their own copies of UnitsML data andwill not be constantly dependent on access to UnitsDB.The ability to edit and view available unit informationwithout specific XML knowledge will make the use ofUnitsML easier. The ability of the tool to connect to theUnitsML web services and update the offline availableunit information is intended.

Development of the UnitsML schema has initiallytaken place at NIST, but completion of the developmentprocess should also include input from the internationalscientific and engineering community. To this end, anOASIS Technical Committee has been created to addressany needed changes in the schema and to publish a finalrecommendation for UnitsML. The release data forUnitsDB and the Web Services tool will be sometimeafter the recommendation for the UnitsML schema hasbeen published.

Disclaimer

Certain commercial software products are identifiedin this document. Such identification does not implyrecommendation or endorsement by the NationalInstitute of Standards and Technology, nor does it implythat the products identified are necessarily the bestavailable for the purpose.


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Fig. 3. UnitsML Web Service.

Acknowledgments

The authors would like to thank Alexander Roth,Ronny Jopp, Jens Bakoczy, Burkhard Schaefer and theNIST UnitsML working group. This project is fundedby NIST’s Systems Integration for ManufacturingApplications (SIMA) Program. SIMA supports NISTprojects, applying information technologies andstandards-based approaches to manufacturing softwareintegration problems.

7. References

[1] Mars Climate Orbiter Failure Board Releases Report.h t t p : / / m a r s . j p l . n a s a . g o v / m s p 9 8 /news/mco990930.html (accessed January 2010).

[2] R. Lloyd, Metric mishap caused loss of NASA orbiter;CNN News: http://www.cnn.com/TECH/space/991110/mars.metric.02/ (accessed January 2010).

[3] R. Monson-Haefel, J2EE Web Services; Addison Wesley:Boston, MA, 2005, Vol. 4, pp 6-32.

[4] XML, from Wikipedia the free encyclopedia.http://en.wikipedia.org/wiki/Xml/ (accessed January 2010).

[5] E. R. Harold, Processing XML with Java; Addison Wesley:Vol. 3, pp 57-119, Boston, MA (2005).

[6] B. A. Schaefer, D. Poetz, G. W. Kramer, Documenting labora-tory workflows using the Analytical Information MarkupLanguage. JALA 2004, 9 (6), p 375.

[7] E. A. Thompson and B. N. Taylor, Guide for the Use of theInternational System of Units (SI); NIST Special Publication811; National Institute of Standards and Technology,Gaithersburg, MD, 2008.

[8] H. S. Thompson, D. Beech, M. Maloney, and N. Mendelsohn,XML Schema Part 1—Structures Second Edition.http://www.w3.org/TR/xmlschema-1/ (accessed January 2010).

About the authors: Ismet Celebi, a former NISTAssociate for the Office of Electronic Commerce inScientific and Engineering Data (ECSED) within thePhysics Laboratory at the National Institute ofStandards and Technology, was supported by the NISTSystems Integration for Manufactuing ApplicationsProgram and the Wiesbaden Computer IntegratedLaboratory (WICIL), RheinMain University of AppliedSciences at the time the first draft of this paper waswritten. Reinhold Schaefer is a retired professor fromWiesbaden Computer Integrated Laboratory (WICIL),RheinMain University of Applied Sciences and aformer President of the Association for LaboratoryAutomation. Robert Dragost is the chair of the OASISUnits Markup Language (UnitsML) TechnicalCommittee and is the manager of ECSED withinthe Physics Laboratory at NIST. Karen Olsen is a

computer scientist of ECSED within the PhysicsLaboratory at NIST. Gary Kramer is a ResearchChemist in the Bioassay Methods Group of theBiochemical Science Division at NIST and chairsASTM Subcommittee E13.15 on Analytical Data. NISTis an agency of the U.S. Department of Commerce.


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115 improving interoperability by incorporating unitsml into

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