7
Annotation modeling with formal ontologies: Implications for informal ontologies L.I. Lumb a, , J.R. Freemantle b , J.I. Lederman b , K.D. Aldridge b a Computing and Network Services, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3 b Earth and Space Science and Engineering, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3 article info Article history: Received 24 April 2007 Received in revised form 21 January 2008 Accepted 29 March 2008 PACS: 91.10.v 91.10.Tq 93.85.Hj 96.60.Ub Keywords: Annotation Formal ontology Informal ontology Ontology Semantic Web XPointer Web Ontology Language abstract Knowledge representation is increasingly recognized as an important component of any cyberinfrastructure (CI). In order to expediently address scientific needs, geoscientists continue to leverage the standards and implementations emerging from the World Wide Web Consortium’s (W3C) Semantic Web effort. In an ongoing investigation, previous efforts have been aimed towards the development of a semantic framework for the Global Geodynamics Project (GGP). In contrast to other efforts, the approach taken has emphasized the development of informal ontologies, i.e., ontologies that are derived from the successive extraction of Resource Description Framework (RDF) representa- tions from eXtensible Markup Language (XML), and then Web Ontology Language (OWL) from RDF. To better understand the challenges and opportunities for incorporating annotations into the emerging semantic framework, the present effort focuses on knowledge-representation modeling involving formal ontologies. Although OWL’s internal mechanism for annotation is constrained to ensure computational completeness and decidability, externally originating annotations based on the XML Pointer Language (XPointer) can easily violate these constraints. Thus, the effort of modeling with formal ontologies allows for recommendations applicable to the case of incorporating annotations into informal ontologies. & 2008 Elsevier Ltd. All rights reserved. 1. Introduction In striking comparison with the original, 1 a recent report 2 appropriately frames knowledge representation in a cyberinfrastructure (CI) context: High quality metadata, which summarize data content, context, structure, interrelationships, and provenance (information on history and origins), are critical to successful information management, annotation, inte- gration and analysis yBecause there is often little awareness of markup language development activities within science and engineering communities, effort is expended reinventing what could be adopted or adapted from elsewhere. Scientists and engineers therefore need access to tools and services that help ensure that metadata are automatically captured or created in real-time. Even though metadata (data about data) receives primary emphasis in the above excerpt, the updated report also places emphasis on current mainstays of knowledge representation such as ontologies. In addition to validat- ing the significance of knowledge representation in the CI context, and annotation in particular, the final two Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/cageo Computers & Geosciences ARTICLE IN PRESS 0098-3004/$ - see front matter & 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.cageo.2008.03.009 Corresponding author. Tel.: +1416 736 5756; fax: +1416 736 5830. E-mail address: [email protected] (L.I. Lumb). URL: http://brunhes.eas.yorku.ca/ (L.I. Lumb). 1 Report of the National Science Foundation Blue-Ribbon Advisory Panel on CI, http://www.nsf.gov/od/oci/reports/toc.jsp. 2 CI vision for 21st century discovery, http://www.nsf.gov/pubs/ 2007/nsf0728/index.jsp. Computers & Geosciences 35 (2009) 855–861

Annotation modeling with formal ontologies: Implications for informal ontologies

  • Upload
    li-lumb

  • View
    214

  • Download
    2

Embed Size (px)

Citation preview

Page 1: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

Contents lists available at ScienceDirect

Computers & Geosciences

Computers & Geosciences 35 (2009) 855–861

0098-30

doi:10.1

� Cor

E-m

URL1 Re

Panel o2 CI

2007/ns

journal homepage: www.elsevier.com/locate/cageo

Annotation modeling with formal ontologies: Implications forinformal ontologies

L.I. Lumb a,� , J.R. Freemantle b, J.I. Lederman b, K.D. Aldridge b

a Computing and Network Services, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3b Earth and Space Science and Engineering, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3

a r t i c l e i n f o

Article history:

Received 24 April 2007

Received in revised form

21 January 2008

Accepted 29 March 2008

PACS:

91.10.�v

91.10.Tq

93.85.Hj

96.60.Ub

Keywords:

Annotation

Formal ontology

Informal ontology

Ontology

Semantic Web

XPointer

Web Ontology Language

04/$ - see front matter & 2008 Elsevier Ltd. A

016/j.cageo.2008.03.009

responding author. Tel.: +1416 736 5756; fax:

ail address: [email protected] (L.I. Lumb).

: http://brunhes.eas.yorku.ca/ (L.I. Lumb).

port of the National Science Foundation Blu

n CI, http://www.nsf.gov/od/oci/reports/toc.js

vision for 21st century discovery, http://

f0728/index.jsp.

a b s t r a c t

Knowledge representation is increasingly recognized as an important component of any

cyberinfrastructure (CI). In order to expediently address scientific needs, geoscientists

continue to leverage the standards and implementations emerging from the World

Wide Web Consortium’s (W3C) Semantic Web effort. In an ongoing investigation,

previous efforts have been aimed towards the development of a semantic framework for

the Global Geodynamics Project (GGP). In contrast to other efforts, the approach taken

has emphasized the development of informal ontologies, i.e., ontologies that are derived

from the successive extraction of Resource Description Framework (RDF) representa-

tions from eXtensible Markup Language (XML), and then Web Ontology Language

(OWL) from RDF. To better understand the challenges and opportunities for

incorporating annotations into the emerging semantic framework, the present effort

focuses on knowledge-representation modeling involving formal ontologies. Although

OWL’s internal mechanism for annotation is constrained to ensure computational

completeness and decidability, externally originating annotations based on the XML

Pointer Language (XPointer) can easily violate these constraints. Thus, the effort of

modeling with formal ontologies allows for recommendations applicable to the case of

incorporating annotations into informal ontologies.

& 2008 Elsevier Ltd. All rights reserved.

1. Introduction

In striking comparison with the original,1 a recentreport2 appropriately frames knowledge representation ina cyberinfrastructure (CI) context:

High quality metadata, which summarize data content,context, structure, interrelationships, and provenance(information on history and origins), are critical to

ll rights reserved.

+1416 736 5830.

e-Ribbon Advisory

p.

www.nsf.gov/pubs/

successful information management, annotation, inte-gration and analysis yBecause there is often littleawareness of markup language development activitieswithin science and engineering communities, effortis expended reinventing what could be adopted oradapted from elsewhere. Scientists and engineerstherefore need access to tools and services that helpensure that metadata are automatically captured orcreated in real-time.

Even though metadata (data about data) receives primaryemphasis in the above excerpt, the updated report alsoplaces emphasis on current mainstays of knowledgerepresentation such as ontologies. In addition to validat-ing the significance of knowledge representation in theCI context, and annotation in particular, the final two

Page 2: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861856

sentences of the excerpt resonate particularly stronglywith the approach taken here. First, this contributioncomprises a component of an ongoing effort to adopt andadapt recent developments3 from the World Wide WebConsortium’s (W3C) Semantic Web effort4 for applicationin an enabling framework for the Global GeodynamicsProject (GGP).5 Second, real-time automation remains akey characteristic of the semantic framework underdevelopment. Although the emphasis here is more onengineering considerations for the framework, the ulti-mate motivation remains scientifically charged (Lumb andAldridge, 2005a):

The requirement to correlate data, in time and space, iscurrently a very manual process that requires geody-namicists and seismologists to specify temporal (e.g.,a period of time, an event in time) and/or spatial (e.g.,global, regional, and specific instruments) details toallow for further analysis.

Thus in the ongoing effort to develop this framework, asemantically based solution is expected to allow for easilyarrived at and scientifically meaningful correlations read-ied for further analysis.

More specifically with respect to the scientific use ofthis framework, Lumb and Aldridge (2006) have focusedon automating the development of informal ontologies forthe GGP. Despite this emphasis on informal ontologies,they anticipated the need for a hybrid approach involvingformal ontologies:

yGRDDL (Gleaning Resource Descriptions from Dia-lects of Languages) is in its earliest stages of develop-ment. Therefore, it is expected that a bottom-upextraction of Resource Description Framework (RDF)from XML [eXtensible Markup Language] via GRDDLwill be well complimented by top-down analysis andprototyping available from ontology tools such asProtege6 and SWOOP.7 In other words, this combinedbottom-up, top-down approach is anticipated toaccelerate the rate of introduction of an RDF-basedmodel for the GGP (Lumb and Aldridge, 2005b). Use ofthese same ontology tools is also anticipated to assistin eventually harmonizing the integration of informalontologies (e.g., that being derived here for the GGP)with SWEET-based8 and other formal ontologies (Lumband Aldridge, 2005b).

It is in this spirit that formal ontologies in general, andannotation in particular, are considered here. In other

3 The need to foster and encourage the adoption and adaptation of

the W3C’s Semantic Web efforts remains highly topical (e.g., Berners-Lee

and Fischetti, 1999; Shadbolt et al., 2006).4 W3C Semantic Web activity, http://www.w3.org/2001/sw/.5 GGP home page, http://www.eas.slu.edu/GGP/ggphome.html.6 The Protege ontology editor and knowledge acquisition system,

http://protege.stanford.edu/.7 SWOOP, Semantic Web ontology editor, http://code.google.com/p/

swoop/.8 SWEET ontologies, http://sweet.jpl.nasa.gov/ontology/.

words, by exploring formal ontologies and their annota-tion, it is expected that recommendations will emerge forthe process of developing annotated informal ontologies.

To initiate the modeling, a formal ontology for the GGPis prototyped by importing an existing formal ontologyand modestly extending it (Section 2.1). This extensionallows for a dual-pronged investigation of annotations informal ontologies. First, through use of functionalityinherent in the Web Ontology Language (OWL), annota-tions of internal origin are considered (Section 2.2).Second, XML Pointer Language (XPointer) is appliedas a means for annotating formal ontologies externally(Section 2.3). The outcome of this dual-pronged investiga-tion of annotating formal ontologies is captured in Section2.4. In Section 3, insight gained by working with formalontologies is applied to informal ontologies. Conclusionsare drawn in Section 4.

2. Annotation modeling with formal ontologies

2.1. A formal ontology prototype

To rapidly create a prototype for modeling purposes, itwas decided that use be made of a pre-existing formalontology. Fortunately, there are a number of candidatesavailable.9 Fairly quickly, it became evident that theformal ontology developed for the Virtual Solar TerrestrialObservatory10 (VSTO) would be appropriate for currentpurposes (Fox et al., 2006). To initiate the investigation,the VSTO formal ontology was imported into Protege, andattention was focused on extending the ontology’s exist-ing Instrument class. Because the primary instrumentused in the GGP is a superconducting gravimeter,11 theGroundBasedInstrument class of the VSTO formalontology was extended to include this and another typeof gravimeter (LaCoste-Romberg). An illustration of theseextensions is provided in Fig. 1 via the OntoViz plug-in forProtege.12 This figure makes explicit the relationships thatexist between a class and both (if applicable) its super-class and subclass. For example, it is clear from this figurethat SuperconductingGravimeter is a subclass ofGravimeter.

By virtue of this extension of the GroundBasedIn-

strument class, the newly defined gravimeters inheritboth the hasLatitude and hasLongitude functionalproperties. In addition to these functional properties thatoriginated in the VSTO ontology, the hasHeight func-tional property was added to the Gravimeter class, andis therefore inherited by the two types of gravimetersdefined here. The relationship between these classes andtheir functional properties is also illustrated in Fig. 1. Useof prefixes (e.g., vsto:) makes namespace considerationsexplicit.

9 Googling and swoogling for ontologies, http://ianlumb.wordpress.

com/2007/04/10/googling-and-swoogling-for-ontologies/.10 VSTO, http://vsto.hao.ucar.edu/.11 Superconducting gravity meters, http://www.gwrinstruments.

com/.12 OntoViz, http://protege.cim3.net/cgi-bin/wiki.pl?OntoViz.

Page 3: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

Fig. 1. Extension of VSTO formal ontology’s GroundBasedInstrument class for current purposes. This schematic was generated automatically by

OntoViz plug-in for Protege.

13 OWL web ontology language reference, W3C Recommendation 10

February 2004, http://www.w3.org/TR/2004/REC-owl-ref-20040210/.

OWL Full does not place constraints on annotation properties.14 Practically, these constraints are required because annotation

properties are designed to be ignored by OWL DL reasoners (Knublauch

et al., 2004).15 Document Object Model (DOM) Level 2 Core Specification,

Version 1.0, W3C Recommendation 13 November, 2000, http://www.w3.

org/TR/DOM-Level-2-Core/.

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861 857

The VSTO formal ontology is based on a variant of theOWL known as OWL description logic (DL). OWL DL isparticularly appealing because it (Singh and Huhns, 2005,Section 8.2):

yprovides maximum expressiveness while ensuringcomputational completeness (all valid conclusions canbe inferred) and decidability (the inferences take finitetime).

Protege allows the variation of OWL to be determined.Thus, as the VSTO ontology is extended for GGP purposes,it is possible to ensure that the resulting ontology remainsOWL DL compliant.

Since extension of the VSTO formal ontology hasresulted in an illustrative prototype for current purposes,attention shifts next to annotating formal ontologies fromwithin (Section 2.2) and without (Section 2.3).

2.2. Internal annotation via OWL annotation properties

OWL allows classes, properties, individuals and eventhe ontology itself, to be annotated with five, pre-definedproperties. These properties are illustrated via the ProtegeOWL Classes view in Fig. 2. In the central foreground, theSelect a property window identifies the availableannotation properties that are illustrated in this figure.GGP-motivated class extensions to the VSTO ontologyappear in the background-left panel (SUBCLASS EX-

PLORER) of Fig. 2, while functional properties associatedwith the highlighted SuperconductingGravimeter

class appear in the background-right-central panel(CLASS EDITOR), and disjoints with this same classappear in the background-lower-right panel. Filledrdfs:comment and rdfs:label annotation propertiesappear in the background-upper-right panel.

Under OWL DL, the following constraints are placed onannotation properties13:

The sets of object properties, datatype properties,annotation properties and ontology properties mustbe mutually disjoint. � Annotation properties must have an explicit typing

triple of the form

AnnotationPropertyID rdf:type owl:AnnotationProperty.

Annotation properties must not be used in propertyaxioms. Thus, in OWL DL one cannot define sub-properties or domain/range constraints for annotationproperties. � The object of an annotation property must be either a

data literal, a Uniform Resource Identifier (URI) refer-ence, or an individual.

Ultimately, of course, these constraints ensure that OWLDL remains computational complete and decidable.14 Animportant corollary in the current context, however, isthat these constraints also ensure consistency with theDocument Object Model (DOM).15

Page 4: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

Fig. 3. An annotated selection of VSTO ontology viewed via Annozilla plug-in for Mozilla Firefox.

Fig. 2. Demonstrative use of several OWL annotation properties in GGP extension of VSTO ontology as illustrated via Protege.

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861858

2.3. External annotation via XPointer

In the case of OWL-based ontologies, annotations aretraditionally created within the ontology via one of five,pre-defined properties (Section 2.2). In addition in thecase of OWL DL, these annotations are constrained to havelocal filler, local class instantiation (an Individual in aProtege context), or make an external reference via a URI.

In Fig. 3, the VSTO formal ontology16 has been openedwith the Mozilla Firefox Web browser.17 Using Annozilla,18

the selection illustrated in the right-hand panel has beenannotated. The yellow ‘‘X’’ in the upper-left corner of thissame panel indicates that the annotation is of typeChange.19 The two left-hand panels of Fig. 3 display an

16 The VSTO ontology, http://dataportal.ucar.edu/schemas/vsto.owl.17 Mozilla Firefox 2, http://www.mozilla.com/firefox/.18 Annozilla (Annotea on Mozilla), http://annozilla.mozdev.org/.19 Annozilla supports the seven annotation types defined in the

http://www.w3.org/2000/10/annotationType annotation type name-

space. Each annotation type has its own yellow icon.

annotation list (upper left-hand panel) and the annotationfiller (lower left-hand panel) corresponding to theselected annotation. The filler of the annotation is alsopresented in Fig. 4. It is clear from this figure that theannotation filler can be formatted, has an identifiedauthor, location (local or on a remote server), a type, anda language preference. Annotations can be updated, andannotated.20

Because the Annozilla-based annotation is external tothe VSTO ontology, the constraints placed on annotationproperties for OWL DL compliance are not violated. Moreprecisely, identified selections are regarded as URI frag-ments that are annotated in a non-invasive manner via

20 In this context, updating an annotation corresponds to editing the

filler of a pre-existing annotation. This is different from annotating a pre-

existing annotation, as in this latter case, a new annotation (with new

filler) is created. Annotations can be annotated by the author, or by

someone else with the appropriate access.

Page 5: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

Fig. 4. An annotated selection in Mozilla Firefox.

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861 859

XPointer. By referencing URI fragments externally, XPoin-ter annotates selections without violating the DOM.

For the selection identified in Fig. 3, Annozilla’s use ofXPointer is detailed in Listing 1. This listing is comprisedof the following:

Namespace declarations: The listing begins with anumber of namespace declarations. Of particular note inthe current context are the annotation-related declara-tions that have been assigned to the variables NS2

and NS3.The annotation target: Using an RDF:Description

element, the target of the annotation is identified. In thisexample, that target is the VSTO ontology that isaccessible at the identified URI. The connection betweenthis specification of the target and the annotation itself ismade through a unique identifier.

The annotation itself : The annotation itself is containedin the final block of the listing. XHTML-formatted21 filler isfollowed by annotation metadata. Of particular note isthe use of XPointer to provide the context metadatafor the annotation. This relatively simple URI fragmentis efficiently and completely described using XPointer’sstring-range function.22

21 XHTML 1.0 The

Edition), http://www.22 string-range

XPointer. http://www

tails on the XPointer

example in detail.

w

.w

Lisiting 1. Annozilla-based annotation via XPointer.

o?xml version ¼ ‘‘1.0’’?4

oRDF:RDF xmlns:NS4 ¼ ‘‘http://purl.org/dc/elements/1.0/’’

xmlns:NS3 ¼ ‘‘http://www.w3.org/2000/10/

annotation-ns#’’

xmlns:NS2 ¼ ‘‘http://www.w3.org/2000/10/

annotationType#’’

xmlns:NS1 ¼ ‘‘http://cnx.rice.edu/annotations/

localServer#’’

xmlns:NC ¼ ‘‘http://home.netscape.com/NC-rdf#’’

xmlns:RDF ¼ ‘‘http://www.w3.org/1999/02/

22-rdf-syntax-ns#’’4

oRDF:Description RDF:about ¼ ‘‘http://dataportal.ucar.edu/schemas/

vsto.owl’’4oNS1:annotatedBy RDF:resource ¼ ‘‘urn:annot9236742601’’/4

o/RDF:Description4

Extensible HyperText Markup Language (Second

3.org/TR/xhtml1/.

is one of a number of functions supported by

3.org/TR/xptr-xpointer/ provides additional de-

scheme. Lumb et al. (2007) describe a related

oRDF:Description

23 The localAnn

/Library/Applicat

identifier4.defau

Profile in Mozilla Fire24 Annozilla (An

mozdev.org/installatio25 Annotea projec26 Welcome to A

Amaya/.

o

i

lt

fo

no

n

t,

m

RDF:about ¼ ‘‘urn:body9236742601’’

NS1:bodyText ¼ ’’<html

xmlns ¼ "http://www.w3.org/1999/

xhtml"><head><title>&&

�!lt;/title></head><body>Latitude and longitude can

be used directly in the gravimeter context. A height

property needs to be added.<br/></body></

html>’’ /4

oNS2:ChangeRDF: about ¼ ‘‘urn:annot9236742601’’

NS4:creator ¼ ‘‘Ian Lumb’’

NS3:created ¼ ‘‘2007-04-16T11:48:18-04:00’’

NS4:date ¼ ‘‘2007-04-16T12:02:21-04:00’’

NS3:context ¼ ‘‘http://dataportal.ucar.edu/

schemas/vsto.owl#&

�!xpointer(string-range(/html[1]/body[1]/

pre[1], "&&

�!quot;, 10874, 626))’’

NS4:language ¼ ‘‘en’’4

oNS3:body RDF:resource ¼ ‘‘urn:body9236742601’’/4oNS3:annotates RDF:resource ¼ ‘‘http://dataportal.ucar.edu/

schemas/vsto.owl&

�!’’/4o/NS2:Change4

o/RDF:RDF4

Annozilla maintains local annotations, such as theone shared via Listing 1, in the file localAnnota-

tions.rdf.23 From the listing and the filename, it isclear that Annozilla annotations are expressed in RDF. Thisis a highly appealing expression, as RDF-based represen-tations can be expressed in OWL and (if desired)incorporated into OWL-based ontologies.

Annozilla is enabled by installing three extensions toMozilla Firefox24:

xpointerlib: A library to allow the use of XPointer.The annotations service: A service allowing access to

annotations.Annozilla: The Annozilla client itself.The Annozilla implementation derives from the Anno-

tea Project.25 And although the availability of an XPointer-based annotation capability in one of the most-widelyused Web browsers is of significant value, Mozilla Firefoxis not the only suitably enabled Web platform. Forexample, the first client implementation of Annotea wasthe W3C’s Amaya Web browser/editor.26

2.4. Internal versus external annotation

In the previous two sections (Sections 2.2 and 2.3), thepossibilities for annotating formal ontologies have beenexplored. Though complimentary, the approaches arequite different. Perhaps the most-significant difference isdrawn out by Fig. 5. OWL annotation properties areinternal to the ontology being annotated. Under con-straints placed upon annotation properties in an OWL DLcontext, both the annotation and its filler are of internal

tations.rdf file is located in the directory

on Support/Firefox/Profiles/ounique

/ on a Mac OS X based system for the default

x.

tea on Mozilla), installation, http://annozilla.

/.

http://www.w3.org/2001/Annotea/.

aya, W3C’s editor/browser, http://www.w3.org/

Page 6: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

Origin

Destination

Internal

External

External

Internal

OWL DL

XPTR

OWL DL

XPTR

Fig. 5. Origin/destination clarification for annotations.

28 T. Berners-Lee, annotation, http://www.w3.org/Design-Issues/

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861860

origin (lower-left quadrant of Fig. 5). In cases whereexternal references are permitted, the annotation is ofinternal origin, whereas the filler is an external URIreference (lower-right quadrant of Fig. 5). In contrast,annotations based on XPointer are of external origin, butthey target URI fragments that are internal to the ontology(upper-left quadrant of Fig. 5). XPointer-based annotationscould also target external URI references in relation to aselection of the ontology (upper-right quadrant of Fig. 5).

One of the appealing characteristics of internallyoriginating annotation properties (Section 2.2) is thatthe annotations and ontology are self-contained. Ofcourse, it would be possible to combine such an ontologywith the externally originating annotations describedhere. Given the less-restrictive nature of externallyoriginating annotations, however, the likelihood of violat-ing the OWL DL-based constraints on annotation proper-ties would be very high. For example, in annotatingmultiple functional properties (Fig. 3), these constraintsare violated. Annotations that annotate existing annota-tions provide another constraint-violating example. Inother words, constraint-violating examples are easilyfound. This does not mean that ontologies (with internallyoriginating annotations) cannot be combined with ex-ternally originating annotations to define an integratedontology. What it does mean, however, is that theresulting ontology is very unlikely to be expressible viaOWL DL. As a further consequence, this also means thatthe resulting ontology is not guaranteed computationalcompleteness and decidability.

The term annotation is used liberally in various OWLspecifications.27 Despite this liberal usage, the term is notdefined. OWL’s usage is essentially consistent with one ofthe earliest definitions of the term in a World Wide Web

27 OWL web ontology language overview, W3C recommendation

10 February 2004, http://www.w3.org/TR/2004/REC-owl-features-

20040210/.

context28: ‘‘Annotation is the linking of a new commen-tary node to someone else’s existing node. It is the essenceof a collaborative hypertext.’’ The approach taken in OWLis also consistent with usage of the term in a CI context29:

Metadata are often associated with data via markuplanguages, representing a consensus around a con-trolled vocabulary to describe phenomena of interestto the community, and allowing detailed annotationsof data to be embedded within a data set.

However, the internal–external distinction captured byFig. 5 becomes problematical in consideration of morecontemporary definitions30:

Annotations are comments, notes, explanations, orother types of external remarks that can be attachedto a Web document or a selected part of the document.As they are external, it is possible to annotate any Webdocument independently, without needing to edit thatdocument. From the technical point of view, annota-tions are usually seen as metadata, as they giveadditional information about an existing piece of data.

Annotation types provide another example of the appar-ent isolation between the OWL and XPointer communitieswithin the W3C. To illustrate this isolation, consider theannotation properties Comment and SeeAlso. As relatedin Section 2.2, OWL defines these and its other annotationproperties within the language. In contrast, XPointerdraws upon an external namespace for its annotationtypes.31

As usage of annotations in formal ontological contextsaccelerates, there will be an increasingly pressing need forthe W3C to develop a much more consistent representa-tion that cross-cuts the current distinctions evident in theOWL and XPointer communities.

3. Implications for annotating informal ontologies

Informal ontologies in general, and their annotation inparticular, have ultimately driven the efforts detailed inthe previous section (Section 2). Thus, attention shiftsnow to applying the findings to the annotation of informalontologies.

The primary finding of the previous section is atendency towards OWL Full when external (i.e., XPointer-based) annotations are involved. This is as applicable tothe annotation of informal ontologies as it was to theannotation of formal ontologies. And while OWL Full isnot inherently problematical there is, however, thepossibility that there will be a corresponding loss ofcomputational completeness and decidability. Such a loss

Annotation.29 CI vision for 21st century discovery, http://www.nsf.gov/pubs/

2007/nsf0728/index.jsp.30 Amaya version 9.52, http://www.w3.org/Amaya/.31 Annotation type namespace, http://www.w3.org/2000/10/

annotationType.

Page 7: Annotation modeling with formal ontologies: Implications for informal ontologies

ARTICLE IN PRESS

L.I. Lumb et al. / Computers & Geosciences 35 (2009) 855–861 861

is of particular concern when use of a reasoner32 isrequired to, for example, determine inferred classes(Horridge et al., 2004).

In addition to the tendency towards OWL Full whenXPointer-based annotations are involved, annotationalso complicates the extraction of OWL from RDF. Forexample, current strategies relating to this conversion arefocused on OWL DL and OWL Lite.33 Thus, annotation’stendency towards OWL Full may necessitate that annota-tions and informal ontologies remain separate, rather thanbeing fully integrated. As alluded to in the previoussection, this is an area in which further research isrequired. This is an important area for research, asit closes the loop in the automated development ofannotated informal ontologies from data-centric repre-sentations based on XML.

4. Conclusions

Knowledge representation is increasingly recognizedas an important component of any CI. And geoscientistsare addressing their scientific needs by leveraging thestandards and implementations emerging from the W3C’sSemantic Web effort. Of recent interest, has been thedevelopment of a semantic framework for the GGP.Because the approach taken has emphasized the devel-opment of informal ontologies, the present effort focusedon knowledge-representation modeling in the more-mature arena of formal ontologies. More specifically,attention has focused here on the incorporation ofannotations into ontologies. OWL possesses an internalmechanism for annotation that is constrained to ensurecomputational completeness and decidability. This allowsfor all-in-one annotations and ontologies. Although all-in-one representations have inherent appeal, there are caseswhere externally originating annotations based on theXML Pointer Language (XPointer) are preferable or evenrequired. Unfortunately, XPointer-based annotations caneasily violate the constraints that apply to OWL’sinternally based annotations. Constraint-violating annota-tions transform OWL DL into OWL Full. All-in-oneannotations and ontologies are still a possibility, however,such a representation is ill advised if computationalcompleteness and decidability are desirable. Fortunately,the dynamic nature of annotations and informal ontolo-gies, allows for decisions in real time and/or multipleoutcomes.

32 RacerPro 1.9, http://www.racer-systems.com/.33 OWL Web Ontology Language, parsing OWL in RDF/XML, W3C

working group note 21 January 2004, http://www.w3.org/TR/owl-

parsing/.

Acknowledgements

Aspects of this work have been financially supported bya Discovery grant from the Natural Sciences and Engineer-ing Research Council of Canada (NSERC) awarded to KDA,and by Computing and Network Services, York University;their contributions and ongoing support are gratefullyacknowledged. Constructive feedback from two anonymousreviewers significantly improved the focus and clarity ofthis paper; their input is graciously acknowledged.

References

Berners-Lee, T., Fischetti, M., 1999. Weaving the Web: The OriginalDesign and Ultimate Destiny of the World Wide Web by Its Inventor.Harper, San Francisco, CA, 461pp.

Fox, P., McGuinness, D., Middleton, D., Cinquini, L., Darnell, J.A., Garcia, J.,West, P., Benedict, J., Solomon, S., 2006. Semantically-enabled large-scale science data repositories. In: Cruz, I., Decker, S., Allemang, D.,Preist, C., Schwabe, D., Mika, P., Uschold, M., Aroyo, L. (Eds.), TheSemantic Web—ISWC 2006. Lecture Notes in Computer Science, vol.4273. Springer, Berlin, Heidelberg, pp. 792–805.

Horridge, M., Knublauch, H., Rector, A., Stevens, R., Wroe, C., 2004. A PracticalGuide To Building OWL Ontologies Using The Protege-OWL Plugin andCO-ODE Tools, 1.0th ed. The University of Manchester, 118pp. URL:hhttp://www.co-ode.org/resources/tutorials/-ProtegeOWLTutorial.pdfi.

Knublauch, H., Fergerson, R.W., Noy, N.F., Musen, M.A., 2004. The ProtegeOWL plugin: an open development environment for Semantic Webapplications. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F.(Eds.), The Semantic Web—ISWC 2004. Lecture Notes in ComputerScience, vol. 3298, Springer, Berlin, Heidelberg, pp. 229–243.

Lumb, L.I., Aldridge, K.D., 2005a. Grid-enabling the Global GeodynamicsProject: the introduction of an XML-based data model. In: Kotsireas,I., Stacey, D. (Eds.), Proceedings of the 19th International Symposiumon High Performance Computing Systems and Applications, HPCS2005. IEEE Computer Society Press, Silver Spring, MD, pp. 216–222.URL: hhttp://ieeexplore.ieee.org/iel5/9779/30845/-01430074.pdfi.

Lumb, L.I., Aldridge, K.D., 2005b. Towards an ontology for the GlobalGeodynamics Project: automated extraction of resource descriptionsfrom an XML-based data model. Eos Transactions AGU 86(52), FallMeeting Supplement, Abstract IN43A-0328.

Lumb, L.I., Aldridge, K.D., 2006. Grid-enabling the Global GeodynamicsProject: automatic RDF extraction from the ESML data descriptionand representation via GRDDL. In: Deupree, R.G., Adams, J.A. (Eds.),20th International Symposium on High-Performance Computing inan Advanced Collaborative Environment, HPCS 2006. IEEE ComputerSociety Press, Silver Spring, MD, pp. 184–191. URL: hhttp://ieeexplore.ieee.org/iel5/10840/34158/01628220.pdfi.

Lumb, L.I., Lederman, J.I., Freemantle, J.R., Aldridge, K.D., 2007. Semanticallyenabling the Global Geodynamics Project: incorporating feature-basedannotations via XML Pointer Language (XPointer). In: 21st Interna-tional Symposium on High-Performance Computing, HPCS 2007. IEEEComputer Society Press, Silver Spring, MD, p. 21. URL: hhttp://ieeexplore.ieee.org/iel5/4215545/4215546/04215570.pdfi.

Shadbolt, N., Hall, W., Berners-Lee, T., 2006. The Semantic Web revisited.Intelligent Systems 21 (3), 96–101.

Singh, M.P., Huhns, M.H., 2005. Service-Oriented Computing: Semantics,Processes, Agents. Wiley, Hoboken, NJ, p. 588.