A short story of

geologic time ontologies and vocabularies

Xiaogang (Marshall) Ma

Tetherless World Constellation

Rensselaer Polytechnic Institute

01-May-2013

TWC eScience presentation

1 The topic

• Ontologies are being applied to harmonize distributed

geoscience data and improve functionalities of data

services on the Web

– Geologic time scale is one of the topics that have received the

most discussion and practices

• This review:

– Recent progress on geologic time ontologies and vocabularies

– Further works

– Recommendations for other geoscience ontology and vocabulary

works

2

Geology

-- the scientific study of the

earth, including the origin

and history of the rocks and

soil of which the earth is

made

3

Image courtesy of Wikipedia Definition from Oxford Collocations Dictionary

Students examining the Wasatch

Fault near Salt Lake City, Utah

GT -- the time which has

elapsed since the

formation of the earth and

the beginning of the

historical period

GTS -- a chronological

(i.e. timeline) framework

for studying the history of

the earth

4 Image courtesy of anonymous author

Geologic time & Geologic time scale

Definition from Oxford English Dictionary

2 Models of geologic time scale

• International Commission on Stratigraphy (ICS)

– Targeting at establish a standard time scale for global correlations

– A primary output: International Stratigraphic Chart

5

2008

2010 2012

2009

6 2013

The standardized nomenclature and hierarchy of

geologic time scale coordinated by ICS is widely

adopted in geological works across the world.

Now let’s see a few models that describe the

primary concepts in geologic time scale

7

We will see some

UML connectors

in the following models

8

Geologic time schema in the

North American Geologic Map

Data Model (NADM) (NADM

Steering Committee 2004)

9

The basic geologic time scale

model of Cox and Richard (2005)

10

The topological

temporal ordinal

reference system

of Michalak

(2005)

11

The schema of geologic time ontology

by Perrin et al. (2011)

Analysis

• The above models share two main concepts in the

geologic time scale: interval (i.e., a period of time) and

instant (i.e., a particular point in time).

– Interval: ‘AgeInterval’, ‘TimeOrdinalEra’, ‘GL_OrdinalTopolEra’ and

‘GeochronologicUnit’

– Instant: ‘AgeDate’, ‘TimeOrdinalEraBoundary’,

‘GL_OrdinalTopolNode’ and ‘GeochronologicBoundary’

• Each model also has feature of its own on some details

– For detailed analysis see Ma and Fox (2013)

12

3 Ontologies and vocabularies of

geologic time scale

• The above-mentioned models describe high-level

concepts behind the nomenclature and hierarchy of

temporal intervals and boundaries

• Besides these abstract models, there are also works on

encodings that represent the contents of geologic time

scale in Semantic Web-compatible formats

13

Table 1 Ontologies and vocabularies of geologic time

scale encoded in Web-compatible formats

14

ID Web address Related publication/webpage

1 http://sweet.jpl.nasa.gov/2.3/stateTimeGeologic.owl (Assessed on 21 March 2012) Raskin and Pan (2005);

http://sweet.jpl.nasa.gov (Assessed on 21 March 2012)

2 http://resource.geolba.ac.at/GeologicTimeScale/GeologicTimeScale/export/GeologicTimeScale.rdf

(Assessed on 21 March 2012)

Ebner (2011);

http://planet.lod2.eu/post/134091850/Marcus-Ebner-In-a-globalized-science-

world (Assessed on 21 March 2012)

3 http://srvgeosciml.brgm.fr/eXist2010/brgm/1GE201001index.html (Assessed on 21 March 2012)

Select “1GE_Ages.xml” in the combo box “GetVocabulary” and click the button “GetVocabulary” to

browse the file

Asch et al. (2010)

4 http://resource.geosciml.org/ISC2009/CGI2011TimeScale.rdf (Assessed on 21 March 2012) https://www.seegrid.csiro.au/wiki/bin/view/CGIModel/ConceptDefinitionsTG

(Assessed on 21 March 2012)

5 https://www.seegrid.csiro.au/subversion/CGI_CDTGVocabulary/tags/SKOSVocabularies/ICS_TimeSc

ale2008.rdf (Assessed on 21 March 2012)

https://www.seegrid.csiro.au/wiki/bin/view/CGIModel/ConceptDefinitionsTG

(Assessed on 21 March 2012)

6 https://www.seegrid.csiro.au/subversion/xmml/ontologies/TBCME/GeologicTimeScale/geologictimesc

ale.rdf (Assessed on 05 February 2011)

The original link is not available now. A copy of the file was archived at:

https://sites.google.com/site/mltgts/mltgts-for-download/geologictimescale.rdf (Assessed on 21 March

2012)

Cox and Richard (2005);

https://www.seegrid.csiro.au/wiki/CGIModel/GeologicTime (Assessed on 21

March 2012)

7 http://def.seegrid.csiro.au/ontology/geotime/isc-2010.ttl (Assessed on 27 June 2012) Cox (2011);

https://www.seegrid.csiro.au/wiki/CGIModel/GeologicTime (Assessed on 21

March 2012)

8 https://sites.google.com/site/mltgts/mltgts-for-download/mtgtsMa2010.rdf (Assessed on 21 March

2012)

Ma et al. (2011)

9 https://sites.google.com/site/mltgts/mltgts-for-download/gtsOwlMa2011.rdf (Assessed on 21 March

2012)

Ma et al. (2012)

10 http://www-

sop.inria.fr/edelweiss/projects/ewok/ontology/dateTimeData/ontologies/GeologicalTimeScale20-1.owl

(Assessed on 03 April 2012)

Perrin et al. (2011);

http://www-sop.inria.fr/edelweiss/projects/ewok/ontologyview/ontologies.html

(Assessed on 03 April 2012)

11 http://resource.geosciml.org/vocabulary/timescale/isc-2012.ttl (Assessed on 14 January 2013) https://www.seegrid.csiro.au/wiki/Siss/VocabularyFormalizationInSKOS

(Assessed on 14 January 2013)

• Now we check the features of a few ontologies and

vocabularies in the above table by using the definition of

‘Lower Triassic’ as an example

16

Ordinal hierarchical structure

hierarchical

Ord

inal

Period Epoch Age Eon Era

17

<gtime:Epoch rdf:about="#LowerTriassic">

<trela:hasEndTime rdf:resource="#245.9MYA" />

<trela:hasStartTime rdf:resource="#251.0MYA" />

<trela:temporalPartOf rdf:resource="#Triassic" />

</gtime:Epoch>

<gtime:Age rdf:about="#Olenekian">

<trela:hasEndTime rdf:resource="#245.9MYA" />

<trela:hasStartTime rdf:resource="#249.5MYA" />

<trela:temporalPartOf rdf:resource="#LowerTriassic" />

</gtime:Age>

<gtime:Age rdf:about="#Induan">

<trela:hasEndTime rdf:resource="#249.5MYA" />

<trela:hasStartTime rdf:resource="#251.0MYA" />

<trela:temporalPartOf rdf:resource="#LowerTriassic" />

</gtime:Age>

<owlt:Instant rdf:about="#245.9MYA">

<screla:hasNumericValue

rdf:datatype="&xsd;double">245.9</screla:hasNumericValue>

</owlt:Instant>

<owlt:Instant rdf:about="#251.0MYA">

<screla:hasNumericValue

rdf:datatype="&xsd;double">251.0</screla:hasNumericValue>

<mrela:hasError rdf:datatype="&xsd;double">0.4</mrela:hasError>

</owlt:Instant>

Geologic time ontology in

SWEET v. 2.3

(ID 1 in Table 1)

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<skos:Concept rdf:about="urn:cgi:classifier:ICS:StratChart:200908:LowerTriassic">

<geosciml:from_Ma xml:lang="en">251 +/-0.4</geosciml:from_Ma>

<geosciml:to_Ma xml:lang="en">245.9</geosciml:to_Ma>

<skos:notation xml:lang="en">a1.1.2.3.3</skos:notation>

<skos:prefLabel xml:lang="bg">Раннен/долен Триас</skos:prefLabel>

<skos:prefLabel xml:lang="cs">Spodní trias</skos:prefLabel>

<skos:prefLabel xml:lang="da">Tidlig/Nedre Triassisk</skos:prefLabel>

<skos:prefLabel xml:lang="de">Frühe/Untere Trias (Buntsandstein)</skos:prefLabel>

<skos:prefLabel xml:lang="en">Early/Lower Triassic</skos:prefLabel>

<skos:prefLabel xml:lang="es">Triásico Inferior</skos:prefLabel>

<skos:prefLabel xml:lang="et">Vara/Alam-Triias</skos:prefLabel>

<skos:prefLabel xml:lang="fi">Varhais/Ala-Trias</skos:prefLabel>

<skos:prefLabel xml:lang="fr">Trias inférieur</skos:prefLabel>

<skos:prefLabel xml:lang="hu">kora/alsó-triász</skos:prefLabel>

<skos:prefLabel xml:lang="it">triassico inferiore</skos:prefLabel>

<skos:prefLabel xml:lang="lt">Ankstyvasis/Apatinis Triasas</skos:prefLabel>

<skos:prefLabel xml:lang="no">Tidlig/undre trias</skos:prefLabel>

<skos:prefLabel xml:lang="nl">Vroeg/Onder Trias</skos:prefLabel>

<skos:prefLabel xml:lang="pl">Wczesny/Dolny Trias</skos:prefLabel>

<skos:prefLabel xml:lang="pt">Triásico Inferior</skos:prefLabel>

<skos:prefLabel xml:lang="sk">rany/spodny trias</skos:prefLabel>

<skos:prefLabel xml:lang="sl">zgodnji/spodnji trias</skos:prefLabel>

<skos:prefLabel xml:lang="sv">äldre/undre trias</skos:prefLabel>

<skos:narrower rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Induan"/>

<skos:narrower rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Olenekian"/>

<skos:broader rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Triassic"/>

</skos:Concept>

Geologic time vocabulary in OneGeology-Europe (1G-E)

(ID 3 in Table 1)

19

isc:LowerTriassic

rdf:type gts:GeochronologicEra , skos:Concept ;

rdfs:comment "younger bound-245.9"@en , "older bound-251 +/-0.4"@en ;

rdfs:label "Lower Triassic Epoch"@en ;

gts:rank gts:Epoch ;

gtrs:end isc:BaseMiddleTriassic ;

gtrs:member isc:Induan , isc:Olenekian ;

gtrs:start isc:BaseMesozoic ;

owl:sameAs <http://dbpedia.org/resource/LowerTriassic> ;

skos:altLabel "下三叠统"@zh , "三畳紀前期"@ja ;

skos:broader isc:Triassic ;

skos:broaderTransitive

isc:Mesozoic , isc:Triassic , isc:Phanerozoic ;

skos:inScheme <http://resource.geosciml.org/classifierscheme/ics/ischart/2010> ;

skos:narrower isc:Olenekian , isc:Induan ;

skos:narrowerTransitive

isc:Induan , isc:Olenekian ;

skos:notation "a1.1.2.3.3"^^gts:EraCode ;

skos:prefLabel "Trias inférieur"@fr , "äldre/undre trias"@sv , "Tidlig/undre

trias"@no , "Tidlig/Nedre Triassisk"@da , "Varhais/Ala-Trias"@fi , "kora/alsó-triász"@hu ,

"zgodnji/spodnji trias"@sl , "Spodní trias"@cs , "Раннен/долен Триаѿ"@bg , "Early/Lower

Triassic"@en , "Vroeg/Onder Trias"@nl , "raný/spodný trias"@sk , "早三叠世"@zh , "前期三畳紀"@ja , "Frühe/Untere Trias (Buntsandstein)"@de , "Wczesny/Dolny Trias"@pl , "Vara/Alam-

Triias"@et , "Ankstyvasis/Apatinis Triasas"@lt , "triassico inferiore"@it , "Triásico

Inferior"@pt , "Triásico Inferior"@es ;

foaf:isPrimaryTopicOf

<http://sweet.jpl.nasa.gov/2.2/stateTimeGeologic.owl#LowerTriassic> .

Geologic time vocabulary by

Cox (2011)

(ID 7 in Table 1)

Analysis

• SWEET geologic time ontology

– Reuses other ontologies in SWEET

– Quantitative time boundaries

– Less qualitative descriptions (but some can be inferred from the

time boundaries, e.g., Induan is a subset of Lower Triassic)

• 1G-E geologic time vocabulary

– A typical application of SKOS

– A point of interest is using multilingual labels for translating

distributed geologic map services in Europe (1G-E portal)

• Geologic time vocabulary by Cox (2011)

– Reuses OWL and SKOS: a overlaid structure

– A point of interest is the SISSVoc vocabulary service

let’s see more about Cox’s work, details in next slides

20

• The general idea of Cox (2011, 2012)

21

A geologic time scale ontology

A vocabulary for each version

of the International Stratigraphic

Chart

Reuse the ontology

2010

2009

2012

2013

2008

22

isc:LowerTriassic

rdf:type gts:GeochronologicEra , skos:Concept ;

rdfs:comment "younger bound-245.9"@en , "older bound-251 +/-0.4"@en ;

rdfs:label "Lower Triassic Epoch"@en ;

gts:rank gts:Epoch ;

gtrs:end isc:BaseMiddleTriassic ;

gtrs:member isc:Induan , isc:Olenekian ;

gtrs:start isc:BaseMesozoic ;

owl:sameAs <http://dbpedia.org/resource/LowerTriassic> ;

skos:altLabel "下三叠统"@zh , "三畳紀前期"@ja ;

skos:broader isc:Triassic ;

skos:broaderTransitive

isc:Mesozoic , isc:Triassic , isc:Phanerozoic ;

skos:inScheme <http://resource.geosciml.org/classifierscheme/ics/ischart/2010>

;

skos:narrower isc:Olenekian , isc:Induan ;

skos:narrowerTransitive

isc:Induan , isc:Olenekian ;

skos:notation "a1.1.2.3.3"^^gts:EraCode ;

skos:prefLabel "Trias inférieur"@fr , "äldre/undre trias"@sv , "Tidlig/undre

trias"@no , "Tidlig/Nedre Triassisk"@da , "Varhais/Ala-Trias"@fi , "kora/alsó-

triász"@hu , "zgodnji/spodnji trias"@sl , "Spodní trias"@cs , "Раннен/долен

Триаѿ"@bg , "Early/Lower Triassic"@en , "Vroeg/Onder Trias"@nl , "raný/spodný

trias"@sk , "早三叠世"@zh , "前期三畳紀"@ja , "Frühe/Untere Trias (Buntsandstein)"@de , "Wczesny/Dolny Trias"@pl , "Vara/Alam-Triias"@et , "Ankstyvasis/Apatinis Triasas"@lt

, "triassico inferiore"@it , "Triásico Inferior"@pt , "Triásico Inferior"@es ;

foaf:isPrimaryTopicOf

<http://sweet.jpl.nasa.gov/2.2/stateTimeGeologic.owl#LowerTriassic> .

Geologic time vocabulary by

Cox (2011)

(ID 7 in Table 1)

OWL and SKOS are overlaid. This

will necessarily be OWL Full

Can you see the difference between: twc:X rdf:type owl:Class;

rdf:type skos:Concept.

and twc:X rdf:type owl:Class;

rdfs:subClassOf skos:Concept.

(cf. Bechhofer and Miles 2008)

SISSvoc

Vocabulary deployment

• Publish SKOS document at ‘vocabulary URI’

– http://def.seegrid.csiro.au/ontology/geotime/isc-2010

• Load SKOS document in triple-store to provide SPARQL

endpoint

– http://def.seegrid.csiro.au/sparql/isc2010

• Configure SISSvoc API

– http://def.seegrid.csiro.au/sissvoc/isc2010/concept

• Configure redirects

– http://resource.geosciml.org/classifier/ics/ischart/LowerTriassic

−http 303→

– http://def.seegrid.csiro.au/sissvoc/isc2012/resource?uri=http://resource.ge

osciml.org/classifier/ics/ischart/LowerTriassic

(Cox, 2012) {URI} vs http://{service}/resource?uri={URI}

4 Discussion on further works

• We are currently in a pragmatic situation

– Organizations and individuals are free to build ontologies,

vocabularies and develop innovative functions

– As long as the developed ontologies/vocabularies and application

functions can be used to tackle research and/or application

problems in efficient ways

24

Geodata harmonization

(Laxton et al. 2010) (Ma et al. 2012)

Exploratory visualization Vocabulary service

(Cox 2012)

• Ontology/vocabulary evolution

– Geologic time concepts and their descriptions are not static but

continuously evolving, e.g., the time boundaries in the geologic

time scale are being updated continuously

– Ontologies/vocabularies with ID ‘4’, ‘5’, ‘7’ and ‘11’ are

corresponding to the International Stratigraphic Charts 2009, 2008,

2010 and 2012, respectively

– Cox discussed the difference between changes made to a concept

and those made to the description of a concept: if a concept is

changed, then it is a new concept, and if only the description of a

concept is changed, the concept remains. See: https://www.seegrid.csiro.au/wiki/Siss/VocabularyFormalizationInSKOS

25

(cf. Ding and Foo 2002; Noy and Klein 2004; Pavel and Euzenat 2012)

• Ontology/vocabulary mapping

– e.g., Geologic time vocabulary by Cox (2011) makes mappings to

equivalent concepts in DBpedia and SWEET by using owl:sameAs and foaf:isPrimaryTopicOf

– e.g., Brodaric and Probst (2009) used the DOLCE foundational

ontology to aid the mapping and integration between two individual

works: the SWEET ontology and the GeoSciML schema

– Need to maintain persistent Uniform Resource Identifiers (URIs)

and metadata for concepts in developed ontologies and

vocabularies, and thus benefit the mappings between ontologies

and vocabularies

26

• Ontology/vocabulary governance

– the activities related to the directing, guiding, development,

evaluation and revision of ontologies on certain topics

• involves interactions and collaborations, e.g., in summer 2012 we (i.e., as the

ontology users) did some inference tests with the ‘isc-2010.ttl’ ontology (ID 7 in

Table 1) created by Cox (i.e., as the ontology manager), and we found some inconsistencies in that ontology, such as ‘isc:MiddleTriassic

skos:broader isc:MiddleTriassic’ and ‘isc:MiddleTriassic

skos:narrower isc:MiddleTriassic’. We then contacted Cox and he

revised the ontology.

– Gruber (1995): guidelines for evaluating an ontology: clarity,

coherence, extendibility, minimal encoding bias, and minimal

ontological commitment

– Fox and Lynnes: evaluation guidelines w.r.t. the use of an

ontology: contextual relevance, maturity, intended use, and fit for

use http://tw.rpi.edu/web/project/SeSF/workinggroups/OntologyEvaluation 27

• Ontology/vocabulary delivery

– Static service: release the RDF document

– A SPARQL endpoint: RESTful, content negotiation

– User-friendly web pages using Application Programming Interfaces

(APIs, e.g., ELDA)

28

5 Recommendations

• Refer to preceding vocabulary or conceptual schema

works

– There is an ontology spectrum

Glossary Taxonomy Thesaurus Conceptual schema Ontology

• Collaborative works to improve the interoperability of

geoscience ontologies/vocabularies and the geodata

underpinned by them

• Expressivity, implementability and maintainability of

geoscience ontology/vocabulary works and applications

29

(McGuinness 2003; Uschold and Gruninger 2004)

(Fox 2012)

6 Wrap up

• The review shows that we are still in the beginning stage of using

Semantic Web technologies in the field of geoscience

• Those items discussed for geologic time ontologies, such as ontology

evolution, ontology mapping, ontology governance, ontology delivery

and multilingual labels are also applicable to other geoscience

ontologies

• More general recommendations:

– Linking current geoscience ontology/vocabulary works to preceding works by

referring to an ontology spectrum

– Collaborative working to improve the interoperability of ontologies and data within

the geoscience community

– Balancing the expressivity, implementability and maintainability to achieve prioritized

applications of geoscience ontologies

30

Thanks

31

See also

Ma, X., Fox, P., 2013. Recent progress on geologic

time ontologies and considerations for future works.

Earth Science Informatics 6 (1), 31–46.

http://dx.doi.org/10.1007/s12145-013-0110-x

Marshall X Ma

max7@rpi.edu

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