The document describes efforts to formalize knowledge in petrology using ontologies. It discusses formalizing facts from databases into sentences in a controlled natural language and then translating those sentences into OWL ontologies. It also discusses developing a definition concentrator ontology to gather and formalize definitions of petrological terms from various sources. The goal is to build a formal theory of petrology through precisely defining concepts and stating relationships between them.

1. Towards OWL-based Knowledge
Representation in Petrology
A.Shkotin, V.Ryakhovsky, D.Kudryavtsev
GIS Department
Vernadsky State Geological Museum
Russian Academy of Sciences
www.sgm.ru
ashkotin@acm.org

2. Contents

Introduction

Fact formalization

Dictionary formalization

Formal definitions

Conclusions and further plans

Acknowledgments

References
2

3. Introduction
Petrology is a science investigating rocks and
their formation conditions.
Large volume of petrological information requiring
systematization, integration and maintenance in a
consistent state is accumulated at present.
These tasks can be solved through knowledge
formalization.
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4. Knowledge Formalization
Final goal: Create a formal theory for the key
concepts of petrology and relationships among
them.
Ontologies, that is conceptual structures
organized on the basis of mathematical logic, play
a pivotal role in the process of creation.
Definitions play a decisive role in a formal theory,
as they specify exactly those concepts whose
properties will be used and studied.
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5. Formal Theory
Building a formal theory of the field of natural
science similar of a mathematical one enables:

Revealing primary concepts

Giving definitions to other concepts

Stating axioms and theorems
5

6. Fact Formalization
6

7. The Approach
Databases are not a knowledge.
They require an essential and thorough
processing to obtain a knowledge.
DB conversion to the traditional form of
knowledge, i.e. knowledge in a natural language,
is the direct way of obtaining knowledge from
data.
The natural language is limited to a CNL. CNL is a
universal means of formal knowledge
presentation. 7

8. 8

9. CNL Sentences. The Approach
Create templates of a CNL sentences to present
all the facts contained in the Proba DB.
Use local (‘internal’) proper names.
Connect words in composite terms using ‘_’ letter.
Global commonly known proper names such as
Iceland, Atlantic_Ocean can be found in a text.
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10. CNL Sentences. Example
PUB5633 is a publication.
PUB5633 title is "A CONTRIBUTION TO THE GEOLOGY OF THE K...".
SAM32994 is a sample. SAM32994 is a rhyolite.
PLC32994 is a place. PLC32994 is a part of Iceland.
SUB469812 is a substance.
WPC469812 is a weight_percent. WPC469812 value is
73.95.
PUB5633 describes SAM32994.
SAM32994 gathering_place is PLC32994.
SAM32994 includes SUB469812.
SUB469812 is a WPC469812 component.
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11. OWL Ontology
All generated sentences are ACE* language
statements.
The sentences are so that the APE* translator
translates them to OWL.
The DB is converted to 1,174 ontologies.
* Attempto Project. http://attempto.ifi.uzh.ch/site/
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12. OWL Ontology #5633
 Classes: place,  Object properties:
publication, rhyolite, component,
sample, substance, gathering_place,
weight_percent. includes, mixture,
part...
 Data properties:  Individuails: Iceland,
authorial_number, PLC32994...,
chemical_formula, PUB5633,
first_page, latitude, SAM32994...,
longitude, reference, SUB469812...,
title, value, year. WPC469812...
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13. Dictionary Ontology
and
Definition Concentrator
13

14. Definition Dictionary
is an important and specific type of knowledge
contains the terms of a subject area and informal
definitions of these terms.
Informal definitions are provided by experts
usually belonging to a scientific school.
Tasks:

Convert a definition dictionary into formal knowledge

Gather definitions given by various schools
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15. Dictionary Entry Example
HARZBURGITE. An ultramafic plutonic rock
composed essentially of olivine and
orthopyroxene. Now defined modally in the
ultramafic rock classification (Fig. 2.9, p.28).
(Rosenbusch, 1887, p.269; Harzburg, Harz
Mts, Lower Saxony, Germany; Tröger 732;
Johannsen v.4, p.438; Tomkeieff p.247)
[IRCGT], p.88
15

16. From Dictionary Text to Ontology
Dictionary
“Dictionary of Terms of Igneous Rocks. 1,567
entries, the overwhelming majority of them being
rock names.
Owner
Inter-Departmental Petrographic Committee in the
Geoscience Division of the Russian Academy of
Sciences.
Text
http://www.igem.ru/site/petrokomitet/slovar.htm
Ontology http://earth.jscc.ru/ontologies/dic.owl
16

17. Definition Concentrator
The goal is to collectively maintain definitions of
scientific terms, including formal definitions.
The ontology of igneous rocks is contained in
webProtege under the dic name.
Some terms are complemented with definitions
from other dictionaries.
Address at Geology portal:
http://earth.jscc.ru/webprotege/
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18. 18

19. Name Spaces
prefix pgc: <http://www.igem.ru/site/petrokomitet/slovar#>
prefix dic: <http://earth.jscc.ru/ontologies/dic.owl#>
prefix gwr: <http://wiki.web.ru/wiki#>
prefix pgcc: <http://www.igem.ru/site/petrokomitet/code#>
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20. Formal Term Meaning Definition
abessedite is
peridotite and mineral_mixture and
contains_mineral only (olivine or hornblende or
phlogopite)
OWL syntax – Manchester.
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21. Formal Definitions
21

22. Primary Source
Le Maitre, L.E., ed. 2002. Igneous Rocks: A
Classification and Glossary of Terms 2nd edition,
Cambridge.
http://amigoreader.com/book/?b=29372
22

23. Building an Algorithm
The classification rules described in
methodologies and recommendations have to be
used to obtain precise definitions and to formalize
them.
We start with a revision of all parts of the
algorithm.
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24. VPC Definitions
Modal content of pyroxenes
VPC_Px(x) = VPC_Opx(x)+VPC_Cpx(x)
Mineral groups for diagrams
VPC_OOC(x) = VPC_Ol(x)+VPC_Opx(x)+VPC_Cpx(x)
VPC_OPH(x) = VPC_Ol(x)+VPC_Px(x)+VPC_hornblende(x)
Modal content of mafic minerals
VPC_M(x) = 100 - (VPC_Q(x)+VPC_A(x)+VPC_P(x)+VPC_F(x))
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25. Qualitative Characteristics
Predicates
pyroclastic, kimberlite, lamproite, lamprophyre,
charnockite, plutonic, volcanic.
Definition
pyroclastic(x) = clastic(x) and
(∀y clast(y) ⋀ part_of(y,x)→ volcanic_eruption_result(y))
DL
Pyroclastic ≡ clastic⊓∀(part_of∘id(clast))-.
volcanic_eruption_result
25

26. 26

27. 27

28. The Use of Reasoners
The described properties can be automatically
verified by loading definitions into a reasoner
working with linear inequalities.
Such reasoners do exist (e.g. Racer), and linear
inequalities can be written using the OWL 2
extension [OWL2LE].
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29. harzburgite
harzburgite(x) =
plutonic(x) and
not (pyroclastic(x) or kimberlite(x) or lamproite(x)
or lamprophyre(x) or charnockite(x))
and VPC_carbonates(x)≤50 and
VPC_melilite(x)≤10 and VPC_M(x) ≥ 90 and
VPC_kalsilite(x)=0 and VPC_leucite(x)=0 and
VPC_hornblende(x)=0 and
0.4*VPC_OOC(x)≤VPC_Ol(x)≤0.9*VPC_OOC(x)
and VPC_Cpx(x)<0.05*VPC_OOC(x)
29

30. Conclusions and Further Plans

A formula is possible Ontology project in

The construction of a petrology:
formal theory started 
Definition

Tools of formal concentrator
knowledge 
Formalization of
maintenance tested [IRCGT]

A definition 
GIS formalization
concentrator 
CRL (Controlled
prototype created Russian language)
30

31. Acknowledgments
We would like to thank

Dr. Stephen M. Richard from Arizona Geological
Survey for comments on the report [otch10], a
helpful discussion and a reference to [BGSRCS]

Pavel Klinov from University of Manchester for
numerous invaluable comments

Dr. Kaarel Kaljurand from Attempto group for the
idea of using proper names
31

32. References
[IRCGT] Le Maitre, L.E., ed. 2002. Igneous Rocks: A
Classification and Glossary of Terms 2nd edition, Cambridge.
url
[BGSRCS] Gillespie, M R, and Styles, M T. 1999. BGS Rock
Classification Scheme, Volume 1, Classification of igneous
rocks. British Geological Survey Research Report, (2nd
edition), RR 99–06. url
[OWL2LE] OWL 2 Web Ontology Language. Data Range
Extension: Linear Equations. url
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