Universitatea Politehnica din Bucuresti

Facultatea de Automatica si Calculatoare

Programul de master Administrarea Bazelor de Date

Ontologies KESE

Masterand: Anghelescu Andreea Maria

Question 1.

i. Add short textual definitions for the concepts Shirt, Collar, Cuff and Sleeve. Use the comment field in
the annotations window, and save the modified OWL file. In your written answer, explain the existing
Description Logic definitions of Shirt, ShirtCollar, and ShirtSleeve in plain English or Romanian.
Marks: 10%
Shirt is a subclass of Garment. Sgt Pepper shirts line has the following subclasses: GeorgeShirt,
JohnShirt, PaulShirt and RingoShirt.
ShirtCollar is a subclass of Collar. An individual is a member of the class ShirtCollar only if it's a
member of Collar and it is part of at least one shirt.
ShirtSleeve is a subclass of Sleeve. An individual is a member of the class ShirtSleeve only if it's
a member of Sleeve, it's part of at least one shirt and has at least one cuff.
Shirt - A long- or short-sleeved garment for the upper part of the body, usually lightweight and
having a collar and a front opening.
Collar The part of a shirt, coat, dress, blouse, etc., that encompasses the neckline of the garment
and is sewn permanently to it, often so as to fold or roll over.
Cuff A fold or band serving as a trimming or finish for the bottom of a sleeve.
Sleeve - The part of a garment that covers the arm, varying in form and length but commonly tubular.
ii. Extend the ontology by adding 6 types of Fabric. Ensure that the appropriate axioms are added.
Describe the new concepts and axioms in your written answer, and save the modified OWL file.
Marks: 10%
I added the following types of fabric: CottonFabric, KnitFabric , LeatherFabric, PolyesterFabric,
SilkFabric and WoolFabric. These classes are disjoint: a shirt can only be made of a single fabric.
iii. Explain why a RingoShirtSleeve must have a Cuff and at least one Button by referring to the
definitions of these concepts, and those of the relations used in the definitions. Show that the reasoner can
make these inferences by adding a superclass to RingoShirtSleeve that asserts the contrary and then
classifying the ontology. State the class restriction used in each case, and describe the result of
classification. Return the ontology to its state on completion of part ii. before answering the following
questions. Note that the parts of a garment may have a specific design that is reflected in their name (e.g.
RingoShirtSleeve), or may be generic (e.g. Cuff and Button).
Marks: 10%
ShirtSleeve parent class requires to have a Cuff - necessary condition for an object to be included
in the class. The condition appears at Least One Button Cuff Some of restriction hasPart because this
class contains also restrictions (hasPart Some Button) and (partOf Some Sleeve). It follows that any
RingoShirtSleeve must have a Cuff, any Cuff must have a Button, and any RingoShirtSleeve must have a
Button.

iv. Add a logical definition for a RingoShirt to require that these items have some RingoShirtSleeve and
lack a Collar. Modify any conflicting definitions to ensure that the ontology remains consistent when it is
classified. Extend the definion of RingoShirt once more to specify the Fabric to be used (use one of the
classes introduced in part ii.). Define any new relationships required, and save the ontology once more.
Marks: 10%
I added the definition for RingoShirt hasPart exactly 0 Collar and hasPart some
RingoShirtSleeve. I deleted the definition hasPart some Collar, because interfered with the new definition
with exactly 0 Collar, and the Reasoner was giving some errors, and the ontology wasnt anymore
consistent.
I also extend the definition of RingoShirt as hasPart some CottonFabric, and the ontology is
still consistent after using the Reasoner.
Question 2.
Choose an ontology that is publicly available, and summarise its development process, level
of formalisation and applications. Make sure to cover the domain, purpose, scope and
granularity when discussing the design, and to give examples of concept definitions.
You may select the DOLCE Ontology, Cyc Ontology (www.cyc.com), Gene Ontology
(www.geneontology.org), Foundational Model of Anatomy
(http://www.digitalanatomist.com/), or the Enterprise Ontology, but you are not required to do
so. However, ensure that the ontology you do select can be cited (i.e. there are papers
published about it) and ensure that you can access the class definitions.
Include the citations, example concept definitions and diagrams in your answer.
Marks: 25% - you should submit an answer of approximately 750 words (excluding
citations).
DOLCE Ontology
Developed by Nicola Guarino and his associates at the Laboratory for Applied Ontology (LOA),
the Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE) is the first module of the
WonderWeb foundational ontologies library. As implied by its acronym, DOLCE has a clear cognitive
bias, in that it aims at capturing the ontological categories underlying natural language and human
common sense. DOLCE, however, does not commit to a strictly referentialist metaphysics related to the
intrinsic nature of the world. Rather, the categories it introduces are thought of as cognitive artifacts,
which are ultimately depending on human perception, cultural imprints and social conventions. In this
sense, they intend to be just descriptive (vs prescriptive) notions, that assist in making already formed
conceptualizations explicit. DOLCE is an ontology of particulars, in the sense that its domain of discourse
is restricted to them. Of course, universals are used to organize and characterize the particulars, but they
are not themselves subject to being organized and characterized (e.g., by means of metaproperties).
The development of this library has been guided by the need of a reliable set of foundational
ontologies that can serve as
- Starting point for building other ontologies,
- Reference point for easy and rigorous comparisons among different ontological approaches,
- Rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata
standards (by manually mapping them into some general module(s) in the library).
A basic choice adopted by DOLCE is the so-called multiplicative approach: different entities can
be co-located in the same space-time. This assumption allows us to make justice of incompatible essential
properties. A classical example is the distinction between a vase and its amount of clay: the vase does not
survive a radical change in shape or topology while the amount of clay does. DOLCE assumes that the
vase and the corresponding amount of clay are two distinct things, yet colocated, so that we can talk of
2

the shape of the vase (but not of the clay) or the mass of the clay (inherited by the vase) without fear of
contradictory claims.
Another foundamental feature of DOLCE is the distinction between enduring and perduring
entities, i.e. between what philosophers usually call continuants and occurrents. For instance, my copy of
the newspaper I bought today is wholly present (and endurant), while some temporal parts of my reading
the newspaper is not (a perdurant). The main relation between endurants and perdurants is that of
participation: an endurant lives in time by participating in some perdurant(s). Other important notions and
relations are characterized in DOLCE, among the notions we recall Qualities, Physical Objects, Social
Objects, Events, Processes, Temporal Regions and Spatial Regions; among the relations let us mention
Participation, Parthood, and Constitution.
DOLCE has quickly become a standard in formal ontology and, thanks to its availability
in several formats (like KIF and OWL) with modules specialized for specific subdomains and
connections to natural languages resources (like WordNet), it is used by several researchers around the
world (see www.loa-cnr.it/DOLCE.html for more information and a partial list of users). Applications
using DOLCE as a formal tool for the semantic integration of data span several areas like computational
linguistics, agriculture, medicine, cultural resources, banking and insurance organization, legal documents
management, software engineering, knowledge engineering, and mobile robotics.

DOLCE Taxonomy
DOLCE's Basic Ontological Choices
Objects (aka continuants or endurants) and Events (aka occurrences or perdurants)
distinct categories connected by the relation of participation.
Qualities
Individual entities inhering in Objects or Events
can live/change with the objects they inhere in
Instance of quality kinds, each associated to a Quality Space representing the "values" (qualia) that
qualities (of that kind) can assume. Quality Spaces are neither in time nor in space.
Multiplicative approach
Different Objects/Events can be spatio-temporally co-localized: the relation of constitution is
considered.
Objects and Events
3

 Objects (3D continuants)

Objects participate to Events
Qualities and qualia
Linguistic evidence
This rose is red
Red is a color
This rose has a color
The color of this rose turned to brown in one week
Red is opposite to green and close to brown
The patients temperature is increasing
The doctor measured the patient's temperature
Each object or event comes with certain qualities that permanently inhere to it and are unique of it
Qualities are perceptually mapped into qualia, which are regions of quality spaces.
Properties hold because qualities have certain locations in their quality spaces.
Each quality type has its own quality space
Qualities and qualia
Linguistic evidence
This rose is red
Red is a color
This rose has a color
The color of this rose turned to brown in one week
Red is opposite to green and close to brown
The patients temperature is increasing
The doctor measured the patient's temperature
Each object or event comes with certain qualities that permanently inhere to it and are unique of it
Qualities are perceptually mapped into qualia, which are regions of quality spaces.
Properties hold because qualities have certain locations in their quality spaces.
Each quality type has its own quality space
Whats special with qualities?
A simple attribute-value structure is not enough as a representation formalism: you need to put
individual qualities in the domain of discourse
Differently from instances of other ottributes, individual qualities are existentially dependent on their
bearers
The so-called determinable/determinate issue is not actually an issue:
All regions in a quality space correspond to determinables
Corresponding properties holding for objects with qualities in these spaces are determinate
Red-color vs. red-thing.
redness (a quality type) is very different from red (a color region) and has a quality space very different
from that of colors...
Abstract vs. Concrete Entities
Concrete:
located (at least) in time
Abstract - two meanings:
- Result of an abstraction process (something common to multiple exemplifications)
- Not located in space-time (no inherent spatial or temporal location)
Examples: propositions, sets, symbols, regions, etc.
Quality regions and quality spaces are abstract entities
Mereological sums (of concrete entities) are concrete, the corresponding sets are abstract.
Physical vs. Non-physical Objects
Physical objects
Inherent spatial localization
4

 Not necessarily dependent on other objects

Non-physical objects
No inherent spatial localization
Dependent on agents
mental (depending on singular agents)
social (depending on communities of agents)
Agentive: a company, an institution
Non-agentive: a law, the Divine Comedy, a linguistic system
Descriptions, an extension of DOLCE
Citations:
From the WonderWeb Deliverable D17 The WonderWeb Library of Foundational Ontologies
Preliminary Report Paper (Claudio Masolo, Stefano Borgo, Aldo Gangemi, Nicola Guarino, Alessandro
Oltramari, Luc Schneider ISTC-CNR c/o ISIB-CNR, C.so Stati Uniti, 4 35127 Padova Italy).
Objects
The main characteristic of objects is that they are endurants with unity. However, they have no common
unity criterion, since different subtypes of objects may have different unity criteria. Differently from
aggregates, (most) objects change some of their parts while keeping their identity, they can have therefore
temporary parts. Often objects (indeed, all endurants) are ontologically independent from occurrences
(discussed below). However, if we admit that every object has a life, it is hard to exclude a mutual
specific constant dependence between the two. Nevertheless, we may still use the notion of dependence to
(weakly) characterize objects as being not specifically constantly dependent on other objects.
Features
Typical examples of features are parasitic entities such as holes, boundaries, surfaces, or stains, which
are generically constantly dependent on physical objects 3 (their hosts). All features are essential wholes,
but, as in the case of objects, no common unity criterion may exist for all of them. However, typical
features have a topological unity, as they are singular entities. Some features may be relevant parts of
their host, like a bump or an edge, or places like a hole in a piece of cheese, the underneath of a table, the
front of a house, which are not parts of their host
Question 3.
Describe the proposals made by Carl Linnaeus for organising living things into a taxonomy,
and the legacy of his work. Academic review articles should be cited; begin with those on the
Nature website: http://www.nature.com/nature/focus/linnaeus300/ Include the citations in
your answer.
Marks: 25% - you should submit an answer of approximately 500 words (excluding citations).
Submission. Submit your written answers on paper. Submit the edited clothing.owl file
electronically.
Carl Linnaeus, also known after his ennoblement as Carl von Linn, was a Swedish botanist,
physician, and zoologist, who laid the foundations for the modern biological naming scheme of binomial
nomenclature. He is known as the father of modern taxonomy, and is also considered one of the fathers of
modern ecology. Many of his writings were in Latin, and his name is rendered in Latin as Carolus
Linnus (after 1761 Carolus a Linn).
In his Imperium Naturae, Linnaeus established three kingdoms, namely Regnum Animale,
Regnum Vegetabile and Regnum Lapideum. This approach, the Animal, Vegetable and Mineral
Kingdoms, survives today in the popular mind, notably in the form of the parlour game question: "Is it
animal, vegetable or mineral?". The work of Linnaeus had a huge impact on science; it was indispensable
as a foundation for biological nomenclature, now regulated by the nomenclature codes. Two of his works,
the first edition of the Species Plantarum (1753) for plants and the tenth edition of the Systema Naturae
(1758), are accepted as part of the starting points of nomenclature; his binomials (names for species) and
5

generic names take priority over those of others. However, the impact he had on science was not because
of the value of his taxonomy.
The establishment of universally accepted conventions for the naming of organisms was
Linnaeus' main contribution to taxonomyhis work marks the starting point of consistent use of binomial
nomenclature. During the 18th century expansion of natural history knowledge, Linnaeus also developed
what became known as the Linnaean taxonomy; the system of scientific classification now widely used in
the biological sciences.
The Linnaean system classified nature within a nested hierarchy, starting with three kingdoms.
Kingdoms were divided into classes and they, in turn, into orders, and thence into genera (singular:
genus), which were divided into Species (singular: species). Below the rank of species he sometimes
recognized taxa of a lower (unnamed) rank; these have since acquired standardised names such as variety
in botany and subspecies in zoology. Modern taxonomy includes a rank of family between order and
genus and a rank of phylum between kingdom and class that were not present in Linnaeus' original
system.
Linnaeus' groupings were based upon shared physical characteristics, and not simply upon
differences. Of his higher groupings, only those for animals are still in use, and the groupings themselves
have been significantly changed since their conception, as have the principles behind them. Nevertheless,
Linnaeus is credited with establishing the idea of a hierarchical structure of classification which is based
upon observable characteristics and intended to reflect natural relationships. While the underlying details
concerning what are considered to be scientifically valid "observable characteristics" have changed with
expanding knowledge (for example, DNA sequencing, unavailable in Linnaeus' time, has proven to be a
tool of considerable utility for classifying living organisms and establishing their evolutionary
relationships), the fundamental principle remains sound.
Citations from http://www.nature.com/nature/focus/linnaeus300/
The legacy of Linnaeus
Every plant and animal has a mitochondrial cytochrome oxidase I gene, and its sequence helps
researchers assign that plant or animal to a given species, with some degree of certainty. The precise
degree of the certainty obtained using this 'barcode' sequence is a matter of some debate, but such
sequences are clearly useful to both taxonomists and those who use applied taxonomy. And the industrialscale sequencing that allowed Craig Venter's ocean-metagenomics consortium to deposit billions of letters
of sequence from hundreds of thousands of microbe genes into the GenBank database this week opens up
even more possibilities.
The ability to peer into living things and inspect the evolutionary scorecard encoded in their
genes has transformed the whole of biology, but few fields have had their core assumptions challenged as
deeply as taxonomy. From the time of Carl Linnaeus, born 300 years ago this May, taxonomy has relied
on the observation and comparison of physical forms. Now it is supplemented by access to what would
once have been seen not as form, but as essence.
Linnaeus himself sought a universal classification of all creation, animal, vegetable and mineral.
His categorizations were not uniformly valuable, but his systematic spirit, his stress on the concept of
species, and the formal but adaptable conventions of nomenclature he introduced have endured. Nature is
glad to celebrate his legacy in this special issue.
Yet Linnaeus's classification was itself a response to a changing world a world in which
Europe's growing hegemony was bringing new species into the realm at headlong speed. Linnaeus's own
experience of it was bounded by France to the south and Lapland to the north, but the 'apostles' who
carried forth his words and sent back samples and descriptions sailed out from Sweden to Arabia, the
Americas north and south, China, Japan and the Pacific. Two sailed with Captain Cook, sending back
samples from the parts of the Pacific now being sieved for genes.
The various inventories that Linnaeus produced grew ever longer. But while today's world
continues to expand in many ways, in some, including those most important to taxonomy, it is shrinking.
The creationist Linnaeus was able to assert that "we can count as many species now as were created at the
6

beginning", but today's taxonomists suspect with near certainty that species are being irretrievably lost to
science at an ever-quickening rate.