The Ontology of Paleobiology
Mathias Brochhausen
Institute of Formal Ontology and Medical Information Science
Saarland University, Saarbruecken, Germany
Paleobiology ontology “tour guide”
What is going on in paleobiology?
What is (an) ontology?
What is going on in biomedical ontologies?
Let‘s get started.
What is paleobiology?
•
Paleobiology (sometimes spelled
palaeobiology) is a growing and comparatively
new discipline which combines the methods
and findings of the natural science biology with
the methods and findings of the earth science
paleontology.
•
Wikipedia, 09 July 2009
What are the subdisciplines?
Paleobotany
Paleozoology
Paleoanthropology
Paleoecology
Taphonomy
Evolutionary developmental paleobiology
Why do we need ontologies in
paleobiology?
In order to make comparative studies both
across time - e.g.in paleoecology - and space
-e.g. in evolutionary developmental
paleobiology, and especially across
paleobiology and recent data.
Data in paleobiology are extremely sparse.
•
Note that this is not a number for paleobiolo-gical
specimens, but for prehistorical ones. We expect
the number for paleobiology to be even smaller.
Time in paleobiology
3 500 000 000 B.P.: Oldest Stromatolite fossils
7 000 000 B.P.:Oldest possible hominine fossil
160 000 B.P.:Oldest Homo sapiens idaltu
State of the art:
What is going on with respect to data
collections for paleobiology?
What is going on with respect to biological
ontologies?
http://www.ucmp.berkeley.edu/pdn/pdnhomelinks.htm
http://paleodb.org/cgi-bin/bridge.pl
Databases from Delson et al., 1
Primate Morphology Online, PRIMO
Human Origins Database, HUD
Smithsonian Paleoanthropology Database
Revealing Human Origins Initiative, RHOI
Neanderthal Studies Professional Online
System, NESPOSAncient Human Occupation
of Britain, AHOB
digital@rchive for Fossil Hominoids
Databases from Delson et al., 2
European Virtual Anthropology Network, EVAN
Siwalik Database Project
Neogene Old World Mammals, NOW
Knowledge-based Archaeological Data
Integration System, KADIS
Transvaal Museum Database
National Museum of Kenya Database, NMK
Databases from Delson et al., 3
National Museum of Kenya Database, NMK
Institute of Vertebrate Paleontology and
Paleoanthropology Site Database, IVPP
AMNH Vertebrate Zoology Catalogue
Paleoportal
The situation regarding paleobiology
relevant databases:
There already exists a huge amount of
distributed data.
Some of the databases are extremely
restricted in coverage, e.g. HUD.
Others are restricted regarding their domain.
This will cause problems with respect to crossdisciplinary studies.
What is an ontology?
•
Ontology is concerned
with categorizing the
elements of reality.
What is an ontology?
Ontology as a branch of philosophy is the
science of what is, of the kinds and structures
of the objects, properties and relations in
every area of reality. In simple terms it seeks
the classification of entities (B. Smith).
What is an ontology?
An ontology is a formal explicit specification of
a shared conceptualization (R. Studer et al.).
What is an ontology?
An ontology is a formal explicit specification of
universals in reality and the relations existing
between these universals. The entities can be
viewed from different perspectives.
Ontologies provide
reference for multiple
sources of data.
The aim is to foster
semantic integration of
data stored in separate
sources.
http://www.obofoundry.org/
What is the OBO Foundry?
•
The OBO Foundry is a collaborative experiment
involving developers of science-based ontologies who
are establishing a set of principles for ontology
development with the goal of creating a suite of
orthogonal interoperable reference ontologies in the
biomedical domain. The groups developing ontologies
who have expressed an interest in this goal are listed
below, followed by other relevant efforts in this domain.
The OBO Foundry and ontology
evaluation
•
The OBO Foundry provides one means to
ensure high quality in ontology development.
•
The principles of the OBO Foundry foster
distributed development according to best
practice.
OBO Foundry ontologies of interest to
paleobiology:
Environment Ontology
Common Anatomy Reference Ontology
Mammalian Phenotype Ontology
Phenotypic Quality Ontology
Gene Ontology
The situation regarding biological
ontologies:
The number of ontologies for the biological
and biomedical arena is growing daily.
Ontologies specifically adressing
paleobiological issues are lacking in the OBO
Foundry.
Case Study Paleoanthropology
An important ontological ressource with
respect to paleoanthropology is the
Foundational Model of Anatomy
(http://sig.biostr.washington.edu/projects/fm),
which is a member in the OBO Foundry.
Cranial measurement points that are
commonly used in Physical Anthropology are
already in the FMA.
The CIDOC-CRM
ISO 21127:2006
http://cidoc.ics.forth.gr/index.html
CIDOC Conceptual Reference Model
...provides definitions and a formal structure
for describing the implicit and explicit concepts
and relationships used in cultural heritage
documentation.
...provides a semantic framework for sharing
information on cultural heritage.
CIDOC Conceptual Reference Model
...provides definitions and a formal structure
for describing the implicit and explicit concepts
and relationships used in cultural heritage
documentation.
...provides a semantic framework for sharing
information on cultural heritage.
We need the means to compare
paleobiological data with recent
biological evidence.
Case Study Paleoanthropology:
•
Physical anthropology
is the science of
human variability in
space and time.
Let‘s get started.
A paleobiology ontology toolkit:
Decide about ontology format and editor.
Decide about Upper Ontology.
Survey the domain.
Identify the tough ontological questions.
Ontology languages
Web Ontology Language, OWL
Open Biological Ontologies, OBO
For details on other languages see GomézPérez et al. (2004) Ontological Engineering,
Springer, London, Berlin, Heidelberg.
OWL sublanguages
OWL Lite
OWL DL
OWL Full
http://www.w3.org/TR/owl-features/
Ontology editors
Protégé (http://protege.stanford.edu)
OBO-edit (http://oboedit.org)
many more, both, commercial and open
source
What is an Upper Ontology?
•
An upper ontology is limited to concepts that
are meta, generic, abstract and philosophical,
and therefore are general enough to address
(...) a broad range of domain areas. Concepts
specific to given domains will not be included;
however, this standard will provide a structure
and a set of general concepts upon which
domain ontologies (...) could be constructed
(http://suo.iee.org).
Examples for Upper Ontologies
Suggested Upper Merged Ontology SUMO
(http://suo.ieee.org/SUO/SUMO/index.html)
Basic Formal Ontology BFO
(http://www.ifomis.org/bfo)
Descriptive Ontology for Linguistic and
Cognitive Engineering DOLCE (http://www.loacnr.it/DOLCE.html)
Why should we use an Upper
Ontology?
Using an Upper Ontology fosters subsequent
harmonisation with other pre-exisiting
ontologies, for instance in the OBO Foundry.
The existence of an Upper level supports
ontology evaluation.
Why should we use an Upper
Ontology?
•
But most of all:
Starting from an Upper Level helps to stay
clear from epistemological considerations. It
provides the right, ontological frame of mind.
Basic Formal Ontology
philosophically sound Upper Ontology
tested for biomedical and topographical
ontology development
developed by P. Grenon and B. Smith
OWL-implementation by H. Stenzhorn
BFO: The basic divide
bfo:Entity
snap:Continuant
span:Occurrent
http://www.ifomis.org/bfo
Continuant
Independent Continuant
Material Object
Object
Fiat Object Part
Object Aggregate
Object Boundary
Site
Dependent Continuant
Quality
Realizable Entity
Disposition
Function
Role
Information Object
http://www.ifomis.org/bfo
Occurent
Processual
Entity
Process
Fiat Process Part
Process Aggregate
Process Boundary
Processual Context
Spatiotemporal
Region
Temporal
Region
A central problem:
bfo:Entity
snap:Continuant
span:Occurrent
Top down
Bottom up
Strategy
Start the ontology development process with
building a sound hierarchy.
Make sure to exclusively use formal is_a
relation in the hierarchy.
Stay clear of multiple inheritance.
Formal is_a
•
Given classes/types/universals A and B
•
A is a proper subclass/subtype/subuniversal of
B
•
if and only if all members of A are members of
B and A is not equal to B
Case Study paleoanthropology
Instances of material objects:
...and paleobiology?
Getting some terms straight:
fossil - “something obtained by digging up”.
Used for both fossilised material and nonfossilised material
to fossilise - to turn into stone, biomaterial
replaced with mineral substances preserving
the form.
Searching for paleobiological evidence we
find:
biological substrate
mineralised morphologies
trace fossils
•
It is important to note that these different types
of specimens are kept separat in the ontology.
•
Especially since the differences lead to
differences in the kind of biological information
we may derive from them.
Bones potentially give
us full biological
information, including
histology and genetics.
Stones conserve some
biological features,
especially the
morphology.
Given the growing
importance of
molecular methods in
paleobiology this
distinction becomes
more and more
important.
Starting with a Middle Ontology for
Paleobiology
span:Object
OrganicObject
AnorganicObject
The organic-anorganic distinction in
paleobiology ontology
Organic Objects are results of biological
processes.
Anorganic Objects are not results of biological
processes.
Note: The organic-anorganic distinction in paleobiology ontology differs
considerably from the same distinction in chemistry.
The artefact problem
Introducing “Taphonomy”
The term stems from the greek word for
“burial.”
Refers to the scientific study of the decay and
fossilisation of (former) organisms.
Reference: Shipman P (1981) Life History of a
Fossil. An Introduction to Taphonomy and
Paleoecology, Cambridge/Mas.
Influences creating artificial results in
paleobiology
Artefact
Geofact
Biofact
Artefact
Biofact
An object that has
An object that has
been changed by
been changed by
non-human,
human influence
biologi-cal
(intentionally).
influence.
Geofact
An object that has
been changed by
geological
influence.
Artefact
Biofact
An object that has
An object that has
been changed by
been changed by
non-human,
human influence
biologi-cal
(intentionally).
influence.
Geofact
An object that has
been changed by
geological
influence.
Physical Thing
is a
Man-Made Thing
is a
Physical Man-Made Object
Examples for man-made thing:
Beethoven’s 5th Symphony
Michelangelo’s David
Einstein’s Theory of General Relativity
The taxon Fringilla coelebs Linnaeus, 1785
Starting with a Middle Ontology for
Paleobiology
span:Object
OrganicObject
AnorganicObject
What about an artefact
consisting of:
a human skull
clay
human hair
some shells?
Is it an object aggregate?
MaterialEntity
Object
ObjectAggregate
Is it an object aggregate?
Definition: A material entity
[snap:MaterialEntity] that is a mereological
sum of separate object [snap:Object] entities
and possesses non-connected boundaries.
Examples: a heap of stones, a group of
commuters on the subway, a collection of
random bacteria, a flock of geese, the patients
in a hospital.
MaterialEntity
Object
OrganicObject
ObjectAggregate
CombinedObject
AnorganicObject
Combined Object
Are by definition composed of proper parts some of
which are organic objects and some of which are
anorganic objects.
From this follows that we need a property (relation)
in our ontology linking proper parts to the objects
they are proper parts of.
For now, we do not need to address the problem
whether combined objects that are not artefacts
exist.
Properties/Relations for the
paleobiology ontology
Representing relations beyond the is_a
relation is one of the chief assets of ontologies
against taxonomies.
The paleobiology ontology ought to be
oriented on biological evidence since
comparative studies with recent biology
constitute one of the main motives.
Introducing: Relation Ontology (RO)
RO contains core relations used in the OBO
Foundry ontologies.
Formal definitions for the relations are given.
RO can be imported into any OWL ontology.
Mineralised morphologies
Fossilised specimens contain information
about morphologies of past organisms.
Morphology is the form of something.
Information on forms can be given in 3DModels both virtual and real based on either
making a cast or executing exact
measurements.
GenericallyDependentContinuant
InformationObject
Shape
Searching for paleobiological evidence we
find:
amount of biological
information
biological substrate
mineralised morphologies
trace fossils
Getting some terms straight:
fossil - “something obtained by digging up”.
Used for both fossilised material and nonfossilised material
to fossilise - to turn into stone, biomaterial
replaced with mineral substances preserving
the form.
SpecificallyDependentContinuant
RealizableEntity
Disposition
Function
Quality
Role
Fossil
Biological Process
Taphonomic
Process
Curation/Research
Process
propagate
breath
die
feed
excrete
decay
fossilize
to be scattered
to be altered by
intention
recovery
conservation
measurement
DNA extraction
Occurrent
ProcessualEntity
Process
BiologicalProcess
TaphonomicProcess
Curation/Research
Additional discussion: What are
species?
In most paleobiological subdisciplines species
play a major role.
Ontologically we need to distinguish between
the status of “species” and individual species.
MaterialEntity
Object
ObjectAggregate
SpecificallyDependentContinuant
RealizableEntity
Disposition
Function
Quality
Role
Conclusions
Building a paleobiology ontology requires to
keep track of ontological issues not commonly
found in other biological ontologies.
Keeping apart the subjects of research and
the research process is far more difficult than
in other biological disciplines.
if you have any questions, comments or in case you
want to cooperate in making paleobiolgy ontology fit for
the OBO Foundry please contact me:
•mathias.brochhausen@ifomis.uni-saarland.de