Post on 12-Jan-2016
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The Ontology of Paleobiology
Mathias BrochhausenInstitute 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
What is going on with respect to data collections for paleobiology?
What is going on with respect to biological ontologies?
State of the art:
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 cross-disciplinary 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.
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-CRMISO 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 Goméz-Pérez 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.loa-cnr.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:Entity
snap:Continuant span:Occurrent
BFO: The basic divide
Continuant
Independent Continuant Dependent Continuant
QualityRealizable EntityDispositionFunctionRoleInformation Object
Material ObjectObjectFiat Object PartObject AggregateObject BoundarySite
Occurent
Processual Entity
Spatiotemporal Region
Temporal Region
ProcessFiat Process PartProcess AggregateProcess BoundaryProcessual Context
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 paleoanthropologyInstances of material objects:
...and paleobiology?
Getting some terms straight:
fossil - “something obtained by digging up”. Used for both fossilised material and non-fossilised 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 GeofactBiofact
An object that has been changed by human influence (intentionally).
An object that has been changed by non-human, biologi-cal influence.
An object that has been changed by geological influence.
Artefact GeofactBiofact
An object that has been changed by human influence (intentionally).
An object that has been changed by non-human, biologi-cal influence.
An object that has been changed by geological influence.
Physical Thing
Physical Man-Made Object
Man-Made Thing
is a is a
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 ObjectAggregate
AnorganicObjectCombinedObjectOrganicObject
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 3D-Models both virtual and real based on either making a cast or executing exact measurements.
GenericallyDependentContinuant
InformationObject
Shape
Searching for paleobiological evidence we find:
biological substrate
mineralised morphologies
trace fossils
amount of biological information
Getting some terms straight:
fossil - “something obtained by digging up”. Used for both fossilised material and non-fossilised material
to fossilise - to turn into stone, biomaterial replaced with mineral substances preserving the form.
SpecificallyDependentContinuant
RealizableEntity
RoleFunctionDisposition
Quality
Fossil
Biological Process
Taphonomic Process
Curation/Research Process
propagatebreath
diefeed
excrete
decayfossilize
to be scattered
to be altered by intention
recoveryconservationmeasurementDNA extraction
Occurrent
ProcessualEntity
Process
Curation/ResearchTaphonomicProcessBiologicalProcess
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
RoleFunctionDisposition
Quality
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