The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical...
-
Upload
gladys-burns -
Category
Documents
-
view
216 -
download
1
Transcript of The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical...
![Page 1: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/1.jpg)
The Ontology of Paleobiology
Mathias BrochhausenInstitute of Formal Ontology and Medical Information Science
Saarland University, Saarbruecken, Germany
![Page 2: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/2.jpg)
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.
![Page 3: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/3.jpg)
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
![Page 4: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/4.jpg)
What are the subdisciplines?
Paleobotany
Paleozoology
Paleoanthropology
Paleoecology
Taphonomy
Evolutionary developmental paleobiology
![Page 5: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/5.jpg)
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.
![Page 6: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/6.jpg)
• 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.
![Page 7: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/7.jpg)
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
![Page 8: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/8.jpg)
What is going on with respect to data collections for paleobiology?
What is going on with respect to biological ontologies?
State of the art:
![Page 10: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/10.jpg)
![Page 12: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/12.jpg)
![Page 13: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/13.jpg)
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
![Page 14: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/14.jpg)
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
![Page 15: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/15.jpg)
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
![Page 16: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/16.jpg)
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.
![Page 17: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/17.jpg)
What is an ontology?
• Ontology is concerned with categorizing the elements of reality.
![Page 18: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/18.jpg)
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).
![Page 19: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/19.jpg)
What is an ontology?
An ontology is a formal explicit specification of a shared conceptualization (R. Studer et al.).
![Page 20: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/20.jpg)
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.
![Page 21: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/21.jpg)
Ontologies provide reference for multiple sources of data.
The aim is to foster semantic integration of data stored in separate sources.
![Page 23: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/23.jpg)
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.
![Page 24: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/24.jpg)
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.
![Page 25: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/25.jpg)
OBO Foundry ontologies of interest to paleobiology:
Environment Ontology
Common Anatomy Reference Ontology
Mammalian Phenotype Ontology
Phenotypic Quality Ontology
Gene Ontology
![Page 26: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/26.jpg)
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.
![Page 27: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/27.jpg)
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.
![Page 28: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/28.jpg)
![Page 29: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/29.jpg)
The CIDOC-CRMISO 21127:2006
http://cidoc.ics.forth.gr/index.html
![Page 30: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/30.jpg)
![Page 31: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/31.jpg)
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.
![Page 32: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/32.jpg)
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.
![Page 33: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/33.jpg)
We need the means to compare paleobiological data with recent
biological evidence.
![Page 34: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/34.jpg)
Case Study Paleoanthropology:
• Physical anthropology is the science of human variability in space and time.
![Page 35: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/35.jpg)
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.
![Page 36: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/36.jpg)
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.
![Page 37: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/37.jpg)
OWL sublanguages
OWL Lite
OWL DL
OWL Full
http://www.w3.org/TR/owl-features/
![Page 38: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/38.jpg)
Ontology editors
Protégé (http://protege.stanford.edu)
OBO-edit (http://oboedit.org)
many more, both, commercial and open source
![Page 39: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/39.jpg)
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).
![Page 40: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/40.jpg)
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)
![Page 41: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/41.jpg)
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.
![Page 42: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/42.jpg)
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.
![Page 43: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/43.jpg)
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
![Page 44: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/44.jpg)
bfo:Entity
snap:Continuant span:Occurrent
BFO: The basic divide
![Page 46: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/46.jpg)
Continuant
Independent Continuant Dependent Continuant
QualityRealizable EntityDispositionFunctionRoleInformation Object
Material ObjectObjectFiat Object PartObject AggregateObject BoundarySite
![Page 48: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/48.jpg)
Occurent
Processual Entity
Spatiotemporal Region
Temporal Region
ProcessFiat Process PartProcess AggregateProcess BoundaryProcessual Context
![Page 49: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/49.jpg)
A central problem:
bfo:Entity
snap:Continuant span:Occurrent
Top down
Bottom up
![Page 50: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/50.jpg)
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.
![Page 51: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/51.jpg)
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
![Page 52: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/52.jpg)
Case Study paleoanthropologyInstances of material objects:
![Page 53: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/53.jpg)
...and paleobiology?
![Page 54: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/54.jpg)
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.
![Page 55: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/55.jpg)
Searching for paleobiological evidence we find:
biological substrate
mineralised morphologies
trace fossils
![Page 56: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/56.jpg)
• 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.
![Page 57: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/57.jpg)
Bones potentially give us full biological information, including histology and genetics.
Stones conserve some biological features, especially the morphology.
![Page 58: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/58.jpg)
Given the growing importance of molecular methods in paleobiology this distinction becomes more and more important.
![Page 59: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/59.jpg)
Starting with a Middle Ontology for Paleobiology
span:Object
OrganicObject AnorganicObject
![Page 60: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/60.jpg)
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.
![Page 61: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/61.jpg)
The artefact problem
![Page 62: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/62.jpg)
![Page 63: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/63.jpg)
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.
![Page 64: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/64.jpg)
![Page 65: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/65.jpg)
![Page 66: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/66.jpg)
Influences creating artificial results in paleobiology
Artefact
Geofact
Biofact
![Page 67: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/67.jpg)
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.
![Page 68: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/68.jpg)
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.
![Page 69: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/69.jpg)
Physical Thing
Physical Man-Made Object
Man-Made Thing
is a is a
![Page 70: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/70.jpg)
Examples for man-made thing:
Beethoven’s 5th Symphony
Michelangelo’s David
Einstein’s Theory of General Relativity
The taxon Fringilla coelebs Linnaeus, 1785
![Page 71: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/71.jpg)
Starting with a Middle Ontology for Paleobiology
span:Object
OrganicObject AnorganicObject
![Page 72: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/72.jpg)
What about an artefact consisting of:
a human skull
clay
human hair
some shells?
![Page 73: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/73.jpg)
Is it an object aggregate?
MaterialEntity
Object ObjectAggregate
![Page 74: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/74.jpg)
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.
![Page 75: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/75.jpg)
MaterialEntity
Object ObjectAggregate
AnorganicObjectCombinedObjectOrganicObject
![Page 76: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/76.jpg)
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.
![Page 77: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/77.jpg)
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.
![Page 78: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/78.jpg)
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.
![Page 79: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/79.jpg)
![Page 80: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/80.jpg)
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.
![Page 81: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/81.jpg)
GenericallyDependentContinuant
InformationObject
Shape
![Page 82: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/82.jpg)
Searching for paleobiological evidence we find:
biological substrate
mineralised morphologies
trace fossils
amount of biological information
![Page 83: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/83.jpg)
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.
![Page 84: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/84.jpg)
SpecificallyDependentContinuant
RealizableEntity
RoleFunctionDisposition
Quality
Fossil
![Page 85: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/85.jpg)
Biological Process
Taphonomic Process
Curation/Research Process
propagatebreath
diefeed
excrete
decayfossilize
to be scattered
to be altered by intention
recoveryconservationmeasurementDNA extraction
![Page 86: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/86.jpg)
Occurrent
ProcessualEntity
Process
Curation/ResearchTaphonomicProcessBiologicalProcess
![Page 87: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/87.jpg)
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.
![Page 88: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/88.jpg)
MaterialEntity
Object ObjectAggregate
![Page 89: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/89.jpg)
SpecificallyDependentContinuant
RealizableEntity
RoleFunctionDisposition
Quality
![Page 90: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/90.jpg)
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.
![Page 91: The Ontology of Paleobiology Mathias Brochhausen Institute of Formal Ontology and Medical Information Science Saarland University, Saarbruecken, Germany.](https://reader035.fdocuments.net/reader035/viewer/2022062801/56649e7d5503460f94b8075f/html5/thumbnails/91.jpg)
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: