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The Ontology of Paleobiology

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?

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The Ontology of Paleobiology

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  1. The Ontology of Paleobiology • Mathias Brochhausen • Institute of Formal Ontology and Medical Information Science • Saarland University, Saarbruecken, Germany

  2. 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.

  3. 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

  4. What are the subdisciplines? • Paleobotany • Paleozoology • Paleoanthropology • Paleoecology • Taphonomy • Evolutionary developmental paleobiology

  5. 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.

  6. 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.

  7. 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

  8. State of the art: • What is going on with respect to data collections for paleobiology? • What is going on with respect to biological ontologies?

  9. http://www.ucmp.berkeley.edu/pdn/pdnhomelinks.htm

  10. http://paleodb.org/cgi-bin/bridge.pl

  11. 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

  12. 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

  13. 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

  14. 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.

  15. What is an ontology? • Ontology is concerned with categorizing the elements of reality.

  16. 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).

  17. What is an ontology? • An ontology is a formal explicit specification of a shared conceptualization (R. Studer et al.).

  18. 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.

  19. Ontologies provide reference for multiple sources of data. • The aim is to foster semantic integration of data stored in separate sources.

  20. http://www.obofoundry.org/

  21. 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.

  22. 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.

  23. OBO Foundry ontologies of interest to paleobiology: • Environment Ontology • Common Anatomy Reference Ontology • Mammalian Phenotype Ontology • Phenotypic Quality Ontology • Gene Ontology

  24. 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.

  25. 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.

  26. The CIDOC-CRMISO 21127:2006http://cidoc.ics.forth.gr/index.html

  27. 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.

  28. 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.

  29. We need the means to compare paleobiological data with recent biological evidence.

  30. Case Study Paleoanthropology: • Physical anthropology is the science of human variability in space and time.

  31. 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.

  32. 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.

  33. OWL sublanguages • OWL Lite • OWL DL • OWL Full http://www.w3.org/TR/owl-features/

  34. Ontology editors • Protégé (http://protege.stanford.edu) • OBO-edit (http://oboedit.org) • many more, both, commercial and open source

  35. 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).

  36. 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)

  37. 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.

  38. 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.

  39. 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

  40. BFO: The basic divide

  41. http://www.ifomis.org/bfo

  42. Continuant Independent Continuant Dependent Continuant Quality Realizable Entity Disposition Function Role Information Object Material Object Object Fiat Object Part Object Aggregate Object Boundary Site

  43. http://www.ifomis.org/bfo

  44. Occurent Processual Entity Spatiotemporal Region Temporal Region Process Fiat Process Part Process Aggregate Process Boundary Processual Context

  45. A central problem:

  46. 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.

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