The Ontology of Paleobiology

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An introduction to the methods and resources of ontology with special reference to the disciplines of paleobiology.

Tutorial by Mathias Brochhausen

The disciplines of paleobiology – including paleozoology, paleobotany, paleoanthropology, paleoecology and paleontology – involve a wide network of researchers, each working on different aspects of a complex problem. With respect to both objects of research and methods employed, paleobiology is a scientific enterprise as diverse as biology itself, but with obvious limitations on the kinds of evidence available. This evidence ranges from data pertaining to aDNA samples, bones, fossilized body parts, and artefacts.

As argued in [1], data sharing will be crucial for future research in anthropology and ways must be found to enable integration of databases such as the Human Origins Database (HOD) [2], the database of the Revealing Human Origins Initiative (RHOI) [3], Neogene of the Old World (NOW) [4]. But such integration is difficult because of the widely different approaches taken by the researchers involved. The most obvious example is the hiatus between anthropology relying on molecular biological methods and the classical morphological anthropology based on the study of phenotypes and comparative anatomy.

We will describe the outlines of a paleobiology ontology to be developed according to the guidelines of the OBO Foundry [5] in such a way as to be interoperable with existing ontologies such as the Gene Ontology (GO) and the Environment Ontology (EnvO).

The anthropology-related portions of the ontology will need to contain representations of hominid taxonomical entities, and of biological, geological and cultural specimens, and thus work well with ontology resources created in the museum field. We have already seen considerable progress in the development of museum ontologies and information models of which CIDOC CRM (ISO 21127) is the most conspicuous example [6]. The tutorial will provide participants with a sketch of portions of an eventual paleobiology ontology pertaining specifically to human evolution and the associated anthropological data, including representation of different types of specimens. Topics to be addressed will include:

  • Introduction to Ontology Building
  • Introduction to the Problems of Data Integration in Paleobiology
  • Taxonomical Considerations
  • Creating the Middle Layer of a Paleobiology Ontology
  • The OBO Foundry
  • CIDOC CRM

The tutorial is directed towards students and professionals with an interest in human phylogeny, general taxonomy, ontological aspects of biology and natural history, and museology.

Faculty

Mathias Brochhausen studied philosophy and anthropology at the University of Mainz. He is a researcher and program director at IFOMIS, the Institute for Formal Ontology and Medical Information Science in Saarbrücken, Germany.

References

[1] Delson E, Harcourt-Smith WEH, Frost SR, Norris CA, Databases, Data Access, and Data Sharing in Paleoanthropology: First Steps. Evolutionary Anthropology, 2007, 16: 161-3.

[2] http://www.humanoriginsdatabase.org.

[3] http://rhoi.berkeley.edu.

[4] http://www.helsinki.fi/science/now.

[5] Smith B, Ashburner M, et al. (2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", Nature Biotechnology 25, 1251 - 1255.

[6] http://cidoc.ics.forth.gr/index.html.

Further Reading

Benton MJ, Harper D (1998) Basic Palaeontology, Prentice Hall, Upper Saddle River NJ.

Henke W, Tattersall I (2007) Handbook of Paleoanthropology (Vol. I-III), Springer, Berlin, London, New York.

http://anthropology.net/2008/01/10/data-portability-in-paleoanthropology.

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