MSE 2016 - Full Program

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Lecture

An ontology-based exploration of biological structures and functions by use of historical biological data

Thursday (29.09.2016)
11:15 - 11:30
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The Historical BioData Explorer is a web platform that supports scientists interested in learning from nature to identify suitable biological systems to study and to compare functionalities of phylogenetically very distant organisms based on historical biological data. From the middle of the 20th century on, the scope of biologists shifted from morphological approaches to molecular biology and genetics, by which a small number of model organisms was investigated in great detail. On the contrary, authors of historical biological literature from the time span of about 1870 to 1941 focused in texts and images on the detailed description of biological structures of a broad range of organisms. For this reason, the historical data is still a valuable source for bio-inspired research, yet it disappeared from the field of view of modern laboratories. The historicity of the material makes it difficult to access and biological terminology further impedes material scientists from systematically approaching a wide-ranging search for model organisms. As a result of the lack of well-searchable structural biological data, model organisms are often identified by chance rather than by systematic search or are conveyed from previous research topics without the analysis of alternative systems. To our knowledge, no tool is available to browse a broad range of organisms for structural aspects.

The Historical BioData Explorer closes this gap. It contains historical texts and images from a) the Challenger Expedition Reports (1880) and b) the Handbook of Zoology (from 1923) with a focus on animal motion. The information is extracted, restructured and annotated to be stored in and searchable through an ontology. Ontologies provide the possibility to use logical rules to deduce information that was not directly put in. The motion ontology is linked to current morphological data through the morphological database MorphDBase as well as to other ontologies and to physical and mechanical data of biomaterials. Additionally, a graph search, text mining and organism selection charts are implemented in an integrative, image-based interface. The historical texts and images are supplemented by objects from the Museum of Natural History Berlin and the scientific collection of the Humboldt University.

Thus, the Historical BioData Explorer combines modern information retrieval methods with historical biological data. It allows researchers working in the field of bio-inspired materials, but also designers and architects, to establish structural or functional relations between phylogenetically very different groups of organisms and to systematically approach the identification of model organisms.

Speaker:
Dr. Friederike Saxe
Humboldt Universität
Additional Authors:
  • Dr. Michael Dürfeld
    Humboldt University, Berlin, Germany
  • Linda Winkler
    Humboldt University, Berlin, Germany
  • Markus Mandalka
    Humboldt University, Berlin, Germany
  • Philipp Schröter
    Humboldt University, Berlin, Germany
  • Anne Lange
    Humboldt University, Berlin, Germany
  • Anika Schultz
    Humboldt University, Berlin, Germany
  • Christian Köhler
    ganzgraph gmbh, Bonn, Germany
  • Dr. Clemens Schmitt
    Humboldt University, Berlin, Germany
  • Prof. Dr. Wolfgang Schäffner
    Humboldt University, Berlin, Germany
  • Prof. Dr. Peter Fratzl
    Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany