Knowledge Management

Background

In the life science a growing amount of data is produced. Many projects process this data, also on a large scale, and produce remarkable results. What is still missing in some cases is the overall view on the data. Are the data from two projects comparable and generated following the same protocol. What are the biological entities represented by the data?

Head of the group: Dr. Dönitz

Research foci

Wordcloud of the project

We work in different projects to make data available to the community. This involves to define data formats, implement processing and deployment pipelines. We also  work with the methods of the semantic web, in particular ontologies and their usage are often a great benefit for projects to better define entities or facilitate a semantic search.

Cooperation with other research groups, e.g. form the biology ensures that the projects have fulfill an important need of the scientific community and stimulate through the interdisciplinary work.

Current projects

MTB-Reporting

In this project we aim to develop a tool that suggest therapies for tumor patients based on their biomarkers. For more details please see the project page.

iBeetle-Base

iBeetle-Base is a joined project together with the Dept. of Evolutionary Developmental Genetics. Initially this database provides access to the phenotypic annotations gathered by a whole genome RNAi screen in the red flour beetle Tribolium castaneum. Currently iBeetle-Base is funded by the DFG in the project titled "iBeetle-Base: Building an Interconnected, Interactive and Extendable Repository for Phenotypic Data". More

TFClass

Transcription factors are a key player in gene regulation. Beside of binding sequence, the evolution and relations of transcription factors are important to understand and predict the function of transcription factors. In the transcription factor classification project we  build up the classification of transcription factores  TFClass based on their DNA binding domain.

MyPathSem

In the MyPathSem project we aim, in a collaboration with other Department of the UMG, to extract the patient specific parts of the molecular networks. For more information please check the project site.

 EndoNet

The intercellular signalling is crucial for every multicellular organism. The manual annotated information ressource EndoNet collects information about the participants of this network, i.e. messenger, receptors, cells or tissues, and combines them with stimuli and phenotypes to network.

Publications

Selected publications:

  • Dönitz J, Gerischer L, Hahnke S, Pfeiffer S, Bucher G. Expanded and updated data and a query pipeline for iBeetle-Base. Nucleic Acids Res. 2018;46:D831–5.
  • Wingender E, Schoeps T, Haubrock M, Krull M, Dönitz J. TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 2018;46:D343–7.
  • Nemajerova A, Kramer D, Siller SS, Herr C, Shomroni O, Pena T, et al. TAp73 is a central transcriptional regulator of airway multiciliogenesis. Genes Dev. 2016;30:1300–12.
  • Ulrich J, Dao VA, Majumdar U, Schmitt-Engel C, Schwirz J, Schultheis D, et al. Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics. 2015;16. doi:10.1186/s12864-015-1880-y.
  • Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, et al. The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat Commun. 2015;6:7822.
  • Dönitz J, Schmitt-Engel C, Grossmann D, Gerischer L, Tech M, Schoppmeier M, et al. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. Nucleic Acids Res. 2015;43:D720–5.

Members of the group

 

    Currently the following people work together to achieve our aims:

    • Jürgen Dönitz, subgroup leader
    • Jingyu Yang, PhD student in the MTB-Report project
    • Kevin Kornrumpf, PhD student in the MTB-Report project
    • Tim Tucholski, student assistant for the MTB-Report project
    • Canh Nguyen Duc, PhD in the iBeetle project
    • Vera Gnass, student assistant for MTB-Report project

    Former members of the group (since September 2019)

    • Tim Tucholski (bachelor student in the TFClass project)
      Title of the thesis "Development of a system for semi-automatic assignment of new sequences to the transcription factor classification TFClass"
    • Karly Conrads, master student in the iBeetle project
    • Charlotte Höltermann, student assistant in the MTB.Report project
    • Vanessa Schlotzig, bachelor student in the MTB Report project
    • Patrick Groos, bachelor student
    • Malte Vosskamp, student assistant for the iBeetle project and MyPathSem (here, the ontology viewer OntoScopeJS)

    iBeetle

    The project provides information about the phenotypes in Tribolium castaneum, collected in a genome wide RNAi screen and enhances the understanding of the development by cross-species analysis.

    Ontologies

    Ontologies are a pillar of the semantic web. With the help of ontologies entities can be identified and the relation-ships between the entities allow an analysis on different levels of abstraction, depending on the data and the specific research question in mind.

    Bachelor or Master thesis

    We offer different topics for Bachelor-, Master-  thesis in this field.
    If you are interessed, please contact Jürgen Dönitz for details.

    Group Leader

    Dr. Jürgen Dönitz

    contact information

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