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A database system for the analysis of biochemical pathways.

Abstract (Expand)

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to … model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.

Authors: I. Rojas, L. Bernardi, E. Ratsch, R. Kania, U. Wittig, J. Saric

Date Published: 18th Jun 2002

Publication Type: Journal

Analysis and comparison of metabolic pathway databases.

Abstract (Expand)

Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism … remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given.

Authors: U. Wittig, A. De Beuckelaer

Date Published: 24th Jul 2001

Publication Type: Journal

The BeeProject: Advanced Digitisation and Creation of a Dataset for the Monitoring of Beehives

Abstract (Expand)

The digitisation of historical documents, particularly those containing tabular data, is becoming increasingly critical for the preservation of information and analysis of long-term trends. However, … this task presents significant challenges, particularly with semi-formal documents like handwritten records, which often need more consistent structure. This paper addresses the challenge of developing an automated approach for transcribing historical handwritten tables. Our presented method works on a mixture of computer vision tools and optical character recognition (OCR) to detect the grid and content of the table. The dataset we collected contains records from beekeepers, consisting of hive weight gain and loss and meteorological conditions. The Institute of Bee Protection at JKI gathered this information from the German beekeeper associations of Lower Saxony, Hesse, Mecklenburg-Vorpommern, Thuringia, and Brandenburg in Germany within the collaborative research project MonViA. This data is crucial for understanding the impact of climate change on bee vitality and contains daily information from each beekeeper over decades, holding valuable insights into past environmental conditions. The success rate of automatically transcribed hive scale data from Lower Saxony was compared with the accuracy of transcription done by human power. Our dataset of 14\,738 handwritten scans, out of which 3819 were manually digitised, provides a large ground truth for future research, paving the way for further exploration and uncovering other historical knowledge.

Authors: Lukrécia Mertová, Severin Polreich, Oleg Lewkovski, Wolfgang Müller

Date Published: No date defined

Publication Type: InProceedings

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