Matthias Lange

Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Saxony-Anhalt, Germany

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Publications (30)16.81 Total impact

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    ABSTRACT: With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous, and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing over 13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance to other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley. © The Author(s) 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.
    Plant and Cell Physiology 12/2014; · 4.98 Impact Factor
  • Data Integration in the Life Sciences; 10th International Workshop, DILS 2014, Lisbon, Portugal, 17-18 July 2014; 07/2014
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    ABSTRACT: The life-science community faces a major challenge in handling "big data", highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, and publication are the three pillars in the "big data life cycle". The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary solutions and lower quality data publication and preservation overall.
    BMC Bioinformatics 06/2014; 15(1):214. · 3.02 Impact Factor
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    ABSTRACT: Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement. In this context, computer aided query expansion and suggestion is one of the most challenging tasks for life science information systems. Existing query front-ends support aspects like spelling correction, query refinement or query expansion. However, the majority of the front-ends only make limited use of enhanced IR algorithms to implement comprehensive and computer aided query refinement workflows. In this work, we present the design of a multi-stage query suggestion workflow and its implementation in the life science IR system LAILAPS. The presented workflow includes enhanced tokenisation, word breaking, spelling correction, query expansion and query suggestion ranking. A spelling correction benchmark with 5,401 queries and manually selected use cases for query expansion demonstrate the performance of the implemented workflow and its advantages compared with state-of-the-art systems.
    Journal of integrative bioinformatics 01/2014; 11(2):237.
  • Approaches in Integrative Bioinformatics, Edited by Ming Chen, Ralf Hofestädt, 01/2014: pages 73-109; Springer Berlin Heidelberg., ISBN: 978-3-642-41281-3
  • 01/2013;
  • Article: Editorial
    Journal of integrative bioinformatics 01/2013; 10(1):226.
  • INFORMATIK 2013 – Informatik angepasst an Mensch, Organisation und Umwelt, Lecture Notes in Informatics edited by Matthias Horbach, 01/2013: pages 1834-1840; Gesellschaft für Informatik e.V. (GI)., ISBN: 978-3-88579-614-5
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    ABSTRACT: Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data is spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a semi-automated data exploration in information retrieval environments, an integrated view to databases is essential. Search engines have the potential of assisting in data retrieval from these structured sources, but fall short of providing a comprehensive knowledge except out of the interlinked databases. A prerequisite of supporting the concept of an integrated data view is to acquire insights into cross-references among database entities. This issue is being hampered by the fact, that only a fraction of all possible cross-references are explicitely tagged in the particular biomedical informations systems. In this work, we investigate to what extend an automated construction of an integrated data network is possible. We propose a method that predicts and extracts cross-references from multiple life science databases and possible referenced data targets. We study the retrieval quality of our method and report on first, promising results. The method is implemented as the tool IDPredictor, which is published under the DOI 10.5447/IPK/2012/4 and is freely available using the URL: http://dx.doi.org/10.5447/IPK/2012/4.
    Journal of integrative bioinformatics 01/2012; 9(2):190.
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    ABSTRACT: The paper presents e!DAL-API, a comprehensive storage backend for primary data management. It stands for (Electronical Data Archive Library) and implements a primary data storage infrastructure, but with an intuitive usability like a classical file system.
    Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on; 01/2012
  • it - Information Technology. 09/2011; 53:234-240.
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    ABSTRACT: ABSTRACT: In modern life science research it is very important to have an efficient management of high throughput primary lab data. To realise such an efficient management, four main aspects have to be handled: (I) long term storage, (II) security, (III) upload and (IV) retrieval. In this paper we define central requirements for a primary lab data management and discuss aspects of best practices to realise these requirements. As a proof of concept, we introduce a pipeline that has been implemented in order to manage primary lab data at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). It comprises: (I) a data storage implementation including a Hierarchical Storage Management system, a relational Oracle Database Management System and a BFiler package to store primary lab data and their meta information, (II) the Virtual Private Database (VPD) implementation for the realisation of data security and the LIMS Light application to (III) upload and (IV) retrieve stored primary lab data. With the LIMS Light system we have developed a primary data management system which provides an efficient storage system with a Hierarchical Storage Management System and an Oracle relational database. With our VPD Access Control Method we can guarantee the security of the stored primary data. Furthermore the system provides high performance upload and download and efficient retrieval of data.
    BMC Research Notes 01/2011; 4:413.
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    ABSTRACT: Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.
    Journal of integrative bioinformatics 04/2010; 7(3).
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    ABSTRACT: Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.
    Journal of integrative bioinformatics 01/2010; 7(2):110.
  • 01/2010;
  • Informatik 2009: Im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.9.-2.10.2009, Lübeck, Proceedings; 01/2009
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    ABSTRACT: To advance the comprehension of complex biological processes occurring in crop plants (e.g. for improvement of growth or yield) it is of high interest to reconstruct and analyse detailed metabolic models. Therefore, we established a pipeline combining software tools for (1) storage of metabolic pathway data and reconstruction of crop plant metabolic models, (2) simulation and analysis of stoichiometric and kinetic models and (3) visualisation of data generated with these models. The applicability of the approach is demonstrated by a case study of cereal seed metabolism.
    Data Integration in the Life Sciences, 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009. Proceedings; 01/2009
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    ABSTRACT: To support the interpretation of measured molecular facts, like gene expression experiments or EST sequencing, the functional or the system biological context has to be considered. Doing so, the relationship to existing biological knowledge has to be discovered. In general, biological knowledge is worldwide represented in a network of databases. In this paper we present a method for knowledge extraction in life science databases, which prevents the scientists from screen scraping and web clicking approaches. We developed a method for extraction of knowledge networks from distributed, heterogeneous life science databases. To meet the requirement of the very large data volume, the method used is based on the concept of data linkage graphs (DLG).We present an efficient software which enables the joining of millions of data points over hundreds of databases. In order to motivate possible applications, we computed networks of protein knowledge, which interconnect metabolic, disease, enzyme and gene function data. The computed networks enabled a holistic relationship among measured experimental facts and the combined biological knowledge. This was successfully applied for a high throughput functional classification of barley EST and gene expression experiments with the perspective of an automated pipeline for the provisioning of controlled annotation of plant gene arrays and chips. Availability: The data linkage graphs (XML or TGF format), the schema integrated database schema (GML or GRAPH-ML) and the graph computation software may be downloaded from the following URL: http://pgrc.ipk-gatersleben.de/dlg/
    http://journal.imbio.de/index.php?paper_id=68. 01/2007;
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    ABSTRACT: The crop expressed sequence tag database, CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/), is a publicly available online resource providing access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200,000 sequences derived from 41 cDNA libraries of four species: barley, wheat, pea and potato. The barley section comprises approximately one-third of all publicly available ESTs. CR-EST deploys an automatic EST preparation pipeline that includes the identification of chimeric clones in order to transparently display the data quality. Sequences are clustered in species-specific projects to currently generate a non-redundant set of approximately 22,600 consensus sequences and approximately 17,200 singletons, which form the basis of the provided set of unigenes. A web application allows the user to compute BLAST alignments of query sequences against the CR-EST database, query data from Gene Ontology and metabolic pathway annotations and query sequence similarities from stored BLAST results. CR-EST also features interactive JAVA-based tools, allowing the visualization of open reading frames and the explorative analysis of Gene Ontology mappings applied to ESTs.
    Nucleic Acids Research 02/2005; 33(Database issue):D619-21. · 8.81 Impact Factor
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    ABSTRACT: Nowadays, huge volumes of molecular biological data are available from different biological research projects. This data often covers overlapping and complemental domains. For instance, the Swiss-Prot database merely contains protein sequences along with their annotations, whereas the KEGG database incorporates enzymes, metabolic pathways and genome data. Due to the fact that this data complements and completes each other, it is desirable to gain a global view on the integrated databases instead of browsing each single data source itself. Unfortunately, most data sources are queried through proprietary interfaces with restricted access and typically support only a small set of simple query operations. Apart from minor exceptions, there is no common data model or presentation standard for the query results. Consequentially, the integration of manifold heterogeneous, distributed databases has become a typical, yet challenging task in bioinformatics. Within this paper, we introduce our own approach called “BioDataServer” which is a user-adaptable integration, storage, analysis and query service for molecular biological data targeted at commercial customers.
    Data Integration in the Life Sciences, First International Workshop, DILS 2004, Leipzig, Germany, March 25-26, 2004, Proceedings; 01/2004

Publication Stats

77 Citations
16.81 Total Impact Points

Institutions

  • 2005–2014
    • Leibniz Institute of Plant Genetics and Crop Plant Research
      • • Department of Molecular Genetics
      • • Research Group Bioinformatics and Information technology
      Gatersleben, Saxony-Anhalt, Germany
  • 2003
    • Bielefeld University
      • Bioinformatics and Medical Informatics
      Bielefeld, North Rhine-Westphalia, Germany