Ontological Modelling and Execution of Phenotypic Queries in the Leipzig Health Atlas.
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Sharing data is of great importance for research in medical sciences. It is the basis for reproducibility and reuse of already generated outcomes in new projects and in new contexts. FAIR data principles … are the basics for sharing data. The Leipzig Health Atlas (LHA) platform follows these principles and provides data, describing metadata, and models that have been implemented in novel software tools and are available as demonstrators. LHA reuses and extends three different major components that have been previously developed by other projects. The SEEK management platform is the foundation providing a repository for archiving, presenting and secure sharing a wide range of publication results, such as published reports, (bio)medical data as well as interactive models and tools. The LHA Data Portal manages study metadata and data allowing to search for data of interest. Finally, PhenoMan is an ontological framework for phenotype modelling. This paper describes the interrelation of these three components. In particular, we use the PhenoMan to, firstly, model and represent phenotypes within the LHA platform. Then, secondly, the ontological phenotype representation can be used to generate search queries that are executed by the LHA Data Portal. The PhenoMan generates the queries in a novel domain specific query language (SDQL), which is specific for data management systems based on CDISC ODM standard, such as the LHA Data Portal. Our approach was successfully applied to represent phenotypes in the Leipzig Health Atlas with the possibility to execute corresponding queries within the LHA Data Portal.

Authors: A. Uciteli, C. Beger, J. Wagner, A. Kiel, F. A. Meineke, S. Staubert, M. Lobe, R. Hansel, J. Schuster, T. Kirsten, H. Herre

Date Published: 24th May 2021

Publication Type: Journal article

Ontology-Based Modelling of Web Content: Example Leipzig Health Atlas
Onto-Med Research Group

Abstract (Expand)

The realisation of a complex web portal, including the modelling of content, is a challenging process. The contents describe different interconnected entities that form a complex structure. The entities … and their relations have to be systematically analysed, and the content has to be specified and integrated into a content management system (CMS). Ontologies provide a suitable solution for modelling and specifying complex entities and their relations. However, the functionality for automated import of ontologies is not available in current content management systems. In order to describe the content of a web portal, we developed an ontology. Based on this ontology, we implemented a pipeline that allows the specification of the portal’s content and its import into the CMS Drupal. Our method is generic. It enables the development of web portals with the focus on a suitable representation of structured knowledge (entities, their properties and relations). Furthermore, it makes it possible to represent existing ontologies in such a way that their content can be understood by users without knowledge of ontologies and their semantics. Our approach has successfully been applied in building the LHA (Leipzig Health Atlas) portal, which provides access to metadata, data, publications and methods from various research projects at the University of Leipzig.

Authors: A. Uciteli, C. Beger, C. Rillich, F. A. Meineke, M. Loffler, H. Herre

Date Published: 2018

Publication Type: InBook

Light-Weighted Automatic Import of Standardized Ontologies into the Content Management System Drupal.
Onto-Med Research Group

Abstract (Expand)

The amount of ontologies, which are utilizable for widespread domains, is growing steadily. BioPortal alone, embraces over 500 published ontologies with nearly 8 million classes. In contrast, the vast … informative content of these ontologies is only directly intelligible by experts. To overcome this deficiency it could be possible to represent ontologies as web portals, which does not require knowledge about ontologies and their semantics, but still carries as much information as possible to the end-user. Furthermore, the conception of a complex web portal is a sophisticated process. Many entities must be analyzed and linked to existing terminologies. Ontologies are a decent solution for gathering and storing this complex data and dependencies. Hence, automated imports of ontologies into web portals could support both mentioned scenarios. The Content Management System (CMS) Drupal 8 is one of many solutions to develop web presentations with less required knowledge about programming languages and it is suitable to represent ontological entities. We developed the Drupal Upper Ontology (DUO), which models concepts of Drupal's architecture, such as nodes, vocabularies and links. DUO can be imported into ontologies to map their entities to Drupal's concepts. Because of Drupal's lack of import capabilities, we implemented the Simple Ontology Loader in Drupal (SOLID), a Drupal 8 module, which allows Drupal administrators to import ontologies based on DUO. Our module generates content in Drupal from existing ontologies and makes it accessible by the general public. Moreover Drupal offers a tagging system which may be amplified with multiple standardized and established terminologies by importing them with SOLID. Our Drupal module shows that ontologies can be used to model content of a CMS and vice versa CMS are suitable to represent ontologies in a user-friendly way. Ontological entities are presented to the user as discrete pages with all appropriate properties, links and tags.

Authors: C. Beger, A. Uciteli, H. Herre

Date Published: 9th Sep 2017

Publication Type: Journal article

Searching for Data Elements in Studies hosted by the LHA
LIFE Adult

All studies and research projects those data are hosted by the Leipzig Health Atlas should follow the FAIR standard. Thus, data are findable, accessible, interoperable, and reusable. To follow the FAIR standard, all data need to be described by rich metadata, on the technical and semantical level. These metadata can then be used to query and search for data elements in a single study or over all studies.

We provide the LHA data portal allowing to searching and accessing data elements in single ...

Creator: Toralf Kirsten

Submitter: René Hänsel

External Link View content
Simple Ontology Loader in Drupal (SOLID)
Onto-Med Research Group

This is a Drupal 8 Module to import nodes and taxonomies into Drupal, using the available API. The module is capable of importing a JSON or OWL file. Idea is to enable users to upload a file containing all information about nodes and their relations. The module will then import all contained information with the Drupal 8 API. Nodes can be specified as "articles" or any other custom node type. The node classification becomes one (or multiple) hierachical vocabulary. Supported import formats are ...

Creator: Christoph Beger

Submitter: Christoph Beger

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