EScience and the Role of Semantic Web-Content-Management-Systems in the Life Sciences

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Within the last decades, research in the life sciences has changed considerably. Today, many researchers use computers for data exploration, compile new and often very large datasets from openly available data and analyze them under new premises. This eScience approach requires data to be openly available through the Internet and utilizes applications of the Semantic Web. Key to the success of eScience is open accessibility and availability of data through corresponding Web-Content-Management-Systems that apply semantic technologies, such as ontologies, for increasing the semantic transparency and enabling computer-parsability of their data. This not only requires the development of eScience-compliant data and metadata standards, but the respective Semantic Web-Content-Management-Systems (SeWCMS) with adequate graphical user interfaces. Currently, we are involved in two projects that address these requirements.

1) Morph·D·Base: eScience-Compliant Standards for Morphology

MDB - Logo 2017
Funded by DFG

The eScience-Compliant Standards for Morphology project is part of the ongoing projects of the online morphological data repository Morph·D·Base. It is presently primarily maintained on funds of the LIS call Standards for Indexing and/or Digitisation of Object Classes in Scientific Collections of the DFG through the Rheinische Friedrich-Wilhelms-Universität Bonn (programming and management), the Foundation Zoological Research Museum Alexander Koenig (ZFMK) (programming, management and use case), the Max Planck Institute of Colloids and Interfaces (use case), the Museum für Naturkunde Berlin (MfN) (use case), and the Universität Rostock (use case). The ZFMK is adding a guarantee for long-term online availability should dedicated project funds run out. In addition, several projects and individuals using the online morphological data repository Morph·D·Base provide a significant contribution to improving the overall functionality of all new features and application-modules developed for Morph·D·Base during this project, as well as suggested eScience-compliant data and metadata standards applied in Morph·D·Base that result from this project.

Draft for the graphical user interface for semantically describing the anatomical organization of a specimen with all its anatomical entity parts in Morph·D·Base

2) Ontology-Controlled Application for Semantic Web-Content-Management-Systems

The Ontology-Controlled Application for Semantic Web-Content-Management-Systems (SeWCMS) we are developing a ready-to-use SeWCMS application that is controlled by a set of application ontologies. This application is not restricted to a particular data scheme or knowledge domain and allows the set up of a SeWCMS and individual customization without requiring a specific informatics background or having to learn how to develop ontologies or how to use ontology editors. The application allows for customization of each instance of the SeWCMS, including the specification of data views, input forms and workflows. With knowledge in CSS, the entire look of the graphical user interface can be customized.

Overall workflow of the application. Left: Jena Tuplestore and the descriptions of data views and workflows in the application ontologies. xxiddle: the Java middleware and the CSS GUI-Elements Catalogue. Right: the Web application based on Angular and nodeJS.

Screenshot VUE File
Ordered sequence of main commands (described in the form of annotations; see top), with each main command possessing a set of variables or sub-commands (described in the form of axiom annotations that often describe a specific triple statement and where it must be stored; see bottom) are used in the application ontologies for describing all individuals and classes involved in specific workflows, data views, etc.

About this Wiki is a technical platform supporting the representation of ongoing work of these two projects. The primary purpose of the platform is to facilitate the ongoing internal communication between the project participants, the representation of intermediate results and preliminary standards as well as accomplished milestones, and the communication of specific contents with external collaborators and the morphological community in general.