Christian Köhler

Christian Köhler
Research Museum Alexander Koenig | ZFMK · Bioinformatic Department

About

23
Publications
2,861
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43
Citations
Introduction
As a CEO of ganzgraph gmb, Bonn, Germany, Christian Köhler tries to bring together biology and technology, helping to manage (big) data. Christian Köhler worked until the End of 2018 at the Bioinformatic Department, Research Museum Alexander Koenig. Christian does research in Zoology, Evolutionary Biology and Ecology. Their current project is 'Morph·D·Base: eScience-Compliant Standards for Morphology'
Additional affiliations
April 2012 - November 2018
Research Museum Alexander Koenig
Position
  • Research Assistant
Description
  • science data portals, science data management (parallel to position CEO ganzgraph)
December 2002 - present
ganzgraph gmbh
Position
  • CEO
Description
  • Including the predecessor of ganzgraph: foundation of internet startup with focus on content management, data management and research related internet internet platforms.
June 2000 - November 2011
Compuvision
Position
  • Developer
Description
  • web developer
Education
April 1994 - December 1998
University of Bonn
Field of study
  • Biology

Publications

Publications (23)
Conference Paper
Full-text available
Automated observations of natural occurrences play a key role in monitoring biodiversity worldwide. With the development of affordable hardware like the AudioMoth (Hill et al. 2019) acoustic logger, large scale and long-term monitoring has come within reach. However, data management and dissemination of monitoring data remain challenging, as the de...
Article
Full-text available
The landscape of currently existing repositories of specimen data consists of isolated islands, with each applying its own underlying data model. Using standardized protocols such as DarwinCore or ABCD, specimen data and metadata are exchanged and published on web portals such as GBIF. However, data models differ across repositories. This can lead...
Preprint
Full-text available
We demonstrate that ontologies are not restricted to modeling a specific domain, but can be used for programming as well. We introduce the Semantic Programming Ontology (SPrO) and its accompanying Java-based middleware, which we use as a semantic programming language. SPrO provides ontology instances as well as annotation, object, and data properti...
Preprint
Full-text available
We introduce SOCCOMAS, a development framework for FAIR Semantic Web Content Management Systems (S-WCMS). Each S-WCMS run by SOCCOMAS has its contents managed through a corresponding knowledge base that stores all data and metadata in the form of semantic knowledge graphs in a Jena tuple store. Automated procedures track provenance, user contributi...
Article
Full-text available
We introduce Semantic Ontology-Controlled application for web Content Management Systems (SOCCOMAS), a development framework for FAIR (‘findable’, ‘accessible’, ‘interoperable’, ‘reusable’) Semantic Web Content Management Systems (S-WCMSs). Each S-WCMS run by SOCCOMAS has its contents managed through a corresponding knowledge base that stores all d...
Chapter
We present a prototype of a semantic version of Morph·D·Base that is currently in development. It is based on SOCCOMAS, a semantic web content management system that is controlled by a set of source code ontologies together with a Java-based middleware and our Semantic Programming Ontology (SPrO). The middleware interprets the descriptions containe...
Preprint
Full-text available
We present a prototype of a semantic version of Morph·D·Base that is currently in development. It is based on SOCCOMAS, a semantic web content management system that is controlled by a set of source code ontologies together with a Java-based middleware and our Semantic Programming Ontology (SPrO). The middleware interprets the descriptions containe...
Presentation
Full-text available
About a decade ago we discussed the Linguistic Problem of Morphology, i.e. lack of standardized morphological terminology and standardized and formalized method of description. Here we report from ongoing development of a description module for Morph∙D∙Base (https://proto.morphdbase.de) that is based on semantic programming technology. The module a...
Presentation
Full-text available
A significant amount of morphological data is still provided as unstructured text. This is unfortunate in times of eScience in which data are increasingly available in a semantically structured format. Here we report on ongoing development of a new description module for Morph∙D∙Base (https://proto.morphdbase.de) that is based on semantic programmi...
Presentation
Full-text available
SOCCOMAS is a ready-to-use Semantic Ontology-Controlled Content Management System (http://escience.biowikifarm.net/wiki/SOCCOMAS). Each web content anagement system (WCMS) run by SOCCOMAS is controlled by a set of ontologies and an accompanying Java-based middleware with the data housed in a Jena tuple store. The ontologies describe the behavior of...
Article
Full-text available
SOCCOMAS is a ready-to-use Semantic Ontology-Controlled Content Management System (http://escience.biowikifarm.net/wiki/SOCCOMAS). Each web content management system (WCMS) run by SOCCOMAS is controlled by a set of ontologies and an accompanying Java-based middleware with the data housed in a Jena tuple store. The ontologies describe the behavior o...
Article
Full-text available
Providing data in a semantically structured format has become the gold standard in data science. However, a significant amount of data is still provided as unstructured text - either because it is legacy data or because adequate tools for storing and disseminating data in a semantically structured format are still missing. We have developed a descr...
Presentation
Full-text available
The talk is divided into three parts. The first part introduces the notion of Semantic Instance Anatomies as an ontology-based method of morphological description (that can be expanded to cover also trait descriptions) that has the potential to establish a new theoretical and methodological framework for comparative biology by enabling the quantifi...
Presentation
Full-text available
The presentation is in German! This is an introduction to SOCCOMAS, a semantic ontology-controlled content management system application with which you can describe within a set of application ontologies all functions of a Web-CMS application, including the structure and composition of its interface, all input forms and data life-cycle, and the app...
Presentation
Full-text available
Ontologies are usually utilized for representing knowledge. Here, we extend this use and demonstrate that ontologies also can be used for describing and controlling semantic Web-Content-Management-Systems (WCMS). We call the resulting application SOCCOMAS: a self-describing and content-independent application for semantic ontology-controlled Web-Co...
Presentation
Full-text available
Creating an application for recording and documenting morphological data in a semantically transparent and reproducible way used to be a challenging task due to the heterogeneous nature of data within this domain. To provide a system for morphologists and taxonomists to work with their research data, collaborate and publish it, we built a Web-based...
Presentation
Full-text available
The graphical user interface is the common primary interface between humans and computer systems. In order to make the complex content of a particular-purpose-system in biodiversity science accessible to the user in an intuitive way, it is often necessary to develop new types of interface modules that meet the specific requirements of the domain. T...
Article
Full-text available
Ontologies are usually utilized for representing knowledge. Here, we extend this use and demonstrate that ontologies also can be used for describing and controlling semantic Web-Content-Management-Systems (WCMS). We call the resulting application SOCCOMAS: a self-describing and content-independent application for semantic ontology-controlled Web-Co...
Article
Full-text available
We demonstrate the early prototype of a new module for Morph·D·Base that allows the generation of highly formalized semantic morphological descriptions (http://escience.bio wikifarm.net/wiki/EScience-Compliant_Standards_for_Morphology). The resulting morphological descriptions follow the individuals-based Instance Anatomy data scheme (as opposed to...
Article
Full-text available
Creating an application for recording and documenting morphological data in a semantically transparent and reproducible way used to be a challenging task due to the heterogeneous nature of data within this domain. To provide a system for morphologists and taxonomists to work with their research data, collaborate and publish it, we built a Web-based...
Conference Paper
Full-text available
The BiNHum project is a collective effort of five natural history museums and research collections of the Humboldt-Ring in Germany to collect, centralize and publish collection data in a unified web portal. The portal and the underlying data workflows provide an extensive set of tools to refine and enrich collection data from various sources. It pr...
Conference Paper
Full-text available
BiNHum (http://wiki.binhum.net) is a project of five natural history museums and research collections representing the Humboldt-Ring: the State Museum of Natural History Karlsruhe (SMNK), the State Museum of Natural History Stuttgart (SMNS), the Zoological Research Museum Alexander Koenig in Bonn (ZFMK), the Bavarian Natural History Collections in...
Article
Full-text available
The mode of visual information processing during visuospatial tasks differs across species and is supposed to depend on evolutionary and ecological factors. Humans show reaction times that increase with angular disparity when tested in mental rotation tasks. Pigeons show a time-independent rotational invariance that possibly evolved in response to...

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Projects

Projects (6)
Project
We develop a Semantic Programming Ontology (SPrO) that is used like a semantic programming language. It consists of specific classes, individuals and properties that represent commands and variables that serve as an ontology-based and thus semantic programming language. SPrO can be used to provide a graphical user interface (GUI), data representations, user interactions, and all workflow processes of a semantic WCMS. A Java-based middleware functions as a compiler that dynamically executes the descriptions by interpreting them as declarative specifications. SPrO is currently used in SOCCOMAS (http://escience.biowikifarm.net/wiki/Ontology-controlled_Application_for_Semantic_Web-Content-Management-Systems).
Project
We develop a Semantic Web Content Management System (WCMS) that is controlled by a set of application ontologies, which describe the respective WCMS. The descriptions use the Semantic Programming Ontology (SPrO). The Java-based middleware of SOCCOMAS dynamically executes programming code based on the descriptions from the application ontologies by interpreting them as declarative specifications of the WCMS. Each WCMS based on this engine stores data as a knowledge base in a tuplestore. The WCMS itself is controlled by a set of ontologies. SOCCOMAS stands for: Semantic Ontology-Controlled COntent MAnagement System. (http://escience.biowikifarm.net/wiki/Ontology-controlled_Application_for_Semantic_Web-Content-Management-Systems)