selected publications

• academic article

  • Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop.  Research Ideas and Outcomes.  9. 2023
  • FAIR scientific information with the Open Research Knowledge Graph.  FAIR Connect.  1:19-21. 2023
  • Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.  Systematic Biology.  72:1084-1100. 2023
  • Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.  Journal of Biomedical Semantics.  13:18. 2022
  • SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC.  Research Ideas and Outcomes.  8. 2022
  • FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example.  Journal of Biomedical Semantics.  12:20. 2021
  • ORKG: Facilitating the Transfer of Research Results with the Open Research Knowledge Graph.  Research Ideas and Outcomes.  7. 2021
  • Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits.  Mammalian Biology.  2021
  • Improving Access to Scientific Literature with Knowledge Graphs.  BIBLIOTHEK Forschung und Praxis.  44:516-529. 2020
  • Transforming the study of organisms: Phenomic data models and knowledge bases.  PLOS Computational Biology.  16:e1008376. 2020
  • FAIR.ReD: Semantic knowledge graph infrastructure for the life sciences.  Biodiversity Information Science and Standards.  3. 2019
  • Anatomy Knowledge Graphs: Toward FAIR morphological data.  Biodiversity Information Science and Standards.  3. 2019
  • From Data to Knowledge: A semantic knowledge graph application for curating specimen data.  Biodiversity Information Science and Standards.  3. 2019
  • Levels and building blocks—toward a domain granularity framework for the life sciences.  Journal of Biomedical Semantics.  10:4. 2019
  • Organizing phenotypic data—a semantic data model for anatomy.  Journal of Biomedical Semantics.  10:12. 2019
  • SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming.  Database.  2019. 2019
  • Using Named Graphs and Knowledge Graph Template Patterns for Efficiently Organizing FAIR Anatomy Data and Metadata.  Biodiversity Information Science and Standards.  3. 2019
  • Entry Life-Cycle with automatic Change-History & Provenance Tracking in collaborative Semantic Web Content Management Systems as implemented in SOCCOMAS.  Biodiversity Information Science and Standards.  2:e26177. 2018
  • The logical basis for coding ontologically dependent characters.  Cladistics.  34:438-458. 2018
  • Towards a semantic approach to numerical tree inference in phylogenetics.  Cladistics.  34:200-224. 2018
  • Using Semantics for morphological Descriptions in Morph•D•Base.  Biodiversity Information Science and Standards.  2:e25535. 2018
  • Assessing similarity: on homology, characters and the need for a semantic approach to non-evolutionary comparative homology.  Cladistics.  33:513-539. 2017
  • Developing a Module for Generating Formalized Semantic Morphological Descriptions for Morph∙D∙Base.  Biodiversity Information Science and Standards.  1:e15141. 2017
  • SOCCOMAS: A Self-Describing and Content-Independent Application for Semantic Ontology-Controlled Web-Content-Management-Systems.  Biodiversity Information Science and Standards.  1:e20033. 2017
  • Semantic Annotations of Text and Images in Morph∙D∙Base.  Biodiversity Information Science and Standards.  1:e14778. 2017
  • Emerging semantics to link phenotype and environment.  PeerJ.  3:e1470. 2015
  • Finding Our Way through Phenotypes.  PLoS Biology.  13:e1002033. 2015
  • Popper and phylogenetics, a misguided rendezvous.  Australian Systematic Botany.  27:85. 2014
  • Why phylogeneticists should care less about Popper's falsificationism.  Cladistics.  30:1-4. 2014
  • The need for data standards in zoomorphology.  Journal of Morphology.  274:793-808. 2013
  • eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth.  Systematics and Biodiversity.  11:257-270. 2013
  • Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities.  PLOS ONE.  7:e30004. 2012
  • Fiat or Bona Fide Boundary—A Matter of Granular Perspective.  PLOS ONE.  7:e48603. 2012
  • Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology.  PLOS ONE.  6:e18794. 2011
  • A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores.  Cladistics.  26:408-437. 2010
  • Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary.  Frontiers in Zoology.  7:29. 2010
  • Spatio-structural granularity of biological material entities.  BMC Bioinformatics.  11:289. 2010
  • The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology.  Zoomorphology.  128:201-217. 2009
  • The linguistic problem of morphology: structure versus homology and the standardization of morphological data.  Cladistics.  26:301-325. 2009
  • The unfalsifiability of cladograms and its consequences.  Cladistics.  24:62-73. 2008
  • A falsificationist perspective on the usage of process frequencies in phylogenetics.  Zoologica Scripta.  36:395-407. 2007
  • Molecular phylogeny of lugworms (Annelida, Arenicolidae) inferred from three genes.  Molecular Phylogenetics and Evolution.  34:673-679. 2005
  • A contribution to sedentary polychaete phylogeny using 18S rRNA sequence data.  Journal of Zoological Systematics and Evolutionary Research.  41:186-195. 2003
  • New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences.  Molecular Phylogenetics and Evolution.  29:279-288. 2003
  • Testing and weighting characters.  Organisms Diversity & Evolution.  2:319-333. 2002
  • Weighting indels as phylogenetic markers of 18S rDNA sequences in Diptera and Strepsiptera.  Organisms Diversity & Evolution.  2:335-349. 2002

• chapter

  • Toward Representing Research Contributions in Scholarly Knowledge Graphs Using Knowledge Graph Cells.  JCDL '20: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries in 2020. 107-116. 2020
  • Using Semantic Programming for Developing a Web Content Management System for Semantic Phenotype Data.  200-206. 2019
  • Taxonomy and the Production of Semantic Phenotypes.  Application of Semantic Technology in Biodiversity Science. 53-77. 2018
  • 20 Documenting Morphology: Morph·D·Base.  475-504. 2014

• dataset

  • COVID-19 Reproductive Number Estimates 2020