Adoption of the Classical Theory of Definition to Ontology Modeling. - Patryk Burek (AIMSA, 2004)

Dually Structured Concepts in the Semantic Web: Answer Set Programming Approach. - Patryk Burek; Rafal Grabos (ESWC, 2005)

Essentialized Conceptual Structures in Ontology Modeling. - Patryk Burek (KES (2), 2005)

A top-level ontology of functions and its application in the Open Biomedical Ontologies. - Patryk Burek; Robert Hoehndorf; Frank Loebe; Johann Visagie; Heinrich Herre; Janet Kelso (ISMB (Supplement of Bioinformatics), 2006)

Ontology of functions: a domain independent framework for modeling functions. - Patryk Burek (2006)

Ontological Analysis of Functional Decomposition. - Patryk Burek; Heinrich Herre; Frank Loebe (SoMeT, 2009)

Assisting the Machine Paradigms for Human-Machine Interaction in Single Cell Tracking. - Nico Scherf; Michael Kunze; Konstantin Thierbach; Thomas Zerjatke; Patryk Burek; Heinrich Herre; Ingmar Glauche; Ingo Roeder (Bildverarbeitung für die Medizin, 2013)

Representation, Realization, and Ascription of Functions for Material Entities. - Patryk Burek; Heinrich Herre (GI-Jahrestagung, 2013)

Search Ontology, a new approach towards Semantic Search. - Alexandr Uciteli; Christoph Goller; Patryk Burek; Sebastian Siemoleit; Breno Faria; Halyna Galanzina; Timo Weiland; Doreen Drechsler-Hake; Wolfram Bartussek; Heinrich Herre (GI-Jahrestagung, 2014)

A UML profile for functional modeling applied to the Molecular Function Ontology. - Patryk Burek; Frank Loebe; Heinrich Herre (ICBO, 2015)

FueL: Representing function structure and function dependencies with a UML profile for function modeling. - Patryk Burek; Frank Loebe; Heinrich Herre (Appl. Ontology, 2016)

Towards refactoring the Molecular Function Ontology with a UML profile for function modeling. - Patryk Burek; Frank Loebe; Heinrich Herre (J. Biomed. Semant., 2017)

Foundations of the Cell Tracking Ontology. - Patryk Burek; Nico Scherf; Heinrich Herre (JOWO, 2019)

A pattern-based approach to a cell tracking ontology. - Patryk Burek; Nico Scherf; Heinrich Herre (KES, 2019)

Ontology patterns for the representation of quality changes of cells in time. - Patryk Burek; Nico Scherf; Heinrich Herre (J. Biomed. Semant., 2019)

On the Formal Representation and Annotation of Cellular Genealogies. - Patryk Burek; Nico Scherf; Heinrich Herre (EKAW, 2020)

Towards GFO 2.0: Architecture, Modules and Applications. - Patryk Burek; Frank Loebe; Heinrich Herre (FOIS, 2020)

On the Ontological Foundations of Cellular Development. - Patryk Burek; Heinrich Herre; Nico Scherf (JOWO, 2020)

A Lightweight Approach to the Multi-perspective Modeling of Processes and Objects. - Patryk Burek; Heinrich Herre (KES, 2020)

Towards a Modern Ontology Development Environment. - Adrian Stadnicki; Filip Filip Pietron; Patryk Burek (KES, 2020)

Developing GFO 2.0 Further - Initiating the Modules of Space and Material Objects. - Frank Loebe; Patryk Burek; Heinrich Herre (JOWO, 2021)

Overview of GFO 2.0 Functions: An ontology module for representing teleological knowledge. - Patryk Burek; Frank Loebe; Heinrich Herre (KES, 2021)

Cybersecurity Ontology for Dynamic Analysis of IT Systems. - Jakub Pastuszuk; Patryk Burek; Bogdan Ksiezopolski (KES, 2021)

GFO: The General Formal Ontology. - Frank Loebe; Patryk Burek; Heinrich Herre (Appl. Ontology, 2022)

Ontology patterns for function modeling with GFO (short paper). - Patryk Burek; Frank Loebe; Heinrich Herre (ER (Companion), 2023)

Balls and Universal Space in GFO. - Bärbel Hanle; Frank Loebe; Patryk Burek; Heinrich Herre (JOWO, 2023)

Ontologically Founded Design Patterns for Situation Modeling. - Patryk Burek; Frank Loebe; Ralph Schäfermeier; Alexandr Uciteli; Bartosz Kondracki; Heinrich Herre (ISD, 2024)