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We are developing infrastructure to support researchers in mapping data related to the peripheral nervous system and other physiological systems, with an emphasis on their relevance to the organs under investigation. The nervous system, a…
This Ontologies are widely used as a means for solving the information heterogeneity problems on the web because of their capability to provide explicit meaning to the information. They become an efficient tool for knowledge representation…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems.…
The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge. It is motivated by the fact that the concepts that are…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
The previously introduced Modular Ontology Modeling methodology (MOMo) attempts to mimic the human analogical process by using modular patterns to assemble more complex concepts. To support this, MOMo organizes organizes ontology design…
Competency Questions (CQs) for an ontology and similar artefacts aim to provide insights into the contents of an ontology and to demarcate its scope. The absence of a controlled natural language, tooling and automation to support the…
Ontologies are useful for automatic machine processing of domain knowledge as they represent it in a structured format. Yet, constructing ontologies requires substantial manual effort. To automate part of this process, large language models…
In this paper, we describe an approach to populate an existing ontology with instance information present in the natural language text provided as input. An ontology is defined as an explicit conceptualization of a shared domain. This…
This paper describes a new technique, called "knowledge patterns", for helping construct axiom-rich, formal ontologies, based on identifying and explicitly representing recurring patterns of knowledge (theory schemata) in the ontology, and…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
Ontologies are a popular way of representing domain knowledge, in particular, knowledge in domains related to life sciences. (Semi-)automating the process of building an ontology has attracted researchers from different communities into a…
Retrieve information resources made by the machine processing may refer to multiple sources. A personal web as part of information resources in the Internet requires a feature that can be understood by computer machines. Therefore, in this…
Modern information systems are changing the idea of "data processing" to the idea of "concept processing", meaning that instead of processing words, such systems process semantic concepts which carry meaning and share contexts with other…
An ontology makes a special vocabulary which describes the domain of interest and the meaning of the term on that vocabulary. Based on the precision of the specification, the concept of the ontology contains several data and conceptual…
Ontologies are known for their ability to organize rich metadata, support the identification of novel insights via semantic queries, and promote reuse. In this paper, we consider the problem of automated planning, where the objective is to…
We propose to use orthologic as the basis for designing type systems supporting intersection, union, and negation types in the presence of subtyping assumptions. We show how to extend orthologic to support monotonic and antimonotonic…
In engineering projects involving various parts from global suppliers, one common task is to determine which parts are best suited for the project requirements. Information about specific parts' characteristics is published in so called…
Machine learning explanation can significantly boost machine learning's application in decision making, but the usability of current methods is limited in human-centric explanation, especially for transfer learning, an important machine…