Related papers: An extensible web interface for databases and its …
To enable materials databases supporting computational and experimental research, it is critical to develop platforms that both facilitate access to the data and provide the tools used to generate/analyze it - all while considering the…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
With the ever-increasing scientific literature, there is a need on a natural language interface to bibliographic information retrieval systems to retrieve related information effectively. In this paper, we propose a natural language…
All natural language processing systems (such as parsers, generators, taggers) need to have access to a lexicon about the words in the language. This thesis presents a lexicon architecture for natural language processing in Turkish. Given a…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
This paper presents our Linked Open Data (LOD) infrastructures for genomic and experimental data related to microRNA biomolecules. Legacy data from two well-known microRNA databases with experimental data and observations, as well as change…
In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters…
Engineering information systems for scientific data analysis presents significant challenges: complex workflows requiring exploration of large solution spaces, close collaboration with domain specialists, and the need for maintainable,…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
In recent years, the DBLP computer science bibliography has been prominently used for searching scholarly information, such as publications, scholars, and venues. However, its current search service lacks the capability to handle complex…
Conversational user interfaces powered by large language models (LLMs) have significantly lowered the technical barriers to database querying. However, existing tools still encounter several challenges, such as misinterpretation of user…
Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is…
Robotic platforms serve different use cases ranging from experiments for prototyping assistive applications up to embedded systems for realizing cyber-physical systems in various domains. We are using 1:10 scale miniature vehicles as a…
The problem of natural language processing over structured data has become a growing research field, both within the relational database and the Semantic Web community, with significant efforts involved in question answering over knowledge…
In this paper, we propose a robot oriented knowledge management system based on the use of the Prolog language. Our framework hinges on a special organisation of knowledge base that enables: 1. its efficient population from natural language…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
This Master's Thesis in Computer Science dives into the design and creation of a user-friendly interface for VoxLogicA, an image analysis tool using spatial model checking with a focus on neuroimaging. The research tackles the problem of…
This paper presents a novel approach to represent enterprise web application structures using Large Language Models (LLMs) to enable intelligent quality engineering at scale. We introduce a hierarchical representation methodology that…