Related papers: An extensible web interface for databases and its …
We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation. The inference engine core is based on a Bayesian model implemented to: (i) allow diverse source of…
A Natural Language Interface (NLI) facilitates users to pose queries to retrieve information from a database without using any artificial language such as the Structured Query Language (SQL). Several applications in various domains…
This paper presents Ellogon, a multi-lingual, cross-platform, general-purpose text engineering environment. Ellogon was designed in order to aid both researchers in natural language processing, as well as companies that produce language…
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…
Even though several publicly accessible pharmacovigilance databases are available, extracting data from them is a technically challenging process. Existing tools typically focus on a single database. We present SurVigilance, an open-source…
Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancer cell's molecular state and its response to anti-cancer therapy. To study the problem, we…
Natural language interfaces (NLIs) provide users with a convenient way to interactively analyze data through natural language queries. Nevertheless, interactive data analysis is a demanding process, especially for novice data analysts. When…
A new family of Intensional RDBs (IRDBs), introduced in [1], extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all preexisting user's…
Protein-Text Question Answering (QA) is crucial for interpreting biological sequences through natural language. The integration of Large Language Models (LLMs) with Retrieval-Augmented Generation (RAG) that efficiently leverages biological…
This article presents a modular, component-based architecture for developing and evaluating AI agents that bridge the gap between natural language interfaces and complex enterprise data warehouses. The system directly addresses core…
As large language models (LLMs) demonstrate increasingly powerful reasoning and orchestration capabilities, LLM-based agents are rapidly proliferating for complex data-related tasks. Despite this progress, the current design of how LLMs…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Translating Natural Language Queries into Structured Query Language (Text-to-SQL or NLQ-to-SQL) is a critical task extensively studied by both the natural language processing and database communities, aimed at providing a natural language…
Background, enhancing interoperability of bioinformatics knowledge bases is a high priority requirement to maximize data reusability, and thus increase their utility such as the return on investment for biomedical research. A knowledge base…
Background: The secure management of sensitive clinical data, particularly human genomics data, has become a critical requirement in modern biomedical research. Although the necessary software and algorithms are readily available, their use…
We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step…
Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…
Since the database update view was standardised in the Prolog ISO standard, the so called logical update view is available in all actively maintained Prolog systems. While this update view provided a well defined update semantics and allows…
This paper presents the first framework for integrating procedural knowledge, or "know-how", into the Linked Data Cloud. Know-how available on the Web, such as step-by-step instructions, is largely unstructured and isolated from other…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…