Related papers: BioInfoBase : A Bioinformatics Resourceome
The objective of automated Question Answering (QA) systems is to provide answers to user queries in a time efficient manner. The answers are usually found in either databases (or knowledge bases) or a collection of documents commonly…
Developing a universal model that can efficiently and effectively respond to a wide range of information access requests -- from retrieval to recommendation to question answering -- has been a long-lasting goal in the information retrieval…
Manual digitization of bibliographic metadata is time consuming and labor intensive, especially for historical and real-world archives with highly variable formatting across documents. Despite advances in machine learning, the absence of…
Curation of biomedical knowledge bases (KBs) relies on extracting accurate multi-entity relational facts from the literature - a process that remains largely manual and expert-driven. An essential step in this workflow is retrieving…
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue…
We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data.…
As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that…
Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and…
The exponential growth of scientific production makes secondary literature abridgements increasingly demanding. We introduce a new open-source framework for systematic reviews that significantly reduces time and workload for collecting and…
Terpenoids are a crucial class of natural products that have been studied for over 150 years, but their interdisciplinary nature (spanning chemistry, pharmacology, and biology) complicates knowledge integration. To address this, the authors…
Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is…
Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable…
The global influence of Big Data is not only growing but seemingly endless. The trend is leaning towards knowledge that is attained easily and quickly from massive pools of Big Data. Today we are living in the technological world that Dr.…
We have recently built a database system called BODHI, intended to store plant bio-diversity information. It is based on an object-oriented modeling approach and is developed completely around public-domain software. The unique feature of…
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds…
F1000 is a post-publication peer review service for biological and medical research. F1000 aims to recommend important publications in the biomedical literature, and from this perspective F1000 could be an interesting tool for research…
Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
We present WebFAQ, a large-scale collection of open-domain question answering datasets derived from FAQ-style schema.org annotations. In total, the data collection consists of 96 million natural question-answer (QA) pairs across 75…
While scientists increasingly recognize the importance of metadata in describing their data, spreadsheets remain the preferred tool for supplying this information despite their limitations in ensuring compliance and quality. Various tools…