2,549 research outputs found
Initial Implementation of a Comparative Data Analysis Ontology
Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs), representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research
Natural Language Interfaces for Tabular Data Querying and Visualization: A Survey
The emergence of natural language processing has revolutionized the way users
interact with tabular data, enabling a shift from traditional query languages
and manual plotting to more intuitive, language-based interfaces. The rise of
large language models (LLMs) such as ChatGPT and its successors has further
advanced this field, opening new avenues for natural language processing
techniques. This survey presents a comprehensive overview of natural language
interfaces for tabular data querying and visualization, which allow users to
interact with data using natural language queries. We introduce the fundamental
concepts and techniques underlying these interfaces with a particular emphasis
on semantic parsing, the key technology facilitating the translation from
natural language to SQL queries or data visualization commands. We then delve
into the recent advancements in Text-to-SQL and Text-to-Vis problems from the
perspectives of datasets, methodologies, metrics, and system designs. This
includes a deep dive into the influence of LLMs, highlighting their strengths,
limitations, and potential for future improvements. Through this survey, we aim
to provide a roadmap for researchers and practitioners interested in developing
and applying natural language interfaces for data interaction in the era of
large language models.Comment: 20 pages, 4 figures, 5 tables. Submitted to IEEE TKD
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