Related papers: Automatic annotation of bioinformatics workflows w…
This paper presents a new annotated corpus of 513 anonymized radiology reports written in Spanish. Reports were manually annotated with entities, negation and uncertainty terms and relations. The corpus was conceived as an evaluation…
Sentiment analysis is often a crowdsourcing task prone to subjective labels given by many annotators. It is not yet fully understood how the annotation bias of each annotator can be modeled correctly with state-of-the-art methods. However,…
Data annotated by humans is a source of knowledge by describing the peculiarities of the problem and therefore fueling the decision process of the trained model. Unfortunately, the annotation process for subjective natural language…
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…
Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies…
The automation of text summarisation of biomedical publications is a pressing need due to the plethora of information available on-line. This paper explores the impact of several supervised machine learning approaches for extracting…
The article presents an overview of current specialized ontology engineering tools, as well as texts' annotation tools based on ontologies. The main functions and features of these tools, their advantages and disadvantages are discussed. A…
Automated text annotation is a compelling use case for generative large language models (LLMs) in social media research. Recent work suggests that LLMs can achieve strong performance on annotation tasks; however, these studies evaluate LLMs…
Obituaries contain information about people's values across times and cultures, which makes them a useful resource for exploring cultural history. They are typically structured similarly, with sections corresponding to Personal Information,…
Automatic summarization has consistently attracted attention due to its versatility and wide application in various downstream tasks. Despite its popularity, we find that annotation efforts have largely been disjointed, and have lacked…
We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for…
The delineation of logical definitions for each class in an ontology and the consistent application of these definitions to the assignment of instances to classes are important criteria for ontology evaluation. If ontologies are specified…
Automatic annotation of documents with controlled vocabulary terms (descriptors) from a conceptual thesaurus is not only useful for document indexing and retrieval. The mapping of texts onto the same thesaurus furthermore allows to…
Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires…
Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the…
Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics,…
Ontologies in the biomedical domain are numerous, highly specialized and very expensive to develop. Thus, a crucial prerequisite for ontology adoption and reuse is effective support for exploring and finding existing ontologies. Towards…
Summary descriptions of subroutines are short (usually one-sentence) natural language explanations of a subroutine's behavior and purpose in a program. These summaries are ubiquitous in documentation, and many tools such as JavaDocs and…
Clinical notes are an efficient way to record patient information but are notoriously hard to decipher for non-experts. Automatically simplifying medical text can empower patients with valuable information about their health, while saving…
Information Extraction is a well-researched area of Natural Language Processing with applications in web search and question answering concerned with identifying entities and relationships between them as expressed in a given context,…