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Third-party annotation is the status quo for labeling text, but egocentric information such as sentiment and belief can at best only be approximated by a third-person proxy. We introduce author labeling, an annotation technique where the…
This article presents the application of the Universal Named Entity framework to generate automatically annotated corpora. By using a workflow that extracts Wikipedia data and meta-data and DBpedia information, we generated an English…
In essence, embedding algorithms work by optimizing the distance between a word and its usual context in order to generate an embedding space that encodes the distributional representation of words. In addition to single words or word…
We describe an effort to annotate a corpus of natural language instructions consisting of 622 wet lab protocols to facilitate automatic or semi-automatic conversion of protocols into a machine-readable format and benefit biological…
While large language models learn sound statistical representations of the language and information therein, ontologies are symbolic knowledge representations that can complement the former ideally. Research at this critical intersection…
The rapidly increasing number of scientific documents available publicly on the Internet creates the challenge of efficiently organizing and indexing these documents. Due to the time consuming and tedious nature of manual classification and…
Nature has inspired various ground-breaking technological developments in applications ranging from robotics to aerospace engineering and the manufacturing of medical devices. However, accessing the information captured in scientific…
Behavioral Profile (BP) annotation is difficult to automate because it requires simultaneous coding across multiple linguistic dimensions. We treat BP annotation as a bundle of annotation skills rather than a single task and evaluate…
Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures. However, annotating these signatures-especially those involving poorly characterized genes-remains a major challenge.…
We describe a formal model for annotating linguistic artifacts, from which we derive an application programming interface (API) to a suite of tools for manipulating these annotations. The abstract logical model provides for a range of…
The large-scale analysis of scholarly artifact usage is constrained primarily by current practices in usage data archiving, privacy issues concerned with the dissemination of usage data, and the lack of a practical ontology for modeling the…
Ontologies play a critical role in Semantic Web technologies by providing a structured and standardized way to represent knowledge and enabling machines to understand the meaning of data. Several taxonomies and ontologies have been…
Materials science literature contains millions of materials synthesis procedures described in unstructured natural language text. Large-scale analysis of these synthesis procedures would facilitate deeper scientific understanding of…
With the rapid development of large language models (LLMs), their application to cell type annotation has drawn increasing attention. However, general-purpose LLMs often face limitations in this specific task due to the lack of guidance…
Despite its scientific, political, and practical value, comprehensive information about human languages, in all their variety and complexity, is not readily obtainable and searchable. One reason is that many language data are collected as…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
This paper introduces a new web-based software tool for annotating text, Text Annotation Graphs, or TAG. It provides functionality for representing complex relationships between words and word phrases that are not available in other…
Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…
The performance of current supervised AI systems is tightly connected to the availability of annotated datasets. Annotations are usually collected through annotation tools, which are often designed for specific tasks and are difficult to…
The digitisation campaigns carried out by libraries and archives in recent years have facilitated access to documents in their collections. However, exploring and exploiting these documents remain difficult tasks due to the sheer quantity…