brat: a Web-based Tool for NLP-Assisted Text Annotation

We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss several case studies of real-world annotation projects using pre-release versions of BRAT and present an evaluation of annotation assisted by semantic class disambiguation on a multicategory entity mention annotation task, showing a 15 % decrease in total annotation time. BRAT is available under an opensource license from

TermEval 2020 : shared task on automatic term extraction using the Annotated Corpora for term Extraction Research (ACTER) dataset

The TermEval 2020 shared task provided a platform for researchers to work on automatic term extraction (ATE) with the same dataset: the Annotated Corpora for Term Extraction Research (ACTER). The dataset covers three languages (English, French, and Dutch) and four domains, of which the domain of heart failure was kept as a held-out test set on which final f1-scores were calculated. The aim was to provide a large, transparent, qualitatively annotated, and diverse dataset to the ATE research community, with the goal of promoting comparative research and thus identifying strengths and weaknesses of various state-of-the-art methodologies. The results show a lot of variation between different systems and illustrate how some methodologies reach higher precision or recall, how different systems extract different types of terms, how some are exceptionally good at finding rare terms, or are less impacted by term length. The current contribution offers an overview of the shared task with a comparative evaluation, which complements the individual papers by all participants

An Infrastructure for acquiring high quality semantic metadata

Because metadata that underlies semantic web applications is gathered from distributed and heterogeneous data sources, it is important to ensure its quality (i.e., reduce duplicates, spelling errors, ambiguities). However, current infrastructures that acquire and integrate semantic data have only marginally addressed the issue of metadata quality. In this paper we present our metadata acquisition infrastructure, ASDI, which pays special attention to ensuring that high quality metadata is derived. Central to the architecture of ASDI is a erification engine that relies on several semantic web tools to check the quality of the derived data. We tested our prototype in the context of building a semantic web portal for our lab, KMi. An experimental evaluation omparing the automatically extracted data against manual annotations indicates that the verification engine enhances the quality of the extracted semantic metadata

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers

Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench

Challenges in creating comprehensive text-processing worklows include a lack of the interoperability of individual components coming from different providers and/or a requirement imposed on the end users to know programming techniques to compose such workflows. In this paper we demonstrate Argo, a web-based system that addresses these issues in several ways. It supports the widely adopted Unstructured Information Management Architecture (UIMA), which handles the problem of interoperability; it provides a web browser-based interface for developing workflows by drawing diagrams composed of a selection of available processing components; and it provides novel user-interactive analytics such as the annotation editor which constitutes a bridge between automatic processing and manual correction. These features extend the target audience of Argo to users with a limited or no technical background. Here, we focus specifically on the construction of advanced workflows, involving multiple branching and merging points, to facilitate various comparative evalutions. Together with the use of user-collaboration capabilities supported in Argo, we demonstrate several use cases including visual inspections, comparisions of multiple processing segments or complete solutions against a reference standard, inter-annotator agreement, and shared task mass evaluations. Ultimetely, Argo emerges as a one-stop workbench for defining, processing, editing and evaluating text processing tasks

Optical tomography: Image improvement using mixed projection of parallel and fan beam modes

Mixed parallel and fan beam projection is a technique used to increase the quality images. This research focuses on enhancing the image quality in optical tomography. Image quality can be defined by measuring the Peak Signal to Noise Ratio (PSNR) and Normalized Mean Square Error (NMSE) parameters. The findings of this research prove that by combining parallel and fan beam projection, the image quality can be increased by more than 10%in terms of its PSNR value and more than 100% in terms of its NMSE value compared to a single parallel beam