Scientific literature encodes a wealth of knowledge relevant to various users. However, the complexity of scientific jargon makes it inaccessible to all but domain specialists. It would be helpful for different types of people to be able to get at least a gist of a paper. Biomedical practitioners often find it difficult to keep up with the information load; but even lay people would benefit from scientific information, for example to dispel medical misconceptions. Besides, in many countries, familiarity with English is limited, let alone scientific English, even among professionals. All this points to the need for simplified access to the scientific literature. We thus present an application aimed at solving this problem, which is capable of summarising scientific text in a way that is tailored to specific types of users, and in their native language. For this objective, we used an LLM that our system queries using user-selected parameters. We conducted an informal evaluation of this prototype using a questionnaire in 3 different languages.

This paper introduces a multi-lingual database containing translated texts of COVID-19 mythbusters. The database has translations into 115 languages as well as the original English texts, of which the original texts are published by World Health Organization (WHO). This paper then presents preliminary analyses on latin-alphabet-based texts to see the potential of the database as a resource for multilingual linguistic analyses. The analyses on latin-alphabet-based texts gave interesting insights into the resource. While the amount of translated texts in each language was small, character bi-grams with normalization (lowercasing and removal of diacritics) was turned out to be an effective proxy for measuring the similarity of the languages, and the affinity ranking of language pairs could be obtained. Additionally, the hierarchical clustering analysis is performed using the character bigram overlap ratio of every possible pair of languages. The result shows the cluster of Germanic languages, Romance languages, and Southern Bantu languages. In sum, the multilingual database not only offers fixed set of materials in numerous languages, but also serves as a preliminary tool to identify the language family using text-based similarity measure of bigram overlap ratio.

Several web services for various natural language processing (NLP) tasks (‘‘NLP-as-a-service” or NLPaaS) have recently been made publicly available. However, despite their similar functionality these services often differ in the protocols they use, thus complicating the development of clients accessing them. A survey of currently available NLPaaS services suggests that it may be possible to identify a minimal application layer protocol that can be shared by NLPaaS services without sacrificing functionality or convenience, while at the same time simplifying the development of clients for these services. In this paper, we hope to raise awareness of the interoperability problems caused by the variety of existing web service protocols, and describe an effort to identify a set of best practices for NLPaaS protocol design. To that end, we survey and compare protocols used by NLPaaS services and suggest how these protocols may be further aligned to reduce variation.

This paper describes an ecosystem consisting of three independent text annotation platforms. To demonstrate their ability to work in concert, we illustrate how to use them to address an interactive domain adaptation task in biomedical entity recognition. The platforms and the approach are in general domain-independent and can be readily applied to other areas of science.

Annotating medical text such as clinical notes with human phenotype descriptors is an important task that can, for example, assist in building patient profiles. To automatically annotate text one usually needs a dictionary of predefined terms. However, do to the variety of human expressiveness, current state-of-the art phenotype concept recognizers and automatic annotators struggle with specific domain issues and challenges. In this paper we present results of an-notating gold standard corpus with a dictionary containing lexical variants for the Human Phenotype Ontology terms. The main purpose of the dictionary is to improve the recall of phenotype concept recognition systems. We compare the method with four other approaches and present results.

This paper presents our findings on the feasibility of doing pronoun resolution for biomedical texts, in comparison with conducting pronoun resolution for the newswire domain. In our experiments, we built a simple machine learning-based pronoun resolution system, and evaluated the system on three different corpora: MUC, ACE, and GENIA. Comparative statistics not only reveal the noticeable issues in constructing an effective pronoun resolution system for a new domain, but also provides a comprehensive view of those corpora often used for this task.

This paper discusses an augmentation of a corpus ofresearch abstracts in biomedical domain (the GENIA corpus) with two kinds of annotations: tree annotation and event annotation. The tree annotation identifies the linguistic structure that encodes the relations among entities. The event annotation reveals the semantic structure of the biological interaction events encoded in the text. With these annotations we aim to provide a link between the clue and the target of biological event information extraction.