This paper presents the integration of Word-Net knowledge resource into ClinIDMap tool, which aims to map identifiers between clinical ontologies and lexical resources.ClinIDMap interlinks identifiers from UMLS, SMOMED-CT, ICD-10 and the corresponding Wikidata and Wikipedia articles for concepts from the UMLS Metathesaurus.The main goal of the tool is to provide semantic interoperability across the clinical concepts from various knowledge bases.As a side effect, the mapping enriches already annotated medical corpora in multiple languages with new labels.In this new release, we add WordNet 3.0 and 3.1 synsets using the available mappings through Wikidata.Thanks to cross-lingual links in MCR we also include the corresponding synsets in other languages and also, extend further ClinIDMap with different domain information.Finally, the final resource helps in the task of enriching of already annotated clinical corpora with additional semantic annotations.

Natural Language Processing (NLP) based on new deep learning technology is contributing to the emergence of powerful solutions that help healthcare providers and researchers discover valuable patterns within insurmountable volumes of health records and scientific literature. Fundamental to the success of such solutions is the processing of negation and speculation. The article addresses this problem with state-of-the-art deep learning approaches from two perspectives: cue and scope labelling, and assertion classification. In light of the real struggle to access clinical annotated data, the study (a) proposes a methodology to automatically convert cue-scope annotations to assertion annotations; and (b) includes a range of scenarios with varying amounts of training data and adversarial test examples. The results expose the clear advantage of Transformer-based models in this regard, managing to overpass a series of baselines and the related work in the public corpus NUBes of clinical Spanish text.

The de-identification of sensible data, also known as automatic textual anonymisation, is essential for data sharing and reuse, both for research and commercial purposes. The first step for data anonymisation is the detection of sensible entities. In this work, we present four new datasets for named entity detection in Spanish in the legal domain. These datasets have been generated in the framework of the MAPA project, three smaller datasets have been manually annotated and one large dataset has been automatically annotated, with an estimated error rate of around 14%. In order to assess the quality of the generated datasets, we have used them to fine-tune a battery of entity-detection models, using as foundation different pre-trained language models: one multilingual, two general-domain monolingual and one in-domain monolingual. We compare the results obtained, which validate the datasets as a valuable resource to fine-tune models for the task of named entity detection. We further explore the proposed methodology by applying it to a real use case scenario.

This paper presents ClinIDMap, a tool for mapping identifiers between clinical ontologies and lexical resources. ClinIDMap interlinks identifiers from UMLS, SMOMED-CT, ICD-10 and the corresponding Wikipedia articles for concepts from the UMLS Metathesaurus. Our main goal is to provide semantic interoperability across the clinical concepts from various knowledge bases. As a side effect, the mapping enriches already annotated corpora in multiple languages with new labels. For instance, spans manually annotated with IDs from UMLS can be annotated with Semantic Types and Groups, and its corresponding SNOMED CT and ICD-10 IDs. We also experiment with sequence labelling models for detecting Diagnosis and Procedures concepts and for detecting UMLS Semantic Groups trained on Spanish, English, and bilingual corpora obtained with the new mapping procedure. The ClinIDMap tool is publicly available.

We describe the MAPA project, funded under the Connecting Europe Facility programme, whose goal is the development of an open-source de-identification toolkit for all official European Union languages. It will be developed since January 2020 until December 2021.

The European MAPA (Multilingual Anonymisation for Public Administrations) project aims at developing an open-source solution for automatic de-identification of medical and legal documents. We introduce here the context, partners and aims of the project, and report on preliminary results.

This paper introduces the first version of the NUBes corpus (Negation and Uncertainty annotations in Biomedical texts in Spanish). The corpus is part of an on-going research and currently consists of 29,682 sentences obtained from anonymised health records annotated with negation and uncertainty. The article includes an exhaustive comparison with similar corpora in Spanish, and presents the main annotation and design decisions. Additionally, we perform preliminary experiments using deep learning algorithms to validate the annotated dataset. As far as we know, NUBes is the largest available corpora for negation in Spanish and the first that also incorporates the annotation of speculation cues, scopes, and events.

HitzalMed is a web-framed tool that performs automatic detection of sensitive information in clinical texts using machine learning algorithms reported to be competitive for the task. Moreover, once sensitive information is detected, different anonymisation techniques are implemented that are configurable by the user –for instance, substitution, where sensitive items are replaced by same category text in an effort to generate a new document that looks as natural as the original one. The tool is able to get data from different document formats and outputs downloadable anonymised data. This paper presents the anonymisation and substitution technology and the demonstrator which is publicly available at https://snlt.vicomtech.org/hitzalmed.

Massive digital data processing provides a wide range of opportunities and benefits, but at the cost of endangering personal data privacy. Anonymisation consists in removing or replacing sensitive information from data, enabling its exploitation for different purposes while preserving the privacy of individuals. Over the years, a lot of automatic anonymisation systems have been proposed; however, depending on the type of data, the target language or the availability of training documents, the task remains challenging still. The emergence of novel deep-learning models during the last two years has brought large improvements to the state of the art in the field of Natural Language Processing. These advancements have been most noticeably led by BERT, a model proposed by Google in 2018, and the shared language models pre-trained on millions of documents. In this paper, we use a BERT-based sequence labelling model to conduct a series of anonymisation experiments on several clinical datasets in Spanish. We also compare BERT with other algorithms. The experiments show that a simple BERT-based model with general-domain pre-training obtains highly competitive results without any domain specific feature engineering.

MOTIVATION: Biomedical literature is one of the most relevant sources of information for knowledge mining in the field of Bioinformatics. In spite of English being the most widely addressed language in the field; in recent years, there has been a growing interest from the natural language processing community in dealing with languages other than English. However, the availability of language resources and tools for appropriate treatment of non-English texts is lacking behind. Our research is concerned with the semantic annotation of biomedical texts in the Spanish language, which can be considered an under-resourced language where biomedical text processing is concerned. RESULTS: We have carried out experiments to assess the effectiveness of several methods for the automatic annotation of biomedical texts in Spanish. One approach is based on the linguistic analysis of Spanish texts and their annotation using an information retrieval and concept disambiguation approach. A second method takes advantage of a Spanish-English machine translation process to annotate English documents and transfer annotations back to Spanish. A third method takes advantage of the combination of both procedures. Our evaluation shows that a combined system has competitive advantages over the two individual procedures. AVAILABILITY AND IMPLEMENTATION: UMLSMapper (https://snlt.vicomtech.org/umlsmapper) and the annotation transfer tool (http://scientmin.taln.upf.edu/anntransfer/) are freely available for research purposes as web services and/or demos. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

OSINT stands for Open Source Intelligence. The CAPER project has built an OSINT solution oriented to the prevention of organised crime. We offer in this paper an overall view of some results, embedding into the system legal and ethical issues raised by the General Data Reform Package (GDRP) in Europe. We briefly describe CAPER architecture, workflow, functionalities, modules and ontologies (European LEAs Interoperability ELIO, and Multi-Lingual Crime Ontology MCO). This paper is focused on the indirect strategy to flesh out Privacy by Design principles (PbD) through the Caper Regulatory Model (CRM).

The Web is a huge virtual space where to express and share individual opinions, influencing any aspect of life, with implications for marketing and communication alike. Social Media are influencing consumersâ preferences by shaping their attitudes and behaviors. Monitoring the Social Media activities is a good way to measure customersâ loyalty, keeping a track on their sentiment towards brands or products. Social Media are the next logical marketing arena. Currently, Facebook dominates the digital marketing space, followed closely by Twitter. This paper describes a Sentiment Analysis study performed on over than 1000 Facebook posts about newscasts, comparing the sentiment for Rai - the Italian public broadcasting service - towards the emerging and more dynamic private company La7. This study maps study results with observations made by the Osservatorio di Pavia, which is an Italian institute of research specialised in media analysis at theoretical and empirical level, engaged in the analysis of political communication in the mass media. This study takes also in account the data provided by Auditel regarding newscast audience, correlating the analysis of Social Media, of Facebook in particular, with measurable data, available to public domain.