Entity normalization (or entity linking) is an important subtask of information extraction that links entity mentions in text to categories or concepts in a reference vocabulary. Machine learning based normalization methods have good adaptability as long as they have enough training data per reference with a sufficient quality. Distributional representations are commonly used because of their capacity to handle different expressions with similar meanings. However, in specific technical and scientific domains, the small amount of training data and the relatively small size of specialized corpora remain major challenges. Recently, the machine learning-based CONTES method has addressed these challenges for reference vocabularies that are ontologies, as is often the case in life sciences and biomedical domains. And yet, its performance is dependent on manually annotated corpus. Furthermore, like other machine learning based methods, parametrization remains tricky. We propose a new approach to address the scarcity of training data that extends the CONTES method by corpus selection, pre-processing and weak supervision strategies, which can yield high-performance results without any manually annotated examples. We also study which hyperparameters are most influential, with sometimes different patterns compared to previous work. The results show that our approach significantly improves accuracy and outperforms previous state-of-the-art algorithms.

This paper presents the fourth edition of the Bacteria Biotope task at BioNLP Open Shared Tasks 2019. The task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts, and the characterization of these entities with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on biodiversity for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, and the challenge organization. We also provide an analysis of the results obtained by participants, and inspect the evolution of the results since the last edition in 2016.

We propose in this paper a semi-supervised method for labeling terms of texts with concepts of a domain ontology. The method generates continuous vector representations of complex terms in a semantic space structured by the ontology. The proposed method relies on a distributional semantics approach, which generates initial vectors for each of the extracted terms. Then these vectors are embedded in the vector space constructed from the structure of the ontology. This embedding is carried out by training a linear model. Finally, we apply a distance calculation to determine the proximity between vectors of terms and vectors of concepts and thus to assign ontology labels to terms. We have evaluated the quality of these representations for a normalization task by using the concepts of an ontology as semantic labels. Normalization of terms is an important step to extract a part of the information containing in texts, but the vector space generated might find other applications. The performance of this method is comparable to that of the state of the art for this task of standardization, opening up encouraging prospects.

The Quæro program that promotes research and industrial innovation on technologies for automatic analysis and classification of multimedia and multilingual documents. Within its context a set of evaluations of Named Entity recognition systems was held in 2009. Four tasks were defined. The first two concerned traditional named entities in French broadcast news for one (a rerun of ESTER 2) and of OCR-ed old newspapers for the other. The third was a gene and protein name extraction in medical abstracts. The last one was the detection of references in patents. Four different partners participated, giving a total of 16 systems. We provide a synthetic descriptions of all of them classifying them by the main approaches chosen (resource-based, rules-based or statistical), without forgetting the fact that any modern system is at some point hybrid. The metric (the relatively standard Slot Error Rate) and the results are also presented and discussed. Finally, a process is ongoing with preliminary acceptance of the partners to ensure the availability for the community of all the corpora used with the exception of the non-Quæro produced ESTER 2 one.