A new synonym-substitution method to enrich the human phenotype ontology

Abstract Background Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technologies in bioinformatics, providing resources for improved natural language processing tasks. However, biomedical ontology-based named entity recognition continues to be a major research problem. Results This paper presents an automated synonym-substitution method to enrich the Human Phenotype Ontology (HPO) with new synonyms. The approach is mainly based on both the lexical properties of the terms and the hierarchical structure of the ontology. By scanning the lexical difference between a term and its descendant terms, the method can learn new names and modifiers in order to generate synonyms for the descendant terms. By searching for the exact phrases in MEDLINE, the method can automatically rule out illogical candidate synonyms. In total, 745 new terms were identified. These terms were indirectly evaluated through the concept annotations on a gold standard corpus and also by document retrieval on a collection of abstracts on hereditary diseases. A moderate improvement in the F-measure performance on the gold standard corpus was observed. Additionally, 6% more abstracts on hereditary diseases were retrieved, and this percentage was 33% higher if only the highly informative concepts were considered. Conclusions A synonym-substitution procedure that leverages the HPO hierarchical structure works well for a reliable and automatic extension of the terminology. The results show that the generated synonyms have a positive impact on concept recognition, mainly those synonyms corresponding to highly informative HPO terms

An Application of Natural Language Processing for Triangulation of Cognitive Load Assessments in Third Level Education

Work has been done to measure Mental Workload based on applications mainly related to ergonomics, human factors, and Machine Learning. The influence of Machine Learning is a reflection of an increased use of new technologies applied to areas conventionally dominated by theoretical approaches. However, collaboration between MWL and Natural Language Processing techniques seems to happen rarely. In this sense, the objective of this research is to make use of Natural Languages Processing techniques to contribute to the analysis of the relationship between Mental Workload subjective measures and Relative Frequency Ratios of keywords gathered during pre-tasks and post-tasks of MWL activities in third-level sessions under different topics and instructional designs. This research employs secondary, empirical and inductive methods to investigate Cognitive Load theory, instructional designs, Mental Workload foundations and measures and Natural Language Process Techniques. Then, NASA-TLX, Workload Profile and Relative Frequency Ratios are calculated. Finally, the relationship between NASA-TLX and Workload Profile and Relative Frequency Ratios is analysed using parametric and non-parametric statistical techniques. Results show that the relationship between Mental Workload and Relative Frequency Ratios of keywords, is only medium correlated, or not correlated at all. Furthermore, it has been found out that instructional designs based on the process of hearing and seeing, and the interaction between participants, can overcome other approaches such as those that make use of videos supported with images and text, or of a lecturer\u27s speech supported with slides

Una herramienta basada en terminologías estandarizadas para la anotación semántica de información textual

El objetivo de esta tesis es el diseño e implementación de técnicas léxicas, sintácticas y semánticas que permitan aprovechar al máximo los recursos de conocimiento disponibles para mejorar la extracción y el análisis de la información relevante contenida en las publicaciones científicas

Additional file 3: of A new synonym-substitution method to enrich the human phenotype ontology

Supplementary information: Full list of the 20 synonyms generated by our method from the release of the HPO from January 13, 2016 and provided by the version of the HPO from April 13, 2017. (CSV 1 kb

Additional file 1: of A new synonym-substitution method to enrich the human phenotype ontology

Supplementary information: Full list of resulting lexical overlaps. (TXT 25 kb