Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes

Twenty-first century mouse genetics is again at an inflection point

The laboratory mouse has been the premier model organism for biomedical research owing to the availability of multiple well-characterized inbred strains, its mammalian physiology and its homozygous genome, and because experiments can be performed under conditions that control environmental variables. Moreover, its genome can be genetically modified to assess the impact of allelic variation on phenotype. Mouse models have been used to discover or test many therapies that are commonly used today. Mouse genetic discoveries are often made using genome-wide association study methods that compare allelic differences in panels of inbred mouse strains with their phenotypic responses. Here we examine changes in the methods used to analyze mouse genetic models of biomedical traits during the twenty-first century. To do this, we first examine where mouse genetics was before the first inflection point, which was just before the revolution in genome sequencing that occurred 20 years ago, and then describe the factors that have accelerated the pace of mouse genetic discovery. We focus on mouse genetic studies that have generated findings that either were translated to humans or could impact clinical medicine or drug development. We next explore how advances in computational capabilities and in DNA sequencing methodology during the past 20 years could enhance the ability of mouse genetics to produce solutions for twenty-first century public-health problems.

Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders

There are >2500 different genetically determined developmental disorders (DD), which, as a group, show very high levels of both locus and allelic heterogeneity. This has led to the wide-spread use of evidence-based filtering of genome-wide sequence data as a diagnostic tool in DD. Determining whether the association of a filtered variant at a specific locus is a plausible explanation of the phenotype in the proband is crucial and commonly requires extensive manual literature review by both clinical scientists and clinicians. Access to a database of weighted clinical features extracted from rigorously curated literature would increase the efficiency of this process and facilitate the development of robust phenotypic similarity metrics. However, given the large and rapidly increasing volume of published information, conventional biocuration approaches are becoming impractical. Here, we present a scalable, automated method for the extraction of categorical phenotypic descriptors from the full-text literature. Papers identified through literature review were downloaded and parsed using the Cadmus custom retrieval package. Human Phenotype Ontology terms were extracted using MetaMap, with 76-84% precision and 65-73% recall. Mean terms per paper increased from 9 in title + abstract, to 68 using full text. We demonstrate that these literature-derived disease models plausibly reflect true disease expressivity more accurately than widely used manually curated models, through comparison with prospectively gathered data from the Deciphering Developmental Disorders study. The area under the curve for receiver operating characteristic (ROC) curves increased by 5-10% through the use of literature-derived models. This work shows that scalable automated literature curation increases performance and adds weight to the need for this strategy to be integrated into informatic variant analysis pipelines. Database URL: https://doi.org/10.1093/database/baac038.

Deep learning-based methods for natural hazard named entity recognition

Natural hazard named entity recognition is a technique used to recognize natural hazard entities from a large number of texts. The method of natural hazard named entity recognition can facilitate acquisition of natural hazards information and provide reference for natural hazard mitigation. The method of named entity recognition has many challenges, such as fast change, multiple types and various forms of named entities. This can introduce difficulties in research of natural hazard named entity recognition. To address the above problem, this paper constructed a natural disaster annotated corpus for training and evaluation model, and selected and compared several deep learning methods based on word vector features. A deep learning method for natural hazard named entity recognition can automatically mine text features and reduce the dependence on manual rules. This paper compares and analyzes the deep learning models from three aspects: pretraining, feature extraction and decoding. A natural hazard named entity recognition method based on deep learning is proposed, namely XLNet-BiLSTM-CRF model. Finally, the research hotspots of natural hazards papers in the past 10 years were obtained through this model. After training, the precision of the XLNet-BilSTM-CRF model is 92.80%, the recall rate is 91.74%, and the F1-score is 92.27%. The results show that this method, which is superior to other methods, can effectively recognize natural hazard named entities.