The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Despite great strides in the development and wide acceptance of standards for exchanging structured information about genomic variants, there is no corresponding standard for exchanging phenotypic data, and this has impeded the sharing of phenotypic information for computational analysis. Here, we introduce the Global Alliance for Genomics and Health (GA4GH) Phenopacket schema, which supports exchange of computable longitudinal case-level phenotypic information for diagnosis and research of all types of disease including Mendelian and complex genetic diseases, cancer, and infectious diseases. To support translational research, diagnostics, and personalized healthcare, phenopackets are designed to be used across a comprehensive landscape of applications including biobanks, databases and registries, clinical information systems such as Electronic Health Records, genomic matchmaking, diagnostic laboratories, and computational tools. The Phenopacket schema is a freely available, community-driven standard that streamlines exchange and systematic use of phenotypic data and will facilitate sophisticated computational analysis of both clinical and genomic information to help improve our understanding of diseases and our ability to manage them.

Natural Language Mapping of Electrocardiogram Interpretations to a Standardized Ontology

Background Interpretations of the electrocardiogram (ECG) are often prepared using software outside the electronic health record (EHR) and imported via an interface as a narrative note. Thus, natural language processing is required to create a computable representation of the findings. Challenges include misspellings, nonstandard abbreviations, jargon, and equivocation in diagnostic interpretations. Objectives Our objective was to develop an algorithm to reliably and efficiently extract such information and map it to the standardized ECG ontology developed jointly by the American Heart Association, the American College of Cardiology Foundation, and the Heart Rhythm Society. The algorithm was to be designed to be easily modifiable for use with EHRs and ECG reporting systems other than the ones studied. Methods An algorithm using natural language processing techniques was developed in structured query language to extract and map quantitative and diagnostic information from ECG narrative reports to the cardiology societies' standardized ECG ontology. The algorithm was developed using a training dataset of 43,861 ECG reports and applied to a test dataset of 46,873 reports. Results Accuracy, precision, recall, and the F1-measure were all 100% in the test dataset for the extraction of quantitative data (e.g., PR and QTc interval, atrial and ventricular heart rate). Performances for matches in each diagnostic category in the standardized ECG ontology were all above 99% in the test dataset. The processing speed was approximately 20,000 reports per minute. We externally validated the algorithm from another institution that used a different ECG reporting system and found similar performance. Conclusion The developed algorithm had high performance for creating a computable representation of ECG interpretations. Software and lookup tables are provided that can easily be modified for local customization and for use with other EHR and ECG reporting systems. This algorithm has utility for research and in clinical decision-support where incorporation of ECG findings is desired.

The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX)

An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.

Un modèle de description de ressources, basé sur des critères didactiques et inscrit dans une perspective EIAHA resource description model, based on didactic criteria and part of an EIAH perspective

RésuméNous présentons dans cette contribution un modèle de description de ressources de type exercices de mathématiques. Ce modèle permet, à partir d’éléments liés aux tâches et aux ostensifs mobilisés dans l’exercice, d’en obtenir une description fondée sur des critères didactiques. Le travail réalisé donne un rôle central à un modèle praxéologique de référence et à sa représentation informatique proposée dans le cadre de référence T4TEL. Il permet de calculer, à partir d’une description initiale basée sur les tâches et les objets ostensifs, plusieurs informations complémentaires sur la ressource afin d’en obtenir une description augmentée.Mots-clés: Ressource, objet ostensif, T4TEL.AbstractWe aim at defining a model of description of resources such as mathematics exercises. Starting from elements related to the tasks and the ostensive objects used in the exercises, this model enables us to get a description based on didactics criteria. The work which is carried on gives a main role to a praxeological model of reference and its computable representation defined in the theoretical framework T4TEL. This model enables to obtain further information from an initial description based on tasks and ostensive objects.Keywords: Ressource, ostensive object, T4TEL.