Corrigendum: A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

[This corrects the article DOI: 10.3389/fpls.2020.

A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

Rice, L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, and , which result from a combination of natural and human selection.

Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties.

Formal definitions allow selecting terms (e.g., identifying all terms related to "Infectious disease" using the query "has causative agent organism") and terminological reasoning (e.

Semantic Queries Expedite MedDRA Terms Selection Thanks to a Dedicated User Interface: A Pilot Study on Five Medical Conditions.

Searching into the MedDRA terminology is usually limited to a hierarchical search, and/or a string search. Our objective was to compare user performances when using a new kind of user interface enabling semantic queries versus classical methods, and evaluating term selection improvement in MedDRA. We implemented a forms-based web interface: OntoADR Query Tools (OQT).

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications.

Background: Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups.

OntoADR a semantic resource describing adverse drug reactions to support searching, coding, and information retrieval.

Introduction: Efficient searching and coding in databases that use terminological resources requires that they support efficient data retrieval. The Medical Dictionary for Regulatory Activities (MedDRA) is a reference terminology for several countries and organizations to code adverse drug reactions (ADRs) for pharmacovigilance. Ontologies that are available in the medical domain provide several advantages such as reasoning to improve data retrieval.

MedDRA® automated term groupings using OntoADR: evaluation with upper gastrointestinal bleedings.

Objective: To propose a method to build customized sets of MedDRA terms for the description of a medical condition. We illustrate this method with upper gastrointestinal bleedings (UGIB).

Research Design And Methods: We created a broad list of MedDRA terms related to UGIB and defined a gold standard with the help of experts.

Open access resources for genome-wide association mapping in rice.

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop.

How we remember what we can do.

According to the motor simulation theory, the knowledge we possess of what we can do is based on simulation mechanisms triggered by an off-line activation of the brain areas involved in motor control. Action capabilities memory does not work by storing some content, but consists in the capacity, rooted in sensory-motor systems, to reenact off-line action sequences exhibiting the range of our powers. In this paper, I present several arguments from cognitive neuropsychology, but also first-person analysis of experience, against this hypothesis.

Bridging data models and terminologies to support adverse drug event reporting using EHR data.

Introduction: This article is part of the Focus Theme of METHODs of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

Background: SALUS project aims at building an interoperability platform and a dedicated toolkit to enable secondary use of electronic health records (EHR) data for post marketing drug surveillance. An important component of this toolkit is a drug-related adverse events (AE) reporting system designed to facilitate and accelerate the reporting process using automatic prepopulation mechanisms.

Describing localized diseases in medical ontology: an FMA-based algorithm.

OntolUrgences is a termino-ontological resource developed to index and retrieve information in electronic Emergency Medical Record. In this project, we improved the ontology coverage to accommodate both anatomical and pathophysiological concepts in emergency medicine. This work lead to the automatic addition of 3,470 concepts and their underlying semantic formalization.

Automatic annotation of ICD-to-MedDRA mappings with SKOS predicates.

Robust alignments between ICD and MedDRA are essential to enable the secondary use of clinical data for pharmacovigilance research. UMLS makes available ICD-to-MedDRA mappings, but they are only poorly specified, which introduces difficulties when exploited in an automatic way. SKOS vocabulary can help achieve quality and machine-processable mappings.

Ci4SeR--curation interface for semantic resources--evaluation with adverse drug reactions.

Evaluation and validation have become a crucial problem for the development of semantic resources. We developed Ci4SeR, a Graphical User Interface to optimize the curation work (not taking into account structural aspects), suitable for any type of resource with lightweight description logic. We tested it on OntoADR, an ontology of adverse drug reactions.

Reasons (not) to Spend a Few Billions More on EHRs: How Human Factors Research Can Help.

Objectives: To select best medical informatics research works published in 2013 on electronic health record (EHR) adoption, design, and impact, from the perspective of human factors and organizational issues (HFOI).

Methods: We selected 2,764 papers by querying PubMed (Mesh and TIAB) as well as using a manual search. Papers were evaluated based on pre-defined exclusion and inclusion criteria from their title, keywords, and abstract to select 15 candidate best papers, finally reviewed by 4 external reviewers using a standard evaluation grid.

Formalizing MedDRA to support semantic reasoning on adverse drug reaction terms.

Although MedDRA has obvious advantages over previous terminologies for coding adverse drug reactions and discovering potential signals using data mining techniques, its terminological organization constrains users to search terms according to predefined categories. Adding formal definitions to MedDRA would allow retrieval of terms according to a case definition that may correspond to novel categories that are not currently available in the terminology. To achieve semantic reasoning with MedDRA, we have associated formal definitions to MedDRA terms in an OWL file named OntoADR that is the result of our first step for providing an "ontologized" version of MedDRA.

Standard-based EHR-enabled applications for clinical research and patient safety: CDISC - IHE QRPH - EHR4CR & SALUS collaboration.

Integration profiles collaboratively developed by CDISC and IHE for integrating data from Electronic Health Records (EHRs) with clinical research and pharmacovigilance are limited to resolving lexical/syntactic data integration issues and do not address semantic barriers. This paper describes the collaboration between two European projects - EHR4CR and SALUS - in implementing ISO/IEC 11179-based metadata registries (MDRs) and semantically integrated cross-platform data access. A common "semantic MDR" provides a framework for bidirectional/cross-MDR mapping and federated queries are enabled using the newly-defined IHE Data Exchange (DEX) profile.

Why Medical Informatics (still) Needs Cognitive and Social Sciences.

Objectives: To summarize current excellent medical informatics research in the field of human factors and organizational issues.

Methods: Using PubMed, a total of 3,024 papers were selected from 17 journals. The papers were evaluated on the basis of their title, keywords, and abstract, using several exclusion and inclusion criteria.

Building a time-saving and adaptable tool to report adverse drug events.

The difficult task of detecting adverse drug events (ADEs) and the tedious process of building manual reports of ADE occurrences out of patient profiles result in a majority of adverse reactions not being reported to health regulatory authorities. The SALUS individual case safety report (ICSR) reporting tool, a component currently developed within the SALUS project, aims to support semi-automatic reporting of ADEs to regulatory authorities. In this paper, we present an initial design and current state of of our ICSR reporting tool that features: (i) automatic pre-population of reporting forms through extraction of the patient data contained in an Electronic Health Record (EHR); (ii) generation and electronic submission of the completed ICSRs by the physician to regulatory authorities; and (iii) integration of the reporting process into the physician's work-flow to limit the disturbance.

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement.

More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers.

Evaluation of automated term groupings for detecting anaphylactic shock signals for drugs.

Signal detection in pharmacovigilance should take into account all terms related to a medical concept rather than a single term. We built an OWL-DL file with formal definitions of MedDRA and SNOMED-CT concepts and performed two queries, Query 1 and 2, to retrieve narrow and broad terms within the Standard MedDRA Query (SMQ) related to 'anaphylactic shock' and the terms from the High Level Term (HLT) grouping related to 'anaphylaxis'. We compared values of the EB05 (EBGM) statistical test for disproportionality with 50 active ingredients randomly selected in the public version of the FDA pharmacovigilance database.

PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants.

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants.

Automatic generation of MedDRA terms groupings using an ontology.

In the context of PROTECT European project, we have developed an ontology of adverse drug reactions (OntoADR) based on the original MedDRA hierarchy and a query-based method to achieve automatic MedDRA terms groupings for improving pharmacovigilance signal detection. Those groupings were evaluated against standard handmade MedDRA groupings corresponding to first priority pharmacovigilance safety topics. Our results demonstrate that this automatic method allows catching most of the terms present in the reference groupings, and suggest that it could offer an important saving of time for the achievement of pharmacovigilance groupings.

HopX1 in Erwinia amylovora functions as an avirulence protein in apple and is regulated by HrpL.

Fire blight is a devastating disease of rosaceous plants caused by the Gram-negative bacterium Erwinia amylovora. This pathogen delivers virulence proteins into host cells utilizing the type III secretion system (T3SS). Expression of the T3SS and of translocated and secreted substrates is activated by the alternative sigma factor HrpL, which recognizes hrp box promoters upstream of regulated genes.

Gramene database in 2010: updates and extensions.

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice.