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Scientific topics: Toxicology  or Data integration and wareho... 

Compartición, análisis y almacenamiento de datos genómicos con RD-Connect GPAP y EGA

El Centro Nacional de Análisis Genómico (CNAG-CRG) y la European Genome-Phenome Archive (EGA) organizan un curso práctico sobre el uso de herramientas para compartir y analizar datos genómicos en el marco del proyecto VEIS - Valorización de EGA para la Industria y la Sociedad. En el primer...

Scientific topics: Data integration and warehousing, Database management, Genomics

Resource type: Video

Compartición, análisis y almacenamiento de datos genómicos con RD-Connect GPAP y EGA http://tess.elixir-uk.org/materials/comparticion-analisis-y-almacenamiento-de-datos-genomicos-con-rd-connect-gpap-y-ega El Centro Nacional de Análisis Genómico (CNAG-CRG) y la European Genome-Phenome Archive (EGA) organizan un curso práctico sobre el uso de herramientas para compartir y analizar datos genómicos en el marco del proyecto VEIS - Valorización de EGA para la Industria y la Sociedad. En el primer módulo del curso se presentará la plataforma RD-Connect GPAP que permite integrar, compartir y analizar datos genómicos y fenotípicos de manera segura entre los equipos clínicos y de investigación autorizados, facilitando el diagnóstico de Enfermedades Raras y la identificación de nuevas asociaciones gen-enfermedad. La interfaz gráfica de la plataforma y sus numerosos recursos conectados permiten analizar e interpretar datos de manera eficaz e intuitiva sin necesidad de tener formación en Bioinformática. La RD-Connect GPAP, coordinada y desarrollada por el CNAG-CRG y reconocida por el International Rare Disease Consortium (IRDiRC), hospeda actualmente datos pseudonimizados de más de 20.000 pacientes y familiares y ha contribuido al diagnóstico de cientos de casos. En el segundo módulo se seguirá la demostración de la plataforma RD-Connect GPAP para el análisis y reanálisis de datos de pacientes con enfermedades raras y se explicará cómo las herramientas ofrecidas por EGA hacen más fácil y segura la compartición y el almacenamiento de los datos. El curso lo impartirán Gemma Bullich y Leslie Matalonga de la Unidad de Bionformática del CNAG-CRG y Teresa d'Altri y Babita Singh de EGA el 17 de diciembre de 10 a 14 h. La agenda del curso es la siguiente: Parte 1. Módulo clínico (RD-Connect GPAP) 1.1 Introducción a la plataforma RD-Connect e importancia del uso de ontologías y estándares (HPO, ORDO, etc) para la integración de datos fenotípicos en el análisis (gen)ómico 1.2 Hands-on: Phenostore: entrada de datos fenotípicos de pacientes con enfermedades raras para el posterior análisis de datos genómicos Parte 2. Módulo genético (EGA y RD-Connect GPAP) 2.1 Secuenciación y análisis de datos genómicos 2.2 European Genome-Phenome Archive y compartición de datos (en inglés) 2.3 Hands-on: Resolución de casos de pacientes con enfermedades raras entrados en parte 1 con RD-Connect GPAP Parte 3. Discusión y preguntas Data integration and warehousing Database management Genomics Clinical Scientists
Making cohort data FAIR

CINECA webinar about how to make data from cohort studies FAIR

Scientific topics: Data management, Data integration and warehousing

Keywords: FAIR data, Cohort data, Ontologies, Standards

Resource type: Video

Making cohort data FAIR http://tess.elixir-uk.org/materials/making-cohort-data-fair CINECA webinar about how to make data from cohort studies FAIR Data management Data integration and warehousing FAIR data, Cohort data, Ontologies, Standards
Annotating data using next generation biobanking ontology (NGBO)

This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO).

Scientific topics: Ontology and terminology, Data integration and warehousing

Keywords: Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary

Resource type: Video

Annotating data using next generation biobanking ontology (NGBO) http://tess.elixir-uk.org/materials/annotating-data-using-next-generation-biobanking-ontology-ngbo This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO). Ontology and terminology Data integration and warehousing Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary
Applying data standards to the harmonization of COVID-19 datasets from different sources

This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations.

Scientific topics: Data integration and warehousing

Keywords: Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies

Resource type: Video

Applying data standards to the harmonization of COVID-19 datasets from different sources http://tess.elixir-uk.org/materials/applying-data-standards-to-the-harmonization-of-covid-19-datasets-from-different-sources This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations. Data integration and warehousing Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Useful ontologies for harmonizing cohort data

This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data.

Scientific topics: Ontology and terminology, Data management, Data integration and warehousing

Keywords: Ontologies, Cohort data, data annotation

Resource type: Video

Useful ontologies for harmonizing cohort data http://tess.elixir-uk.org/materials/useful-ontologies-for-harmonizing-cohort-data This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data. Ontology and terminology Data management Data integration and warehousing Ontologies, Cohort data, data annotation Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Annotating data using ontologies

This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems.

Scientific topics: Ontology and terminology, Data integration and warehousing, Data management

Keywords: Ontologies, Annotation, Data integration

Resource type: Video

Annotating data using ontologies http://tess.elixir-uk.org/materials/annotating-data-using-ontologies This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems. Ontology and terminology Data integration and warehousing Data management Ontologies, Annotation, Data integration
Solutions for overcoming cohort data integration challenges using ontology: an introduction

Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups.

Scientific topics: Data management, Data integration and warehousing, Ontology and terminology

Keywords: Ontologies, Data integration, Annotation

Resource type: Video

Solutions for overcoming cohort data integration challenges using ontology: an introduction http://tess.elixir-uk.org/materials/solutions-for-overcoming-cohort-data-integration-challenges-using-ontology-an-introduction Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups. Data management Data integration and warehousing Ontology and terminology Ontologies, Data integration, Annotation
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop http://tess.elixir-uk.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Adding nanomaterial data http://tess.elixir-uk.org/materials/adding-nanomaterial-data This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format. Database management Toxicology nanotoxicology, enanomapper, resource description framework, ontology programmers data entering