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12 materials found

Scientific topics: Sample collections  or Ontology and terminology 

Expanding the SPHN RDF Schema

This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor.

Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

Operations: Editing, Ontology visualisation, Visualisation, Data handling

Keywords: Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL

Resource type: Video, Training materials, E-learning

Expanding the SPHN RDF Schema http://tess.elixir-uk.org/materials/expanding-the-sphn-rdf-schema This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor. Kristin Gnodke Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Training Primer (RDF and SPARQL)

This training provides a first introduction to RDF and SPARQL.

Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology

Operations: Query and retrieval, Database search, Data handling, Data retrieval

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology

Resource type: Video, Training materials, E-learning

Training Primer (RDF and SPARQL) http://tess.elixir-uk.org/materials/training-primer-rdf-and-sparql This training provides a first introduction to RDF and SPARQL. Sabine Österle Computer science Data management FAIR data Medical informatics Ontology and terminology Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Semantic Standards

This training module provides an introduction on the key semantic standards used within SPHN.

Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

Operations: Standardisation and normalisation, Data handling

Keywords: Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD

Resource type: Video, Training materials, E-learning

Semantic Standards http://tess.elixir-uk.org/materials/semantic-standards This training module provides an introduction on the key semantic standards used within SPHN. Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
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
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
Data harmonization and enrichment using EMBL-EBI ontology tools

This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators...

Scientific topics: Ontology and terminology, Data submission, annotation, and curation, Data management

Keywords: CINECA, data harmonization, Annotation, Ontologies

Resource type: Video

Data harmonization and enrichment using EMBL-EBI ontology tools http://tess.elixir-uk.org/materials/data-harmonization-and-enrichment-using-embl-ebi-ontology-tools This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators access the tools through their respective websites. REST APIs are available for software developers who want to build systems based on these services. Ontology and terminology Data submission, annotation, and curation Data management CINECA, data harmonization, Annotation, Ontologies biocurators software developers, bioinformaticians
bio.tools documentation

Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal.

Scientific topics: Ontology and terminology, Computational biology, Data submission, annotation, and curation, Bioinformatics

Operations: Data retrieval

Keywords: Tools, Curation, Software, Sofware curation, Tool curation

Resource type: Documentation, API reference

bio.tools documentation http://tess.elixir-uk.org/materials/bio-tools-documentation Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal. Ontology and terminology Computational biology Data submission, annotation, and curation Bioinformatics Tools, Curation, Software, Sofware curation, Tool curation Researchers Software providers Developers Curators
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
Ontology Lookup Service (OLS)

This webinar will introduce the OLS system and show how it can be used to find ontologies and ontology terms. We will also cover how you can use OLS services to map existing data to ontologies.

Scientific topics: Ontology and terminology

Resource type: Webinar

Ontology Lookup Service (OLS) http://tess.elixir-uk.org/materials/ontology-lookup-service-ols This webinar will introduce the OLS system and show how it can be used to find ontologies and ontology terms. We will also cover how you can use OLS services to map existing data to ontologies. Ontology and terminology life scientists biocurators
Sample prep for Proteomics

Sample prep for proteomics by Monica Schenone.

Scientific topics: Proteomics, Sample collections

Sample prep for Proteomics http://tess.elixir-uk.org/materials/sample-prep-for-proteomics Sample prep for proteomics by Monica Schenone. Proteomics Sample collections