9 materials found

Scientific topics: Database management 


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 https://tess.elixir-europe.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
A Critical Guide to the PDB

This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures. The rationale for creating the resource and the kinds of information it provides are discussed,...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures

A Critical Guide to the PDB https://tess.elixir-europe.org/materials/a-critical-guide-to-the-pdb This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures. The rationale for creating the resource and the kinds of information it provides are discussed, and issues relating to its evolution and growth are explored. Specifically, this Guide introduces the principal features of the PDB, the nature (and quality) of its contents and how these may be interrogated. On reading this Guide, users will be able to: i) explain some of the ways in which knowledge of protein structures is useful; ii) identify the constituent databases of the wwPDB; iii) explain key features of the RCSB PDB in terms of its data distribution, growth and redundancy statistics; iv) search the PDB using simple and advanced keywords and full sequences, and analyse differences between them; and v) explain various structural quality criteria, and infer the quality of individual PDB entries. Database management Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures Beginners 2018-09-08
A Critical Guide to InterPro

This Critical Guide in the Introduction to Bioinformatics series provides an introduction to the InterPro database, the largest, most comprehensive, integrated protein family database in the world. The rationale for creating the resource, the nature of its contributing databases and the kinds of...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis

A Critical Guide to InterPro https://tess.elixir-europe.org/materials/a-critical-guide-to-interpro This Critical Guide in the Introduction to Bioinformatics series provides an introduction to the InterPro database, the largest, most comprehensive, integrated protein family database in the world. The rationale for creating the resource, the nature of its contributing databases and the kinds of information they provide are discussed, and the role of InterPro in protein classification and function-annotation projects is outlined. Specifically, this Guide introduces the principal components of the InterPro database, the differences between them, and how their integration creates a resource whose diagnostic power is greater than the sum of its parts. On reading this Guide, users will be able to: i) explain how protein family databases are used to help annotate uncharacterised protein sequences; ii) identify InterPro’s constituent data resources and explain the main methods that underpin them; iii) search InterPro using keywords and full sequences; iv) analyse and interpret search results in terms of protein family hierarchies, their structural domains and functional features; and v) track the provenance of InterPro’s annotations. Database management Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis Beginners 2018-09-08
A Critical Guide to the UniProtKB Flat-file Format

This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data. Web-based interfaces have made databases more user-friendly, but knowledge of the underlying file format offers a deeper understanding of how to navigate...

Scientific topics: Database management

Keywords: Flat file databases, Flat files, Introduction bioinformatics, Uniprotkb flat file format

A Critical Guide to the UniProtKB Flat-file Format https://tess.elixir-europe.org/materials/a-critical-guide-to-the-uniprotkb-flat-file-format This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data. Web-based interfaces have made databases more user-friendly, but knowledge of the underlying file format offers a deeper understanding of how to navigate and mine the information they contain, so that humans and machines can get the most out of them. This Guide explores the file format that underpins one of today’s most popular protein sequence databases – UniProtKB. Specifically, this Guide introduces the concept of database ‘flat-files’, and examines features of the UniProtKB flat-file format. On reading this Guide, users will be able to: i) identify key fields within UniProtKB/Swiss-Prot and UniProtKB/TrEMBL flat-files; ii) explain what these fields mean, what information they contain and what the information is used for; iii) analyse the information in different fields and infer structural and functional features of a sequence; iv) examine and investigate the provenance of annotations; and v) compare annotations at different time-points and evaluate the likely impact of annotation changes. Database management Flat file databases, Flat files, Introduction bioinformatics, Uniprotkb flat file format Beginners 2018-09-08
A Critical Guide to UniProtKB

This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the UniProt protein sequence database, with a particular focus on the UniProt Knowledgebase – UniProtKB. The rationale for creating the resource, its contributing databases and the kinds of information...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction uniprot, Protein sequence databases, Uniprot knowledgebase

A Critical Guide to UniProtKB https://tess.elixir-europe.org/materials/a-critical-guide-to-uniprotkb This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the UniProt protein sequence database, with a particular focus on the UniProt Knowledgebase – UniProtKB. The rationale for creating the resource, its contributing databases and the kinds of information they provide are discussed, and issues behind the quality of their annotations are explored. Specifically, this Guide introduces the principal components of the UniProt Knowledgebase, and the differences between them. On reading this Guide, users will be able to: i) identify and explain the characteristic features of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entries; ii) distinguish annotations that are computed, and hence not experimentally validated; iii) search UniProtKB using keywords, full sequences and peptides, and interpret the results; iv) analyse and track the provenance of annotations; and v) infer which annotations are likely to be accurate and which erroneous. Database management Introduction bioinformatics, Introduction uniprot, Protein sequence databases, Uniprot knowledgebase Beginners 2018-09-08
Intermine 2.0

Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015 Created at: 2nd BiVi Annual Meeting.

Scientific topics: Database management

Keywords: Databases

Resource type: Slideshow

Intermine 2.0 https://tess.elixir-europe.org/materials/intermine-2-0 Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015 Created at: 2nd BiVi Annual Meeting. Ms. Yo Yehudi Database management Databases 2017-02-03
Reactome

Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Scientific topics: Database management, Pathway or network

Keywords: Pathway, Databases

Resource type: Slideshow

Reactome https://tess.elixir-europe.org/materials/reactome Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Konstantinos Sidiropoulos Database management Pathway or network Pathway, Databases 2017-02-03
Zegami: Digital Data Integration, Visualisation and Management

Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated...

Scientific topics: Database management

Keywords: Cells and Organisms, Databases

Resource type: Video

Zegami: Digital Data Integration, Visualisation and Management https://tess.elixir-europe.org/materials/zegami-digital-data-integration-visualisation-and-management Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated metadata) on a massive scale allowing querying and organisation of large image based collections. The talk will show various examples of its usage in biology and beyond, and will look at new features such as annotation to build training sets for machine learning. Created at: 3rd BiVi Annual Meeting (2017). Stephen Taylor Database management Cells and Organisms, Databases 2017-05-12
TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/tgac_seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data analysis for plant species data Data quality checks Estimation of reproducibility Batch effects Statistical concepts Importance of standards Data formats Data integration What will I learn? To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions Identify key challenges, opportunities and bottlenecks Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics Sequence analysis Plant biology Database management Bioinformatics Ngs, Ngs bioinformatics, Plants bioinformatics PhD students plant researchers post-docs 2015-06-22 2017-10-09