Genetic variation is fundamental to the evolution of all species and is what makes us individuals. Our genes have a large influence on our lives. They affect what we look like, our personalities and preferences and our susceptibility to disease. By studying genetic variation we hope to understand the molecular processes that contribute to life on earth.

By the end of the course you will be able to:
List examples of genetic variation databases
Describe the type of data found in different genetic variation databases
Explore genetic variation data within publicly available resources

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Soil and sediment microorganisms are remarkably diverse and are critical for ecosystem health. However, they are underrepresented in public databases, and assembling new metaproteomic datasets is challenging, which makes it difficult to characterize the microorganisms in specific soil samples. To increase the outputs of soil metaproteomic studies, a recent study compared various database construction strategies. Search strategies using either sample-specific metagenomic databases or public databases produced comparable peptide-spectrum matches for a floodplain soil core. However, a two-step cascaded search combining both types of databases led to greater peptide-spectrum matching. The combination strategy also improved functional annotation of the peptides, and the resulting metaproteome (MetaP) annotations correlated well with the metagenome (MetaG) annotations..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This quick tour provides a brief introduction to the EMBL-EBI's molecular interactions database, IntAct.

By the end of the course you will be able to:
Describe IntAct and how it can help you to find information on molecular interactions
Explore where to find out more about IntAct

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites – the metabolome – with that of genes, transcripts, and proteins (the genome, transcriptome, and metabolome).

The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive, high quality and freely accessible resource of protein sequences and functional information. UniProtKB integrates, interprets and standardizes data from a range of sources including the scientific literature, tools for protein sequence analysis, other knowledge resources and databases, and automatic annotation systems, to provide a detailed overview of the available protein knowledge.

This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge.

Who is this course for?
This webinar targets life scientists and bioinformaticians who study enzymes and small molecules, particularly those interested in linking or bridging the two domains. No prior knowledge of bioinformatics or cheminformatics is required, but an undergraduate level knowledge of biology/ biochemistry would be useful.

Outcomes
By the end of the webinar you will be able to:

Describe how UniProt annotates enzyme and transporter function, and where the data comes from
Find and retrieve information about specific enzymes, transporters and the metabolites on which they act, by searching UniProtKB using text, chemical structures, and chemical classifications
Help us develop the representation of small molecule data in UniProtKB by providing valuable feedback

Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as genes and proteins, metabolites, species, mutations, phosphorylations, interactions, associations, and many more.

This webinar will demonstrate how to access text-mined literature evidence programmatically, and how to supplement it with bibliographic information for advanced use cases. Two of such use cases, mapping of tropical disease research by author affiliation geoparsing and comparison of applicability of analytical chemistry techniques, will be introduced by invited speaker, Dr. Magnus Palmblad.

Who is this course for?
This webinar is aimed at individuals who wish to learn about accessing text-mined literature evidence programmatically. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

This course provides an insight into the different protein family building methodologies employed by three InterPro member databases, namely SFLD (Structure Function Linkage Database), TIGRFAMs and PANTHER. It also describes an automated approach to comparing protein signatures and predicting hierarchical relationships between them.

By the end of the course you will be able to:
Identify differences and similarities in methodologies of protein signature creation by SFLD, TIGRFAMs and PANTHER
Illustrate how protein signatures can be compared to predict relationships between them

InterPro is a classification database that provides predictive information about protein sequences.

By the end of the course you will be able to:
search the InterPro database in a number of different ways
interpret the information in an InterPro entry page
review the graphical representation of the signature matches on an InterPro protein page

This quick tour provides a brief introduction to InterPro, EMBL-EBI's database of protein families, domains and functional sites.

By the end of the course you will be able to:
explain what InterPro is and how it can help you to relate protein architecture to function
determine where to find out more about InterPro

This webinar is about InterProScan, the underlying software application that scans both protein and nucleic acid sequences against InterPro's predictive models, which are provided by the InterPro’s member databases. InterPro is a freely available resource used to classify sequences into protein families and to predict the presence of important domains and sites.

Who is this course for?
This webinar is aimed at scientists and bioinformaticians with an interest in using InterProScan for protein functional analysis or anyone with interest in protein sequence annotation using InterPro. A basic knowledge of using the command line interface is recommended for this webinar.

The International Mouse Phenotyping Consortium (IMPC) portal provides a freely available comprehensive catalogue of mammalian gene function, using the mouse as a model. By applying a standardised phenotyping pipeline to single-gene knockout mouse lines, the IMPC identifies the physiological systems that are disrupted when a gene is disabled and thus establish gene-phenotype associations. This course will show you how to navigate the IMPC portal to find phenotypes, disease models and knockout mouse strains for a gene of interest.

By the end of the course you will be able to:
Describe what the IMPC is and what data you can find within the IMPC portal
Determine whether there are phenotypes and/or potential disease models for your gene of interest
Identify whether there are genes associated with a phenotype you are interested in
Establish whether there are knockout mouse strains available for your gene of interest and know how to order them

The IMPC is an international research infrastructure, comprised by 21 of the leading mouse genetics centres worldwide, that is systematically identifying the function of every protein-coding gene in the mouse genome. Despite having sequenced the entire genomes of many species, the exact function of most genes remains unknown. To address this, the IMPC is coordinating the production of a knockout mouse strain per protein-coding gene, which are then characterised using a standardised, broad-based phenotyping pipeline, giving insights into the function for genes for which very little is known. Our open-access database now includes phenotyping data for nearly 6,500 mouse genes.

This webinar will discuss some of the exciting discoveries in genetic disease, development and sexual dimorphism that biologists and clinical researchers are making using IMPC resources. The IMPC strives to generate data that ultimately help understand human health and disease and identify new targets for therapeutic intervention. This data is also useful for research focusing on other mammalian species, including evolutionary research studies seeking to understand adaptation.

All IMPC data is freely available to use and can be accessed at www.mousephenotype.org. The IMPC would like to encourage researchers to get in touch via the IMPC website if they are interested in using IMPC data and would like further guidance on how to use our data.

Who is this course for?
This webinar is suitable for anyone interested in learning more about the IMPC. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended.

Outcomes
By the end of the webinar you will be able to:

List the aims of the IMPC
Describe discoveries made using IMPC resources
Navigate www.mousephenotype.org to access IMPC data

This webinar will provide an interactive introduction to the new UniProt Disease Portal: a single centralised resource of UniProt disease-centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability.

The UniProt knowledgebase (UniProtKB) supports biomedical research by providing a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. To do this, UniProt integrates, interprets and standardises data from a range of sources including scientific literature, protein sequence analysis tools, other databases and automatic annotation systems to provide a detailed overview of the available protein knowledge.

This webinar will introduce you to the UniProt Disease Portal which aims to help researchers explore and access current genomic disease-related data from the UniProtKB database, but in a single centralised resource. The portal incorporates UniProt functional annotations, protein network visualisations, genomic variant and drug-related data, and organises in a way that allows users to easily visualise and compare data to identify similarities using variants, protein interactions, diseases, and drug data.

The Disease Portal is currently in its first beta release, so we hope that this interactive introduction will give you an understanding of how to access disease-centric protein data in UniProt and encourage your feedback to assist ongoing development of the Portal to further suit the requirements of our users.

Who is this course for?
This webinar is aimed at individuals who have an interest in protein disease biology, would like an interactive introduction to the new disease portal, and/or wish to learn about how disease data is collected and annotated in UniProt. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Navigate the beta UniProt disease portal to find and discover information on proteins and therapeutic drugs of interest
Understand how UniProt annotates disease data and identify where the data comes from
Help us develop the UniProt Disease Portal by providing valuable feedback

This webinar will give an introduction to programmatic access at PDBe, highlighting the type of data that is available and how this can be utilised.

This webinar is part of a 6-part PDBe API webinar series, introducing different levels of programmatic access at PDBe.The series will range from basic data retrieval and search using the PDBe API to more advanced features, including access and reuse of PDBe data visualisation components.

Who is this course for?
This webinar is open to anyone who is interested in learning about the programmatic access of PDBe.

Outcomes
By the end of the webinar you will be able to:

Discover how to programmatically access data at PDBe
Explore the type of data available at PDBe

European Genome-phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects.

This webinar aims to cover a quick introduction to EGA by exploring topics ranging from searching and accessing data in EGA to interpreting Data Use Ontology (DUO) codes. We will also demonstrate downloading data with an EGA test account.

Who is this course for?
Anyone who is interested in secure archiving or accessing distribution services for controlled access to human biomedical omics data. An undergraduate level knowledge of biology, and in particular some knowledge of genetics and genomics, would be an advantage.

Outcomes
By the end of the webinar you will be able to:

Explore the scope of EGA
Explain the usage of DUO codes
Access and download data from EGA

This webinar will introduce the Complex Portal, an encyclopaedic database for information on macromolecular complexes. In this webinar we will explain the coverage and curation priorities of the Complex Portal, show how to search for complexes using a variety of accession numbers, keywords and how to use the organism search. We will also demonstrate examples of complex details pages that include visualisation tools and link-outs to related database.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about the Complex Portal. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Explore the Complex Portal resource
Search for the information on macromolecular complexes
Identify data visualisation tools

This curated pathway brings together a number of online tutorials and recorded webinars to provide an introduction to bioinformatics, a brief tour of the resources available from EMBL-EBI and more details about some of those resources, including Ensembl, UniProt and Expression Atlas.

By the end of the course you will be able to:
Outline what bioinformatics is
Describe the importance of data management
Recall which resources are available from EMBL-EBI
Know where to find information about genes
View information on gene expression
Search for protein information
Know where to find out more about EMBL-EBI resources

This webinar will include a brief introduction to the GWAS Catalog, followed by hands-on demonstrations and exercises covering different methods for accessing GWAS Catalog data, focusing on the most common use-cases. This will include our web-based search interface, with a number of different tools for data access and visualisation, and download of filtered datasets. We will also briefly introduce and describe how to submit your own data.

Who is this course for?
This webinar will be suitable to a wide range of scientists, clinicians and statisticians who are interested in the applications of GWAS Catalog that includes prioritising candidate loci, gathering statistics on traits or populations of interest, exploring disease mechanisms, predicting risk of disease, and discovering drug targets, among other goals.

Outcomes
By the end of the webinar you will be able to:

Describe the role of the GWAS Catalog
Search the GWAS Catalog website
Know how to submit data

LIMSwiki is a collaborative wiki dedicated to the scientific community, featuring organized, documented, and up-to-date content regarding all aspects of laboratory informatics, bioinformatics, and health informatics. LIMSwiki also strives to maintain relevant knowledge about laboratory equipment as well as commercial and open-source software likely to be used in a laboratory setting. This also includes the vendors of such equipment and software.