ELIXIR-UK Fellowship

GTN tutorial. Making clinical datasets FAIR

Wed, 01 Nov 2023 00:00:00 +0000

The life science community is generally very good at sharing omics data on platforms such as GEO and ArrayExpress. However, the metadata and clinical data associated with the omics datasets are often incredibly sparse. Tracking down the meta- and clinical data of omics datasets can be time-consuming for both data owner and researcher and is a significant hurdle when trying to explore enriched omics data.

In this tutorial, you will learn the benefits of making clinical datasets FAIR (Findable, Accessible, Interoperable, and Reusable) and how to make them FAIR.

Using a data catalogue within a research team

Wed, 04 Oct 2023 00:00:00 +0000

Learn what is a basic data catalogue, understand how it can help you manage data files and start with the first steps to create a simple data catalogue using a given example.

00:00 Learning objectives
00:25 Definition of a data catalogue
03:00 Metadata for data catalogues
04:06 Benefits of a well-managed catalogue
05:31 Example of data
06:50 Acknowledgements

Data catalogues for large projects

Wed, 04 Oct 2023 00:00:00 +0000

Understand how to make a data catalogue work for your project, manage details of projects that feed into yours and make the data catalogue easy to use.

00:00 Learning objectives
00:43 Data catalogue: definition
01:44 Study tab
02:25 Data dictionary for the data catalogue
03:47 Tips
05:16 Acknowledgments

Data catalogues for different data types

Wed, 04 Oct 2023 00:00:00 +0000

Capture details of transcriptomic data in a data catalogue, adapt your data catalogue for different data types and understand how to link together related datasets.

00:00 Learning objectives
00:30 Data catalogue: definition
00:58 Example: transcriptomic metadata
01:49 Columns relevant to transcriptomic data
02:40 Image datasets
05:32 Grouping linked datasets
05:00 Acknowledgments

GTN tutorial. Sequence data submission to ENA

Sat, 30 Sep 2023 00:00:00 +0000

In this Galaxy Training Network tutorial you will learn:

To populate ENA metadata objects through the Webin portal
To submit raw reads to ENA using FTP

Time estimation: 1 hour

Tutorial for Canto – PomBase's online community curation tool

Thu, 28 Sep 2023 00:00:00 +0000

Canto is PomBase’s online community curation tool. It enables researchers to participate directly in curating data from new publications to support the small staff of professional curators. This step-by-step tutorial helps these community contributors to curate papers using Canto.

Screenshot of Canto tutorial

GTN tutorial. FAIR data management solutions

Wed, 27 Sep 2023 00:00:00 +0000

The FAIR (Findable, Accessible, Interoperable, Reusable) data stewardship created the foundation for sharing and publishing digital assets, especially data. This apply to machine accessibility and emphasize that all digital assets should share data in a way that will enable maximum use and reuse.

This tutorial is a short introduction to the FAIR data management framework.

FAIRytale. Common themes in data management emerge at the MRC’s open data workshop

Mon, 25 Sep 2023 00:00:00 +0000

In October of 2022, I hosted an all-day seminar at the MRC Biostatistics unit to give a community of like-minded researchers a chance to discuss and explain the implications of open-data practice for their research [1]. The day was a resounding success, with a number of excellent talks and conversations. One thing I found particularly interesting – as a member of the research support team – was how often the same themes re-emerged despite the range of research interests represented. This feeling has only strengthened during my time as a fellow.

While all the conference attendees were from fields broadly considered ‘the life sciences’, the event had an interdisciplinary feel. Even so, throughout various applications, the data needs (and challenges) remained remarkably consistent. Many attendees had heard of the FAIR principles [2][3][4] before, but those that were new to the concepts were surprised by how well FAIR captures the challenges they faced. The dominant feeling over our four sessions was that often, researchers get half/most of the way with their open data effort but then undervalue how important those final steps are.

One ‘final step’ that was often missed was providing long-term hosting solutions for data, and several conversations revolved around how important this is. We heard several horror stories of important data sets that were (in theory) ‘available on request from the corresponding author’ but in actuality, could not be accessed, sometimes as close to 6 months after publication date. Similarly, several attendees had navigated to self-hosted websites that gave 404 errors within a year of being mentioned in published research. While this might seem disheartening, this is something of a solved problem with Figshare [5] and Zenodo [6] providing hosting platforms that will last for as good as forever.

The presence (or absence) of appropriate metadata was a second key finding of our workshop. This was particularly important to researchers using genetics data as minor convention/naming differences could cause several hours to be lost when trying to run the data through a new algorithm. Unfortunately, it can be difficult to establish one-size-fits-all metadata principles as the required information tends to be very field-specific. In an ideal world, everyone would provide ‘as much metadata as possible’, but several colleagues were keen to point out that this is often impractical and leads to crude full data dumps in which useful information is drowned out by unhelpfully large numbers of files containing information of little to no value.

The workshop had a huge range of perspectives, and I found the day fascinating. I hope this FAIRy Tale has helped to illustrate that doing the basics really well can be a huge source of value for both you and future researchers. In particular, it’s essential to use a long-term, stable hosting platform for as much of your research data as possible and to provide accurate, complete and (ideally) concise metadata so that a new researcher can get up to speed with your data as quickly as possible.

GTN tutorial. REMBI, Recommended Metadata for Biological Images – metadata guidelines for bioimaging data

Mon, 11 Sep 2023 00:00:00 +0000

In this Galaxy Training Network tutorial you will:

Organise bioimage metadata
Find out what REMBI is and why it is useful
Categorise what metadata belongs to each of the submodules of REMBI
Gather the metadata for an example bioimage dataset

Time estimation: 15 minutes

GTN tutorial. Filter, plot and explore single-cell RNA-seq data

Mon, 11 Sep 2023 00:00:00 +0000

You’ve done all the work to make a single cell matrix, with gene counts and mitochondrial counts and buckets of cell metadata from all your variables of interest. Now it’s time to fully process your data, to remove low quality cells, to reduce the many dimensions of data that make it difficult to work with, and ultimately to try to define clusters and to find biological meaning and insights.

This tutorial works with Scanpy, because currently Galaxy hosts the most Scanpy tools of all of those options.

ELIXIR-UK Fellowship

GTN tutorial. Making clinical datasets FAIR

Using a data catalogue within a research team

Data catalogues for large projects

Data catalogues for different data types

GTN tutorial. Sequence data submission to ENA

Tutorial for Canto – PomBase's online community curation tool

GTN tutorial. FAIR data management solutions

FAIRytale. Common themes in data management emerge at the MRC’s open data workshop

Further reading

GTN tutorial. REMBI, Recommended Metadata for Biological Images – metadata guidelines for bioimaging data

GTN tutorial. Filter, plot and explore single-cell RNA-seq data