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506 changes: 0 additions & 506 deletions episodes/01-OS-and-FAIR.md
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140 changes: 0 additions & 140 deletions episodes/02-Intro-to-metadata.md
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---
title: "Introduction to metadata"
<<<<<<< HEAD
teaching: 15
exercises: 20
=======
teaching: 11
exercises: 14
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---

:::::::::::::::::::::::::::::::::::::: questions
Expand All @@ -18,11 +13,7 @@ exercises: 14

::::::::::::::::::::::::::::::::::::: objectives

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- Recognize what metadata is
=======
- Recognise what metadata is
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- Distinguish different types of metadata
- Know how to decide what to include in metadata

Expand All @@ -31,7 +22,6 @@ exercises: 14



<<<<<<< HEAD
(13 min teaching)

## What is (or are) metadata?
Expand All @@ -44,19 +34,6 @@ Simply put, metadata is data about the data. Sound confusing? Let's clarify: met
This is a confocal microscopy image of a *C. elegans* nematode strain used
as a proteostasis model (Pretty! Isn't it?). The image is part of the raw data
associated with [Goya et al., 2020](https://doi.org/10.1016/j.celrep.2019.12.078),
=======
(5 min teaching)

## What is (or are) metadata?

Simply put, metadata is data about the data. Sound confusing? Lets clarify: metadata is the *description of data*. It allows deeper understanding of data and provides insight for its interpretation. Hence, your metadata should be considered as important as your data. Further, metadata plays a very important role in making your data FAIR. It should be continuously added to your research data (not just at the beginning or end of a project!). Metadata can be produced in an automated way (e.g. when you capture a microscopy image usually the accompanying software saves metadata as part of it) or manually.

<ins>Let's take a look at an example:</ins>

This is a confocal microscopy image of a *C. elegans* nematode strain used
as a proteostasis model (Pretty! Isn't it?). The image is part of the raw data
associated to [Goya et al., 2020](https://doi.org/10.1016/j.celrep.2019.12.078),
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which was deposited in a Public Omero Server
[Project](https://publicomero.bio.ed.ac.uk/webclient/?show=project-58)
[Figure1 set](https://publicomero.bio.ed.ac.uk/webclient/?show=dataset-231)
Expand Down Expand Up @@ -142,7 +119,6 @@ This is a lot of information!

## Types of metadata

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According to [How to FAIR](https://howtofair.dk/), we can distinguish between three main types of metadata:

* **Administrative metadata:** Data about a project or resource that is relevant for managing it; for example, project/resource owner, principal investigator, project collaborators, funder, project period, etc. They are usually assigned to the data before you collect or create them.
Expand All @@ -151,35 +127,11 @@ According to [How to FAIR](https://howtofair.dk/), we can distinguish between th

Descriptive and structural **metadata should be added continuously** throughout the project.

=======
According to [How to FAIR](https://howtofair.dk/) we can distinguish
between three main types of metadata:

* **Administrative metadata:** data about a project or resource
that are relevant for managing it; E.g. project/resource owner,
principal investigator, project collaborators, funder, project period,
etc. They are usually assigned to the data, before you collect or create
them.
* **Descriptive or citation metadata:** data about a dataset or
resource that allow people to discover and identify it; E.g.
authors, title, abstract, keywords, persistent identifier, related
publications, etc.
* **Structural metadata:** data about how a dataset or resource
came about, but also how it is internally structured. E.g. the unit
of analysis, collection method, sampling procedure, sample size,
categories, variables, etc. Structural metadata have to be gathered by
the researchers according to best practice in their research community
and will be published together with the data.

Descriptive and structural **metadata should be added
continuously** throughout the project.
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### Examples of metadata

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ere we have an Excel spreadsheet that contains project metadata for a made-up experiment of plant metabolites:

![Metadata in data table example](./fig/04-metadatafull_spreadsheet_solution.png)
Expand All @@ -192,36 +144,13 @@ Different types of metadata (administrative, descriptive, structural) are presen
- Structural metadata marked in green

Embedding metadata with your data as in the example is a very useful technique as the metadata remain joined to the data. As you can see, typically the metadata can be found in column headers (e.g., Strain, Media) or as key-value pairs (e.g., Funder, Protocols).
=======
Here we have an excel spreadsheet that contains project metadata for
a made-up experiment of plant metabolites
![Metadata in data table example](./fig/04-metadatafull_spreadsheet_solution.png)
*Figure credits: Tomasz Zielinski and Andrés Romanowski*

Different types of metadata (administrative,
descriptive, structural) are present in this example.

* Administrative metadata marked in blue
* Descriptive metadata marked in orange
* Structural metadata marked in green

Embedding metadata with your data as in the example is very useful technique
as the metadata remain joined to the data.
As you can see typically the metadata can be found in column headers (eg. Strain, Media) or as key value pairs (eg. Funder, Protocols)
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(6 min teaching)

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Another form of storing metadata is the creation of a README file.

For example, check the README files of two datasets:
=======
Another form of storing metadata is creation of README file.

For example check the README files of two datasets
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* [NMJ analysis](https://github.com/Boehmin/NMJ_analysis)
* [COVID wastewater data](https://github.com/BioRDM/COVID-Wastewater-Scotland)
Expand All @@ -233,53 +162,28 @@ Check what sections the readme files typically include.

## Where does data end and metadata start?

<<<<<<< HEAD
What is "data" and what is "metadata" can be a matter of perspective: Some researchers' metadata can be other researchers' data.

For example, a funding body is categorized as typical administrative metadata; however, it can be used to calculate numbers of public datasets per funder and then used to compare the effects of different funders' policies on open practices.

=======
What is "data" and what is "metadata" can be a matter of
perspective: Some researchers' metadata can be other researchers'
data.

For example, a funding body is categorised as typical administrative metadata,
however, it can be used to calculate numbers of public datasets per funder
and then used to compare effects of different funders' policies on open practices.
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::::

## Adding metadata to your experiments

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Good metadata is crucial for assuring the reusability of your outcomes. Adding metadata is also a very time-consuming process if done manually, so collecting metadata should be done incrementally during your experiment.

As we saw, metadata can take many forms, from as simple as including a ReadMe.txt file, embedding them inside the Excel files, to using domain-specific metadata standards and formats.

=======
Good metadata are crucial for assuring re-usability of your outcomes.
Adding metadata is also a very time-consuming process if done manually,
so collecting metadata should be done incrementally during your experiment.

As we saw metadata can take many forms
from as simple as including a ReadMe.txt file,
by embedding them inside the Excel files,
to using domain specific metadata standards and formats.
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But,
* **What should be included in metadata?**
* **What terms should be used in descriptions?**

::::::::::::: challenge

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## Exercise 1: What to include - discussion
(5 minutes breakout + 7 discussing results)
=======
## Exercise 1: What to include - discussion (5 minutes)
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Think of the data you generate in your projects,
and imagine you are going to share them.
Expand Down Expand Up @@ -313,7 +217,6 @@ Some typical elements are:
:::::::::::::

## Minimal Information Standard
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For many assay methods and experiment types, there are defined recommendations and guidelines called **Minimal Information Standards (MIS)**.

The minimum information standard is a set of guidelines for reporting data derived by relevant methods in the biosciences. Following these guidelines ensures that the data can be easily:
Expand All @@ -335,27 +238,6 @@ Individual minimum information standards are developed by communities of cross-d


![Minimum information standards](./fig/02-MinimumInformationStandarts.png)
=======

For many assay methods and experiment types, there are defined recommendations
and guidelines called **Minimal Information Standards**.


The minimum information standard is a set of guidelines for reporting data
derived by relevant methods in biosciences.
If followed, it ensures that the data can be easily verified,
analysed and clearly interpreted by the wider scientific community.
Keeping with these recommendations also facilitates the foundation of structuralized
databases, public repositories and development of data analysis tools.

Individual minimum information standards are brought by the communities of cross-disciplinary
specialists focused on issues of the specific method used in experimental biology.

Minimum Information for Biological and Biomedical Investigations [(MIBBI)](https://fairsharing.org/collection/MIBBI)
is the collection of the most known standards.

![Minimum information standards](./fig/02-MinimumInformationStandarts.png)
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Figure. Some of the MIBBI minimum information standards from fairsharing.org


Expand All @@ -365,20 +247,12 @@ for finding standards
::::::::::::: challenge

## Exercise 2: Minimal information standard example (5 min)
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(about 4 + 2 discussion)

Look at the document titled "**Minimum Information About a Neuroscience Investigation (MINI) Electrophysiology**" (Gibson, F. et al. Nat Prec (2008): [https://www.nature.com/articles/npre.2008.1720.1.pdf](https://www.nature.com/articles/npre.2008.1720.1.pdf)), which contains recommendations for reporting the use of electrophysiology in a neuroscience study.
(*Neuroscience (or neurobiology) is the scientific study of the nervous system*).


=======

Look at ***Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology***
[Gibson, F. et al. Nat Prec (2008)](https://www.nature.com/articles/npre.2008.1720.1.pdf).
which contains recommendations for reporting the use of electrophysiology in a neuroscience study.
(*Neuroscience (or neurobiology) is the scientific study of the nervous system*).
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Scroll to *Reporting requirement* and decide which of the points 1-8 are:

Expand All @@ -399,7 +273,6 @@ Look at the document titled "**Minimum Information About a Neuroscience Investig
:::::::::::::


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(3 min)

## Metadata and FAIR guidelines
Expand All @@ -410,19 +283,6 @@ Since metadata is data about data, all of the FAIR principles (Findable, Accessi

Ideally, metadata should be not only machine-readable but also interoperable so that computer systems can interlink or reason about it.

=======


## Metadata and FAIR guidelines
Metadata provides extremely valuable information for us and others to be able to
interpret, process, reuse and reproduce the research data it accompanies.

Because metadata are data about data, all of the FAIR principles i.e.
Findable, Accessible, Interoperable and Reusable apply to metadata.

Ideally, metadata should not only be machine-readable, but also interoperable
so that they can interlink or be reasoned about by computer systems.
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## Attribution
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