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Add metadata and ontologies informations #104

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5 changes: 4 additions & 1 deletion docs/_Getting-Started/03-contributors.md
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4. Konrad U. Förstner (ORCID ID: [0000-0002-1481-2996](http://orcid.org/0000-0002-1481-2996))
5. Paul M. J. Klemm (ORCID ID: [0000-0002-3609-5713](https://orcid.org/0000-0002-3609-5713))
6. Uta Parmaksiz (ORCID ID: [0000-0002-0087-5056](https://orcid.org/0000-0002-0087-5056))
7. \<Enter your name here>
7. Charlie Pauvert (ORCID ID: [0000-0001-9832-2507](https://orcid.org/0000-0001-9832-2507))
8. Maja Magel (ORCID ID: [0009-0004-2517-0791](https://orcid.org/0009-0004-2517-0791))
9. Martin Bole (ORCID ID: [0009-0004-9189-8852](https://orcid.org/0009-0004-9189-8852))
10. \<Enter your name here>
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# Metadata

## What is metadata?
## What is metadata?

Before we delve into specifications on what Metadata standards for the Microbiology community are or would be, let us explain what metadata is and how you have probably already used it at least once.
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Before we delve into specifications on what Metadata standards for the Microbiology community are or would be, let us explain what metadata is and how you have probably already used it at least once.
Before we delve into specifications on what metadata standards for the microbiology community are, let us explain what metadata is and how to use it. Maybe you are already doing it unintentionally.


In the simplest terms, metadata is **data** about data. So, in general, metadata provides us with information about other data but does not tell us anything about the content of the data itself.

For example, when you use your smartphone camera to take photos of your loved one, your device automatically creates the corresponding metadata regarding that photograph. The metadata, in this case, should at least contain the following (depending on your device settings):
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For example, when you use your smartphone camera to take photos of your loved one, your device automatically creates the corresponding metadata regarding that photograph. The metadata, in this case, should at least contain the following (depending on your device settings):
For example, when you use your smartphone camera to take photos of your loved one, your device automatically creates the corresponding metadata regarding that photograph. In this case, the metadata should at least contain the following (depending on your device settings):


1. Name of file (e.g., *20221110_141434.jpg)*)
2. Type of file (e.g. *JPEG image (image/jpeg)*)
3. Size of file (e.g. *1,2 MB (1.213.634 bytes)*)
4. Camera information: Lens, focal length, aperture, exposure, ISO speed, flash, shutter count
6. Creation date of file (e.g., *2024-02-14 09:53:47*)
7. Width of photograph (e.g. 2435 pixels)
8. Height of photograph (e.g., 2435 pixels)
9. Location stamp (if enabled in the device) (e.g., 51.312568, 12.412855)
10. Several permissions and locations of the file (owner, access, etc.)

Several years later, you find the photo on your **new mobile device**, and you start to wonder **where** and **when** you took the picture. You open up the photograph file description, and there it is. Even on your new device, you can still access the metadata of the photograph you took several years before. So you can correctly recall when the photo was taken and where it was created. If the environmental conditions match, you can replicate the photograph using the Camera information.
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It is worth noting here that in this particular case, your metadata was interoperable (you could access it even on your new mobile device - by you and your device), and it was reusable (in theory, you could use the metadata of the original photo to replicate it, even several years later). Still, it was not findable or accessible for anyone else. If you do not know to what we are hinting here, we advise you to read the [**FAIR Data Principles**](./04-fair.md) section of this repository.

In this particular case, we could consider ourselves lucky as the metadata for our photograph was created automatically. That might not always be the case when dealing with (meta)data generated in our research.

## When to collect your metadata?

As is usually the case in sciences, your research (and the wider microbiological community) can benefit highly from the rigorous and timely planning of your experiments, including metadata collection. In this case, we refer you to other subsections of this KnowledgeBase <insert_appropriate_links_inside_repo> that should be considered when planning your experiments.

Metadata collection should be planned, but at the same time, it can be overwhelming. What is enough to describe it? Was it crucial to note down the pipette I was using? Will one year older me understand what I wrote down in my notebook/ELN? Will other researchers make sense of the (meta)data I collected? Will other researchers be able to replicate my research if I did not note down my in-house DNA extraction protocol? These and other considerations not noted here should be thoroughly thought out before the start of experimental procedures. Some of the metadata can even be collected and documented before the start of experiments if you already know how to collect your samples, sequence them (if sequencing is a part of the analysis), and analyze them.



# Metadata standards

Once a community agrees to a set of relevant metadata for their field, they can devise metadata standards.
A metadata standard is usually defined for a given type of data and by different stakeholders (e.g., users community, data repositories).
For every metadata fields part of a metadata standard, one could expect a human-readable description of the metadata field paired with a machine-readable persistent identifier of the field, then an indication of the level of requirements of this field in the standard and how many values of this field are expected (that is the cardinality).


[More than a thousand standards are listed by the organisation `FAIRsharing.org`](https://fairsharing.org/search?fairsharingRegistry=Standard) which can be overwhelming.
We compiled a [list of widely used metadata standards in the fied of microbiome research](https://github.com/NFDI4Microbiota/MetadataStandards)


# Metadata management

# Metadata quality control
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