From f07c087d04373f8dbceb5f5030e3c8ac5d6e71ca Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:10:04 +0100 Subject: [PATCH 01/17] Update - initial header03-md.md --- docs/_Research-Data-Management/03-md.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 3b911b87..f11c469b 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -5,11 +5,16 @@ layout: default docs_css: markdown redirect_from: /Research-Data-Management empty: true -hide: true +hide: false --- # 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 probably already used it at least once in your life. + +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. + # Metadata standards # Metadata management From 64ffc97f4a74339955549c343f9a75b4732b529d Mon Sep 17 00:00:00 2001 From: cpauvert Date: Thu, 15 Feb 2024 11:18:37 +0100 Subject: [PATCH 02/17] remove empty attribute and fix header space --- docs/_Research-Data-Management/03-md.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index f11c469b..ab5b368c 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -4,13 +4,14 @@ category: Research-Data-Management layout: default docs_css: markdown redirect_from: /Research-Data-Management -empty: true +empty: false hide: false --- # 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 probably already used it at least once in your life. 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. From d848ea3165ce6eaec4433a78e5209d98701fa4bd Mon Sep 17 00:00:00 2001 From: magelm <101332248+magelm@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:35:11 +0100 Subject: [PATCH 03/17] Update 03-md.md skeleton suggestion for md standards --- docs/_Research-Data-Management/03-md.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index ab5b368c..4d600461 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -17,6 +17,12 @@ Before we delve into specifications on what Metadata standards for the Microbiol 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. # Metadata standards +1. from general to more specific more microbiology? >other github page +2. metadatastandards intro for microbiology: etc + +?? file type standards/ technical metadata + + # Metadata management From eb04a60c7fed541f976fc67eda2ffee3a7d5dcee Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:39:03 +0100 Subject: [PATCH 04/17] General metadata description 03-md.md --- docs/_Research-Data-Management/03-md.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 4d600461..d7f1b5be 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -16,6 +16,14 @@ Before we delve into specifications on what Metadata standards for the Microbiol 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 encapsulates: +1. Name of file +2. Type of file +3. Size of file +4. Creation date of file +5. Width of photograph +6. Height of photograph + # Metadata standards 1. from general to more specific more microbiology? >other github page 2. metadatastandards intro for microbiology: etc From a320115f83d7c3e1f3003bf2693ecd9dbd2db89a Mon Sep 17 00:00:00 2001 From: cpauvert Date: Thu, 15 Feb 2024 12:17:07 +0100 Subject: [PATCH 05/17] draft a section on metadata standards with reference to the N4M github --- docs/_Research-Data-Management/03-md.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index d7f1b5be..fe2e8794 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -25,12 +25,15 @@ For example: When you use your smartphone camera to take photos of your loved on 6. Height of photograph # Metadata standards -1. from general to more specific more microbiology? >other github page -2. metadatastandards intro for microbiology: etc -?? file type standards/ technical metadata +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 From 29792e02da765255171b0e2f51da7c166ee76298 Mon Sep 17 00:00:00 2001 From: cpauvert Date: Thu, 15 Feb 2024 12:22:33 +0100 Subject: [PATCH 06/17] add names to contributor lists --- docs/_Getting-Started/03-contributors.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md index 7649ea03..68649946 100644 --- a/docs/_Getting-Started/03-contributors.md +++ b/docs/_Getting-Started/03-contributors.md @@ -11,4 +11,7 @@ docs_css: markdown 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. \ +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. \ From 591cbd22455715676b6819ff0ba259f6fc8e42e6 Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 12:32:21 +0100 Subject: [PATCH 07/17] ## What is metadata and ## when to collect metadata 03-md.md --- docs/_Research-Data-Management/03-md.md | 37 +++++++++++++++++++------ 1 file changed, 28 insertions(+), 9 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index fe2e8794..cb2457ed 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -11,18 +11,37 @@ hide: false # 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. + +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): + +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. + +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. + +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 that should be considered when planning your experiments. -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 probably already used it at least once in your life. +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. -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 encapsulates: -1. Name of file -2. Type of file -3. Size of file -4. Creation date of file -5. Width of photograph -6. Height of photograph # Metadata standards From 4d6229e91f58ca347d8d471332a9ff47a55043ec Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:31:23 +0100 Subject: [PATCH 08/17] minor correction 03-md.md Added reference to FAIR data principles page of this repo --- docs/_Research-Data-Management/03-md.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index cb2457ed..63310eaa 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -31,7 +31,7 @@ For example, when you use your smartphone camera to take photos of your loved on 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. -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. +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**)[./docs/_Research-Data-Management/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. From 86d51a1c95928e7aa67ea50b08fbf29649d34c60 Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:32:44 +0100 Subject: [PATCH 09/17] Quickfix syntax hyperlink 03-md.md --- docs/_Research-Data-Management/03-md.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 63310eaa..6ad32dd4 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -31,7 +31,7 @@ For example, when you use your smartphone camera to take photos of your loved on 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. -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**)[./docs/_Research-Data-Management/04-fair.md] section of this repository. +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**](./docs/_Research-Data-Management/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. From f97d550f2b90e33a92bf7e2cc9847a1420600c9f Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:35:16 +0100 Subject: [PATCH 10/17] quickfix V2 03-md.md --- docs/_Research-Data-Management/03-md.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 6ad32dd4..af2c654a 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -31,7 +31,7 @@ For example, when you use your smartphone camera to take photos of your loved on 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. -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**](./docs/_Research-Data-Management/04-fair.md) section of this repository. +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. From c2ec26c61fe2366b79fcba40e21ea8106d23fd59 Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:42:51 +0100 Subject: [PATCH 11/17] QF v3 Update 03-md.md --- docs/_Research-Data-Management/03-md.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index af2c654a..70453ade 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -10,12 +10,11 @@ hide: false # 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. -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. +Metadata is information that describes other information in order to help you understand or use it. 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): @@ -31,7 +30,7 @@ For example, when you use your smartphone camera to take photos of your loved on 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. -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. +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 don't know what we hint at here, please 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. From c63c70a6b6d0e6f156d58a81b2a30dddab84c9bb Mon Sep 17 00:00:00 2001 From: cpauvert Date: Thu, 15 Feb 2024 14:31:55 +0100 Subject: [PATCH 12/17] precise that we is NFDI4Microbiota and typos --- docs/_Research-Data-Management/03-md.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 70453ade..0d9457a2 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -48,9 +48,8 @@ Once a community agrees to a set of relevant metadata for their field, they can 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) +At NFDI4Microbiota, we compiled a [list of widely used metadata standards in the fied of microbiome research](https://github.com/NFDI4Microbiota/MetadataStandards) that you can browse and use for the different types of data collected during your investigations. # Metadata management From 09c1678f367a7d68a695795c44f879e7a5f35b75 Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 15:37:34 +0100 Subject: [PATCH 13/17] Changed flow and purpose 03-md.md Changed flow of the first section on Metadata is data about data, renamed some headers, added links to existing resources, quality of life improvements --- docs/_Research-Data-Management/03-md.md | 33 +++++++++++-------------- 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 0d9457a2..cd66d95a 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -10,36 +10,31 @@ hide: false # Metadata -## What is metadata? +## Metadata is data about data -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 or would be, let us explain what metadata is. -Metadata is information that describes other information in order to help you understand or use it. 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. +Metadata is information that describes other information in order to help you understand or use it. 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): +If you find our explanation lacking, we refer you to the [FAIR Cook Book](https://faircookbook.elixir-europe.org/content/home.html), more specifically to the [FAIR and the notion of metadata](https://faircookbook.elixir-europe.org/content/recipes/introduction/metadata-fair.html) section. -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.) +## When should you collect your metadata -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. +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: [**Data Management Plans (DMPs)**](./08-dmp.md) that could help you plan your experiments. -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 don't know what we hint at here, please read the [**FAIR Data Principles**](./04-fair.md) section of this repository. +Metadata collection should be planned, but at the same time, it can be overwhelming. What amount of metadata is enough to describe your data? Was it crucial to note down the pipette I was using, or should I have noted down the location of the sampling site? 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? -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. +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. -## When to collect your metadata? +## Metadata collection example -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 that should be considered when planning your experiments. +We will look into an example of microbiological environmental metadata, where we gather samples from a forest environment, specifically plant rhizosphere, and we will be doing amplicon and metagenomic sequencing. We will not dive specifically into all omics types and biological/environmental on this page. Instead, we encourage readers to read our [MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards/tree/main) resource repository. -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. +Our proposal for a sampling campaign to analyze plant-rhizosphere microbiomes was accepted. In the proposal, we outlined the purpose and goal of our campaign. Since our funding is public, our funding agency requires us to submit our generated and gathered data to a public repository (e.g., ENA, NCBI, DDBJ). We immediately jump to [**ENA's Sample Checklist browser**](https://www.ebi.ac.uk/ena/browser/checklists) and find a checklist that best corresponds to our sampling campaign. After some scrolling, we discover the [GSC MIxS plant associated; Checklist: ERC000020](https://www.ebi.ac.uk/ena/browser/view/ERC000020), that list some of the **Mandatory** metadata fields that need to be filled out for data submission, along with their **Field Format** and **Field restriction** and **Optional** fields. The metadata fields correspond to technical metadata (e.g., sequencing method, sample volume or weight for DNA extraction, nucleic acid extraction, library size, etc.) along with some metadata fields corresponding to the biological and environmental metadata (e.g., broad-scale environmental context, local environmental context, environmental medium, geographic location (latitude) and geographic location (longitude), host metadata, sample collection metadata, etc.) +Alternatively, we can hop over to the [MetadataStandards/Plant-associated microbiome biological-environmental metadata](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md) where we can find a similar (but stripped down) checklist with some filed out examples for biological and environmental metadata. For the technical metadata corresponding to this example samling campaign we would refer the reader the [Amplicon sequencing](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Technical/Amplicon_Technical_Metadata.md) and [Metagenome sequencing](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Technical/Metagenome_Technical_Metadata.md) section of our [Technical MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards/tree/main/Technical) part of repository. + +By now, we should have a rough estimation of what kind of biological/environmental metadata we can collect before sampling, during sampling, and what could be collected during the processing of samples. # Metadata standards From 875315c6ca6043449da2a6f31b27641c278b4d4a Mon Sep 17 00:00:00 2001 From: Martin Bole <113352405+MartinBoleSlo@users.noreply.github.com> Date: Thu, 15 Feb 2024 16:22:25 +0100 Subject: [PATCH 14/17] Disclaimer on where to do public repo data deposition 03-md.md --- docs/_Research-Data-Management/03-md.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index cd66d95a..c2403494 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -30,7 +30,9 @@ These and other considerations not noted here should be thoroughly thought out b We will look into an example of microbiological environmental metadata, where we gather samples from a forest environment, specifically plant rhizosphere, and we will be doing amplicon and metagenomic sequencing. We will not dive specifically into all omics types and biological/environmental on this page. Instead, we encourage readers to read our [MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards/tree/main) resource repository. -Our proposal for a sampling campaign to analyze plant-rhizosphere microbiomes was accepted. In the proposal, we outlined the purpose and goal of our campaign. Since our funding is public, our funding agency requires us to submit our generated and gathered data to a public repository (e.g., ENA, NCBI, DDBJ). We immediately jump to [**ENA's Sample Checklist browser**](https://www.ebi.ac.uk/ena/browser/checklists) and find a checklist that best corresponds to our sampling campaign. After some scrolling, we discover the [GSC MIxS plant associated; Checklist: ERC000020](https://www.ebi.ac.uk/ena/browser/view/ERC000020), that list some of the **Mandatory** metadata fields that need to be filled out for data submission, along with their **Field Format** and **Field restriction** and **Optional** fields. The metadata fields correspond to technical metadata (e.g., sequencing method, sample volume or weight for DNA extraction, nucleic acid extraction, library size, etc.) along with some metadata fields corresponding to the biological and environmental metadata (e.g., broad-scale environmental context, local environmental context, environmental medium, geographic location (latitude) and geographic location (longitude), host metadata, sample collection metadata, etc.) +Our proposal for a sampling campaign to analyze plant-rhizosphere microbiomes was accepted. In the proposal, we outlined the purpose and goal of our campaign. Since our funding is public, our funding agency requires us to submit our generated and gathered data to a public repository (e.g., ENA, NCBI, DDBJ). To find where you can deposit your data, we refer our readers to the [Data Repositories](./22-data-repositories.md) section of this KnowledgeBase. There we see that our Nucleic acid sequences can be deposited in ENA. + +We immediately jump to [**ENA's Sample Checklist browser**](https://www.ebi.ac.uk/ena/browser/checklists) and find a checklist that best corresponds to our sampling campaign. After some scrolling, we discover the [GSC MIxS plant associated; Checklist: ERC000020](https://www.ebi.ac.uk/ena/browser/view/ERC000020), that list some of the **Mandatory** metadata fields that need to be filled out for data submission, along with their **Field Format** and **Field restriction** and **Optional** fields. The metadata fields correspond to technical metadata (e.g., sequencing method, sample volume or weight for DNA extraction, nucleic acid extraction, library size, etc.) along with some metadata fields corresponding to the biological and environmental metadata (e.g., broad-scale environmental context, local environmental context, environmental medium, geographic location (latitude) and geographic location (longitude), host metadata, sample collection metadata, etc.) Alternatively, we can hop over to the [MetadataStandards/Plant-associated microbiome biological-environmental metadata](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md) where we can find a similar (but stripped down) checklist with some filed out examples for biological and environmental metadata. For the technical metadata corresponding to this example samling campaign we would refer the reader the [Amplicon sequencing](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Technical/Amplicon_Technical_Metadata.md) and [Metagenome sequencing](https://github.com/NFDI4Microbiota/MetadataStandards/blob/main/Technical/Metagenome_Technical_Metadata.md) section of our [Technical MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards/tree/main/Technical) part of repository. From d6845edd09f0f2710023f148d4a32a13e3001107 Mon Sep 17 00:00:00 2001 From: Charlie Pauvert Date: Thu, 15 Feb 2024 16:46:25 +0100 Subject: [PATCH 15/17] reformulate metadata introduction Co-authored-by: magelm <101332248+magelm@users.noreply.github.com> --- docs/_Research-Data-Management/03-md.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index c2403494..9171ed14 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -14,7 +14,7 @@ hide: false Before we delve into specifications on what Metadata standards for the Microbiology community are or would be, let us explain what metadata is. -Metadata is information that describes other information in order to help you understand or use it. 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. +In general, metadata provides us with information about other data but does not tell us anything about the content of the data itself. Instead, it describes other types of information to help you understand or use the data you are working with. In the simplest terms, metadata is **data** about data. If you find our explanation lacking, we refer you to the [FAIR Cook Book](https://faircookbook.elixir-europe.org/content/home.html), more specifically to the [FAIR and the notion of metadata](https://faircookbook.elixir-europe.org/content/recipes/introduction/metadata-fair.html) section. From 761484ae685aa6cb98b4b5c57c953d00df171850 Mon Sep 17 00:00:00 2001 From: Charlie Pauvert Date: Thu, 15 Feb 2024 16:56:49 +0100 Subject: [PATCH 16/17] fix typos and reformulate metadata section Co-authored-by: magelm <101332248+magelm@users.noreply.github.com> --- docs/_Research-Data-Management/03-md.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index 9171ed14..d9ec5ce4 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -20,9 +20,9 @@ If you find our explanation lacking, we refer you to the [FAIR Cook Book](https: ## When should you 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: [**Data Management Plans (DMPs)**](./08-dmp.md) that could help you plan your experiments. +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 Knowledge Base: [**Data Management Plans (DMPs)**](./08-dmp.md) that could help you plan your experiments. -Metadata collection should be planned, but at the same time, it can be overwhelming. What amount of metadata is enough to describe your data? Was it crucial to note down the pipette I was using, or should I have noted down the location of the sampling site? 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? +Metadata collection should be planned, but at the same time, it can be overwhelming. What amount of metadata is enough to describe your data? Was it crucial to note down the pipette I was using, or should I have noted down the location of the sampling site? Will I still understand in a year 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. From 16c4d97c6f4846b52b927d62fc481cee5d50ca8d Mon Sep 17 00:00:00 2001 From: Charlie Pauvert Date: Thu, 15 Feb 2024 16:59:00 +0100 Subject: [PATCH 17/17] precise cookbook link, reformulation and slim down links Co-authored-by: magelm <101332248+magelm@users.noreply.github.com> --- docs/_Research-Data-Management/03-md.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md index d9ec5ce4..f1af20c0 100644 --- a/docs/_Research-Data-Management/03-md.md +++ b/docs/_Research-Data-Management/03-md.md @@ -12,11 +12,11 @@ hide: false ## Metadata is data about data -Before we delve into specifications on what Metadata standards for the Microbiology community are or would be, let us explain what metadata is. +Before we delve into specifications on what metadata standards for the microbiology community are, let us explain what metadata is. In general, metadata provides us with information about other data but does not tell us anything about the content of the data itself. Instead, it describes other types of information to help you understand or use the data you are working with. In the simplest terms, metadata is **data** about data. -If you find our explanation lacking, we refer you to the [FAIR Cook Book](https://faircookbook.elixir-europe.org/content/home.html), more specifically to the [FAIR and the notion of metadata](https://faircookbook.elixir-europe.org/content/recipes/introduction/metadata-fair.html) section. +For more details on the distinction between different types of metadata, we refer you to the FAIR Cookbook recipe [FAIR and the notion of metadata](https://w3id.org/faircookbook/FCB068) section. ## When should you collect your metadata @@ -24,11 +24,11 @@ As is usually the case in sciences, your research (and the wider microbiological Metadata collection should be planned, but at the same time, it can be overwhelming. What amount of metadata is enough to describe your data? Was it crucial to note down the pipette I was using, or should I have noted down the location of the sampling site? Will I still understand in a year 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. +These and other considerations should be thoroughly thought out before the start of your experimental procedures. Some of the metadata can even be collected and documented before starting the experiments if you already know how to collect your samples, process, sequence them (if sequencing is a part of the analysis), and analyze them. ## Metadata collection example -We will look into an example of microbiological environmental metadata, where we gather samples from a forest environment, specifically plant rhizosphere, and we will be doing amplicon and metagenomic sequencing. We will not dive specifically into all omics types and biological/environmental on this page. Instead, we encourage readers to read our [MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards/tree/main) resource repository. +We will look into an example of microbiological environmental metadata, where we gather samples from a forest environment, specifically plant rhizosphere, and we will be doing amplicon and metagenomic sequencing. We will not dive specifically into all omics types and biological/environmental on this page. Instead, we encourage readers to read our [MetadataStandards](https://github.com/NFDI4Microbiota/MetadataStandards) resource repository. Our proposal for a sampling campaign to analyze plant-rhizosphere microbiomes was accepted. In the proposal, we outlined the purpose and goal of our campaign. Since our funding is public, our funding agency requires us to submit our generated and gathered data to a public repository (e.g., ENA, NCBI, DDBJ). To find where you can deposit your data, we refer our readers to the [Data Repositories](./22-data-repositories.md) section of this KnowledgeBase. There we see that our Nucleic acid sequences can be deposited in ENA.