From fb2240885b636ad6e059539f97834cc0634ff703 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Thu, 15 Feb 2024 11:53:02 +0100
Subject: [PATCH 01/27] Update 22-data-repositories.md

-added protein structure data repositories (PDBe, PDBj, RCSB PDB)
-minor spelling correction
-added link to DB resource page (NAR journal help page)
---
 docs/_Research-Data-Management/22-data-repositories.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/docs/_Research-Data-Management/22-data-repositories.md b/docs/_Research-Data-Management/22-data-repositories.md
index 9322e93a..55275dfb 100644
--- a/docs/_Research-Data-Management/22-data-repositories.md
+++ b/docs/_Research-Data-Management/22-data-repositories.md
@@ -33,8 +33,8 @@ Below are listed criteria you might want to consider when selecting a repository
 4. A cost-free interdisciplinary repository (e.g. [Figshare](https://figshare.com/), [Zenodo](https://zenodo.org/)).
 5. Another repository that you can search for using the above-mentioned criteria in a repository finder. 
 
-## Well-established repositories in microbiology
-Below are liste well-established repositories in microbiology. For each repository, the FAIRsharing and re3data pages are linked. On the FAIRsharing page, you will find information such as which journals endorse the repository (under "Collections & Recommendations" and then "In Policies"). On the re3data page, you will find information such as the above-mentioned criteria to select a trusted repoository.
+## Well-established repositories for data deposition in microbiology
+Below are listed well-established repositories in microbiology. For each repository, the FAIRsharing and re3data pages are linked. On the FAIRsharing page, you will find information such as which journals endorse the repository (under "Collections & Recommendations" and then "In Policies"). On the re3data page, you will find information such as the above-mentioned criteria to select a trusted repoository.
 
 | Data type 	| Data repository 	| FAIRsharing 	| re3data 	| 
 |---	|---	|---	|---	|
@@ -45,6 +45,9 @@ Below are liste well-established repositories in microbiology. For each reposito
 |  	| [Cell Image Library](http://www.cellimagelibrary.org/home) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.8t18te) 	| [re3data](https://www.re3data.org/repository/r3d100000023) 	|
 | **Linked genotype and phenotype data** 	| European Genome-phenome Archive ([EGA](https://ega-archive.org/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.mya1ff) 	| [re3data](https://www.re3data.org/repository/r3d100011242) 	|
 | **Macromolecular structures** 	| Worldwide Protein Data Bank ([wwPDB](http://www.wwpdb.org/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.mckkb4) 	| [re3data](https://www.re3data.org/repository/r3d100011104) 	|
+|     | RCSB Protein Data Bank ([RCSB PDB](https://www.rcsb.org))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.2t35ja) 	| [re3data](https://www.re3data.org/repository/r3d100010327) 	|
+|     | Protein Data Bank of Japan ([PDBj](https://pdbj.org))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.rs2815) 	| [re3data](https://www.re3data.org/repository/r3d100010910) 	|
+|     | Protein Data Bank of Europe ([PDBj](https://www.ebi.ac.uk/pdbe/))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.26ek1v) 	| [re3data](https://www.re3data.org/repository/r3d100010538) 	|
 |  	| Biological Magnetic Resonance Data Bank ([BMRB](https://bmrb.io/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.p06nme) 	| [re3data](https://www.re3data.org/repository/r3d100010191) 	|
 | **Electron microscopy data** 	| Electron Microscopy Data Bank ([EMDB](https://www.ebi.ac.uk/emdb/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.651n9j) 	| [re3data](https://www.re3data.org/repository/r3d100010562) 	|
 |  	| Electron Microscopy Public Image Archive ([EMPIAR](https://www.ebi.ac.uk/empiar/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.dff3ef) 	| [re3data](https://www.re3data.org/repository/r3d100012356) 	|
@@ -155,6 +158,9 @@ For more details, see this [guide](https://www.openaire.eu/zenodo-guide).
 * To find a suitable interdisciplinary repository: [Generalist Repository Comparison Chart](https://doi.org/10.5281/zenodo.3946720)
 * To find Open Access repositories: [OpenDOAR](https://v2.sherpa.ac.uk/opendoar/): Directory of Open Access Repositories
 
+## See Also
+* [Data Deposition and Standardization](https://academic.oup.com/nar/pages/data_deposition_and_standardization) help page of the [Oxford Academic](https://academic.oup.com) Nucleic Acids Research ([NAR Journal](https://academic.oup.com/nar)).
+
 ## References
 * Engelhardt, C., Biernacka, K., Coffey, A., Cornet, R., Danciu, A., Demchenko, Y., Downes, S., Erdmann, C., Garbuglia, F., Germer, K., Helbig, K., Hellström, M., Hettne, K., Hibbert, D., Jetten, M., Karimova, Y., Kryger Hansen, K., Kuusniemi, M. E., Letizia, V., … Zhou, B. (2022). D7.4 How to be FAIR with your data. A teaching and training handbook for higher education institutions (V1.2.1). Zenodo. [https://doi.org/10.5281/ZENODO.6674301](https://doi.org/10.5281/ZENODO.6674301)
 * Lindlar, M., Rudnik, P., Horton, L., & Jones, S. (2020). “You say potato, I say potato” - Mapping Digital Preservation and Research Data Management Concepts towards Collective Curation and Preservation Strategies. [https://doi.org/10.5281/ZENODO.3672773](https://doi.org/10.5281/ZENODO.3672773)

From c656d13bf15bc763c45bba8d12db2ffed9e17a84 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Thu, 15 Feb 2024 12:48:47 +0100
Subject: [PATCH 02/27] Update 26-data-reuse.md

-added data resources for re-use table
---
 .../26-data-reuse.md                          | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md
index 0b8dc122..545b4854 100644
--- a/docs/_Research-Data-Management/26-data-reuse.md
+++ b/docs/_Research-Data-Management/26-data-reuse.md
@@ -22,6 +22,29 @@ For researchers who publish their data, preparing datasets for reuse is time-con
 
 For researchers reusing data, there are risks such as unknown quality and denormalisation (i.e. "the same data is stored multiple times in the same database under different names/identifiers"). There is also the challenge of comparing and integrating datasets from different sources {% cite sielemann_2020 %}.
 
+
+## Resources to facilitate data re-use in microbiology
+Below are listed widely used resources in microbiology which facilitate the re-use of raw data found in the data repositories (see section above). These so-called "secondary databases" provided added value through additional data types for example from data integration or from processing of raw data. For each resource and when available, the FAIRsharing and re3data pages are linked. On the FAIRsharing page, you will find information such as which journals endorse the resource (under "Collections & Recommendations" and then "In Policies"). On the re3data page, you will find information such as the above-mentioned criteria to select a trusted resource. DB = database.
+
+| Domain, Data Type	| Data repository 	| FAIRsharing 	| re3data 	| 
+|---	|---	|---	|---	|
+| **Viruses, Knowledge resources** 	| [ViralZone](https://viralzone.expasy.org/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.tppk10) 	| [re3data](https://www.re3data.org/repository/r3d100013314) 	|
+|     | International Committee for the Taxonomy of Viruses [ICTV](https://ictv.global/) 	| - 	| - 	|
+| **Viruses, Virus-host databases** | [Virus-HostDB](https://www.genome.jp/virushostdb) 	| - 	| - 	|
+|     | Viral Host-Range DB [VHRDB](https://viralhostrangedb.pasteur.cloud/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.7a4bbd) 	| - 	|
+| **Viruses, Sequence analysis platforms** 	| ([NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.d38075) 	| - 	|
+|     | ([BV-BRC](https://www.bv-brc.org/)) | [FAIRsharing](https://fairsharing.org/FAIRsharing.2ea3ef) 	| [re3data](https://www.re3data.org/repository/r3d100014100) 	|
+| **Viruses, Nucleic acid sequence downloads** | ([RVDB](https://rvdb.dbi.udel.edu/)) 	| - 	| - 	|
+|     | ([inphared](https://github.com/RyanCook94/inphared)) 	| -	| - |
+| **Viruses, Macromolecular structures** 	| VIPERdb ([VIPERdb](https://viperdb.org/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.45e0f5) 	| [re3data](https://www.re3data.org/repository/r3d100012362) 	|
+| **Viruses, Protein sequences** 	| Virus Orthologous Groups ([VOGdb](https://vogdb.org/)) 	| - | - |
+|    	| Phage Orthologous Groups ([PHROGs](https://phrogs.lmge.uca.fr/index.php)) 	| - | - |
+| **Viruses, -omics datasets** 	| [IMG/VR](https://img.jgi.doe.gov/cgi-bin/vr/main.cgi) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.2KIa7T) 	| - 	|
+|  	| Multi-Omics Portal of Virus Infection ([MVIP](https://mvip.whu.edu.cn/)) 	| - | - |
+| **All, Protein sequence search** 	| [InterPro](https://www.ebi.ac.uk/interpro/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.pda11d) 	| [re3data](https://www.re3data.org/repository/r3d100010798) 	|
+{: .table .table-hover}
+
+
 # Relevant licenses and terms of use
 See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/25-licenses).
 

From 2c314c02ef3fb45e31928e2fc81c89c9ea575420 Mon Sep 17 00:00:00 2001
From: Ka-Markus <77575423+Ka-Markus@users.noreply.github.com>
Date: Thu, 15 Feb 2024 15:57:55 +0100
Subject: [PATCH 03/27] Update 08-dmp.md

subsection Digital Preservation in DMPs added
---
 docs/_Research-Data-Management/08-dmp.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/_Research-Data-Management/08-dmp.md b/docs/_Research-Data-Management/08-dmp.md
index 54b4fe77..8ded9beb 100644
--- a/docs/_Research-Data-Management/08-dmp.md
+++ b/docs/_Research-Data-Management/08-dmp.md
@@ -23,6 +23,13 @@ In a DMP, researchers usually describe the data, their generation and processing
 * Legal aspects and anonymisation
 * Deletion
 
+## Digital Preservation in DMPs
+Data Management Plans usually ask for “long-term archiving” or “long-term preservation” of research data, “data preservation”, “long-term data accessibility” or sometimes “data sharing”. Exact terminology varies according to the different funders and their DMP templates and research data guidelines.
+For long-term archiving, preservation and accessibility/sharing, publication of research data in a Trusted Digital Repository (TDR) / trustworthy repository is recommended {% cite OpenAIRE_2024 england_2023_10125224 %}. TRD fall usually into two categories:
+* a repository that has a CoreTrustSeal, nestor seal (DIN 31644) or ISO 16363 certification
+* a repository that is commonly used and endorsed by the international research communities
+For finding a TDR, check the [Data Repository page of the Knowledge Base](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/22-data-repositories).
+
 # Benefits
 When implemented correctly, a DMP can [benefit all stakeholders](https://doi.org/10.1371/journal.pcbi.1006750) of a research project despite the initial overhead of creating the DMP itself:
 

From f978a97eebfcb9a4b2f51006af6c73a99787d69b Mon Sep 17 00:00:00 2001
From: Jonas C Kasmanas <54112176+JotaKas@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:10:11 +0100
Subject: [PATCH 04/27] Kasmanas - Update 03-contributors.md

---
 docs/_Getting-Started/03-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index 646dae39..4141cf5d 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -16,3 +16,4 @@ docs_css: markdown
 9. Martin Bole (ORCID ID: [0009-0004-9189-8852](https://orcid.org/0009-0004-9189-8852))
 10. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423))
 11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237))
+12. Jonas Coelho Kasmanas (ORCID ID: [0000-0001-6513-5350](https://orcid.org/0000-0001-6513-5350))

From 14947d6e88469f5c6d5f9d5de7ba4d0e0d4ca6b0 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:11:10 +0100
Subject: [PATCH 05/27] Update 03-contributors.md

added contributor
---
 docs/_Getting-Started/03-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index 646dae39..e02ecfea 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -16,3 +16,4 @@ docs_css: markdown
 9. Martin Bole (ORCID ID: [0009-0004-9189-8852](https://orcid.org/0009-0004-9189-8852))
 10. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423))
 11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237))
+12. Noriko Cassman (ORCID ID: [0000-0003-1655-0931](https://orcid.org/0000-0003-1655-0931))

From 69b5a6dc189608e2547e0f4f34c1cc16078374dc Mon Sep 17 00:00:00 2001
From: MVock <144668763+nighthog80@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:12:28 +0100
Subject: [PATCH 06/27] Update 03-contributors.md

added myself
---
 docs/_Getting-Started/03-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index 646dae39..fb1dd63c 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -16,3 +16,4 @@ docs_css: markdown
 9. Martin Bole (ORCID ID: [0009-0004-9189-8852](https://orcid.org/0009-0004-9189-8852))
 10. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423))
 11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237))
+12. Michael Vockenhuber (ORCID ID: [0009-0006-8111-1723](https://orcid.org/0009-0006-8111-1723))

From f41480b9ad7226f0850c23f7feb6f644114e5d1a Mon Sep 17 00:00:00 2001
From: Uta Parmaksiz <62014584+UParmaksiz@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:21:21 +0100
Subject: [PATCH 07/27] Update 25-digital-preservation.md

headline shortend
---
 docs/_Research-Data-Management/25-digital-preservation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/25-digital-preservation.md b/docs/_Research-Data-Management/25-digital-preservation.md
index f548400d..b07eaccb 100644
--- a/docs/_Research-Data-Management/25-digital-preservation.md
+++ b/docs/_Research-Data-Management/25-digital-preservation.md
@@ -4,7 +4,7 @@ category: Research-Data-Management
 layout: default
 docs_css: markdown
 ---
-# Definition of digital preservation
+# Definition
 Digital preservation is the act of ensuring continued findability and access to digital material and maintaining it independently understandable and reusable by a designated community, and with evidence supporting its authenticity, for as long as necessary. Preservation actions include:
 * Data cleaning
 * Data validation

From 6ad8698003a67032a02e63f2e87adfd875253fd6 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:26:26 +0100
Subject: [PATCH 08/27] Update 26-data-reuse.md

---
 docs/_Research-Data-Management/26-data-reuse.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md
index 545b4854..031b4ddc 100644
--- a/docs/_Research-Data-Management/26-data-reuse.md
+++ b/docs/_Research-Data-Management/26-data-reuse.md
@@ -32,11 +32,11 @@ Below are listed widely used resources in microbiology which facilitate the re-u
 |     | International Committee for the Taxonomy of Viruses [ICTV](https://ictv.global/) 	| - 	| - 	|
 | **Viruses, Virus-host databases** | [Virus-HostDB](https://www.genome.jp/virushostdb) 	| - 	| - 	|
 |     | Viral Host-Range DB [VHRDB](https://viralhostrangedb.pasteur.cloud/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.7a4bbd) 	| - 	|
-| **Viruses, Sequence analysis platforms** 	| ([NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.d38075) 	| - 	|
+| **Viruses, Sequence analysis platforms** 	| [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.d38075) 	| - 	|
 |     | ([BV-BRC](https://www.bv-brc.org/)) | [FAIRsharing](https://fairsharing.org/FAIRsharing.2ea3ef) 	| [re3data](https://www.re3data.org/repository/r3d100014100) 	|
-| **Viruses, Nucleic acid sequence downloads** | ([RVDB](https://rvdb.dbi.udel.edu/)) 	| - 	| - 	|
+| **Viruses, Nucleic acid sequence downloads** | [RVDB](https://rvdb.dbi.udel.edu/) 	| - 	| - 	|
 |     | ([inphared](https://github.com/RyanCook94/inphared)) 	| -	| - |
-| **Viruses, Macromolecular structures** 	| VIPERdb ([VIPERdb](https://viperdb.org/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.45e0f5) 	| [re3data](https://www.re3data.org/repository/r3d100012362) 	|
+| **Viruses, Macromolecular structures** 	| [VIPERdb](https://viperdb.org/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.45e0f5) 	| [re3data](https://www.re3data.org/repository/r3d100012362) 	|
 | **Viruses, Protein sequences** 	| Virus Orthologous Groups ([VOGdb](https://vogdb.org/)) 	| - | - |
 |    	| Phage Orthologous Groups ([PHROGs](https://phrogs.lmge.uca.fr/index.php)) 	| - | - |
 | **Viruses, -omics datasets** 	| [IMG/VR](https://img.jgi.doe.gov/cgi-bin/vr/main.cgi) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.2KIa7T) 	| - 	|

From ffa6ff9ef9c237a58fe07cd1bf8f98a408c7f999 Mon Sep 17 00:00:00 2001
From: Ka-Markus <77575423+Ka-Markus@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:27:43 +0100
Subject: [PATCH 09/27] Update 03-contributors.md

added Katharina Markus
---
 docs/_Getting-Started/03-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index 646dae39..c76c8aab 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -16,3 +16,4 @@ docs_css: markdown
 9. Martin Bole (ORCID ID: [0009-0004-9189-8852](https://orcid.org/0009-0004-9189-8852))
 10. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423))
 11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237))
+12. Katharina Markus (ORCID ID: [0000-0002-9316-8982](https://orcid.org/0000-0002-9316-8982))

From 95222f0445fb2396d3a60de693322c9da740729f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rabea=20M=C3=BCller?=
 <42644523+RabeaMue@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:31:29 +0100
Subject: [PATCH 10/27] Update 03-contributors.md

---
 docs/_Getting-Started/03-contributors.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index 646dae39..2c6cee80 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -5,14 +5,14 @@ layout: default
 docs_css: markdown
 ---
 
-1. Barbara Götz (ORCID ID: [0000-0002-6382-7211](https://orcid.org/0000-0002-6382-7211))
+1. Barbara Götz (ORCID ID: [0000-0002-6382-7211](https://orcid.org/0000-0002-6382-7211), Wikidata: [Q94745883](https://www.wikidata.org/wiki/Q94745883))
 2. Ekaterina Smirnova
-3. Justine Vandendorpe (ORCID ID: [0000-0002-9421-8582](https://orcid.org/0000-0002-9421-8582))
-4. Konrad U. Förstner (ORCID ID: [0000-0002-1481-2996](http://orcid.org/0000-0002-1481-2996))
+3. Justine Vandendorpe (ORCID ID: [0000-0002-9421-8582](https://orcid.org/0000-0002-9421-8582), Wikidata: [Q62930742](https://www.wikidata.org/wiki/Q62930742))
+4. Konrad U. Förstner (ORCID ID: [0000-0002-1481-2996](http://orcid.org/0000-0002-1481-2996), Wikidata: [Q18744528](https://www.wikidata.org/wiki/Q18744528))
 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. Charlie Pauvert (ORCID ID: [0000-0001-9832-2507](https://orcid.org/0000-0001-9832-2507))
+7. Charlie Pauvert (ORCID ID: [0000-0001-9832-2507](https://orcid.org/0000-0001-9832-2507), Wikidata: [Q103017355](https://www.wikidata.org/wiki/Q103017355))
 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. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423))
-11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237))
+10. Frank Förster (ORCID ID: [0000-0003-4166-5423](https://orcid.org/0000-0003-4166-5423), Wikidata: [Q42155371](https://www.wikidata.org/wiki/Q42155371))
+11. Rabea Müller (ORCID ID: [0000-0002-3096-8237](https://orcid.org/0000-0002-3096-8237), Wikidata: [Q95461538](https://www.wikidata.org/wiki/Q95461538))

From 324701b62f08ac9e97677f8dde165f7ec0b79d3b Mon Sep 17 00:00:00 2001
From: catgonzftw1 <120124695+catgonzftw1@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:40:06 +0100
Subject: [PATCH 11/27] Update references.bib

added reference for ELN to COS
---
 docs/_bibliography/references.bib | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib
index ddf927fe..6e8fdfbf 100644
--- a/docs/_bibliography/references.bib
+++ b/docs/_bibliography/references.bib
@@ -356,3 +356,9 @@ @misc{england_2023_10125224
   doi          = {10.5281/zenodo.10125224},
   url          = {https://doi.org/10.5281/zenodo.10125224}
 }
+
+@misc{nosek_COS,
+  title = {Strategy for Culture Change},
+  howpublished = {\url{https://www.cos.io/blog/strategy-for-culture-change}},
+  note = {Accessed: 2024-02-15}
+}

From 404e6cf3e1961b10db58ad29a2e73dc9798e02a0 Mon Sep 17 00:00:00 2001
From: catgonzftw1 <120124695+catgonzftw1@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:44:17 +0100
Subject: [PATCH 12/27] Update 12-eln.md

Added paragraph for culture change
---
 docs/_Research-Data-Management/12-eln.md | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md
index bc900d6b..70cfb98b 100644
--- a/docs/_Research-Data-Management/12-eln.md
+++ b/docs/_Research-Data-Management/12-eln.md
@@ -57,7 +57,6 @@ ELNs also prevent data loss by eliminating problems with data deletion {% cite b
 Finally, ELNs contribute to GSP by providing for data security and collaboration (see Data sharing and publishing) {% cite lma_rdmwg %}.
 
 # Criteria to select an ELN
-
 ## Basic systems
 Basic systems allow for traditional text entry, which can be searched and made available on multiple devices via the cloud. They also allow files (e.g. images, spreadsheets) to be attached to text and the attachments to be viewed, annotated and searched. Such systems include Word, Evernote and Dropbox. Basic systems have the advantage of being inexpensive, easily accessible and already familiar to many researchers. However, considerable effort is required to achieve the functionality of a traditional ELN with such a system {% cite bobrov_2021 vandendorpe_2020 %}.
 
@@ -70,6 +69,17 @@ High-end systems have all the features of specialised systems and more. High-end
 ## Electronic Lab Notebooks *vs.* Laboratory Information Management System (LIMS)
 ELNs are sometimes confused with Laboratory Information Management Systems (LIMS). They both streamline laboratory workflow and data management and are complementary, but they have different functionalities and features. A LIMS is a comprehensive software for managing and tracking laboratory operations and data. A LIMS covers sample management, workflow management and automation, quality control and sample tracking throughout the laboratory. On the other hand, an ELN focuses on experimental data acquisition, experiment documentation and (real-time) collaboration {% cite eln_lims_linkedin eln_lims_sapio %}.
 
+# Implementing an ELN
+## Changing Culture
+A cultural change is needed in order to transition researchers not only to ELNs from physical notebooks but to adhere to FAIR principles thus working towards open science. According to Nosek, at the Center for Open Science there are “five levels of intervention” which starts at the bottom with infrastructure {% cite nosek_COS %}. 
+
+Changes to infrastructure would help ease the transition to an ELN by making such it possible to adopt. Covering costs for the use of an ELN at the institutional level, rather than leaving it up to individually funded research projects, would make it possible for groups to justify their use. The next step would be to ensure a good experience with ELNs through a user-friendly interface, training researchers how to use the ELN, and incorporating it into existing workflows.
+
+A community of researchers will begin to form who use ELNs as a common practice. Provide incentives to researchers in order to ensure the continued use of the ELN. According to the Center for Open Science there are over 100 journals which offer badges that indicate when there is data or materials available to the reader. These badges incentivize researchers to share data as it adds more credibility to their findings. After moving through the bottom four levels of infrastructure, experience, community, and incentives the top level policy change will be possible. At the policy level the institution can now make the transition to ELN a requirement for its affiliated researchers.
+
+While there are still researchers who may be apprehensive regarding sharing their data this will change as the culture surrounding research transitions to more transparency.
+
+
 # Further resources
 * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria.
 * ELN Filter - Selection of ELNs that are suitable for the life sciences and that can be filtered out according to criteria ([English](https://www.publisso.de/fileadmin/user_upload/PUBLISSO/PUBLISSO_ELN-Filter_2021-06_english.xlsx), [German](https://www.publisso.de/fileadmin/user_upload/PUBLISSO/PUBLISSO_ELN-Filter_2020-12-01.xlsx)).

From bf37dcc12ed9f1ba4c4d35fa803d41f947a4c3a1 Mon Sep 17 00:00:00 2001
From: catgonzftw1 <120124695+catgonzftw1@users.noreply.github.com>
Date: Fri, 16 Feb 2024 09:47:53 +0100
Subject: [PATCH 13/27] Update references.bib

added reference for Guerrero2016 to be used in the ELN doc
---
 docs/_bibliography/references.bib | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib
index 6e8fdfbf..13730b72 100644
--- a/docs/_bibliography/references.bib
+++ b/docs/_bibliography/references.bib
@@ -362,3 +362,19 @@ @misc{nosek_COS
   howpublished = {\url{https://www.cos.io/blog/strategy-for-culture-change}},
   note = {Accessed: 2024-02-15}
 }
+
+@article{Guerrero2016,
+  title = {Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute},
+  volume = {11},
+  ISSN = {1932-6203},
+  url = {http://dx.doi.org/10.1371/journal.pone.0160428},
+  DOI = {10.1371/journal.pone.0160428},
+  number = {8},
+  journal = {PLOS ONE},
+  publisher = {Public Library of Science (PLoS)},
+  author = {Guerrero,  Santiago and Dujardin,  Gwendal and Cabrera-Andrade,  Alejandro and Paz-y-Miño,  César and Indacochea,  Alberto and Inglés-Ferrándiz,  Marta and Nadimpalli,  Hima Priyanka and Collu,  Nicola and Dublanche,  Yann and De Mingo,  Ismael and Camargo,  David},
+  editor = {Martens,  Lennart},
+  year = {2016},
+  month = aug,
+  pages = {e0160428}
+}

From 20c383594d06a309571beb2ef9917c4d5a67a736 Mon Sep 17 00:00:00 2001
From: catgonzftw1 <120124695+catgonzftw1@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:01:44 +0100
Subject: [PATCH 14/27] Update 12-eln.md

added pros and cons of physical lab notebook
---
 docs/_Research-Data-Management/12-eln.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md
index 70cfb98b..31257249 100644
--- a/docs/_Research-Data-Management/12-eln.md
+++ b/docs/_Research-Data-Management/12-eln.md
@@ -20,6 +20,17 @@ ELNs offer features and functions that can pave the way for significant time sav
 ELNs are not data publishing platforms and are not suitable for storing large files. Large files require special technology for secure storage (e.g. Object Store, Nextcloud), but can still be linked in the ELN {% cite rehwald_2022 %}.
 
 # Benefits and drawbacks
+## Pros & Cons of Physical Lab Notebooks
+
+Historically, documentation of experiments have been done in a physical, paper and pen notebook. For some researchers this is still a preferred method of documentation. It’s easy and inexpensive to use as it does not require computers nor internet access. However, with the technological advancement in data collection and processing there is a greater amount of data produced than ever before and with it there is a need for data to be digitised and managed electronically. 
+
+Also with advances in communication and travel it is even easier to work collaboratively with researchers at different institutes around the world. This collaboration would be difficult or hindered if scans of physical lab notebooks would need to be shared. Of course, this also does not take into consideration the legibility of the experiment notes or the ability to make general sense of it.
+
+These drawbacks outweigh the benefits of a physical laboratory notebook. Adoption of an ELN is one of the essential steps needed in making research data FAIR. The purpose of adherence to the FAIR principles is so that the data can continue to be reused, validated, and expanded by researchers in the future. The data life cycle starts with planning and goes through the production and analysis followed by storage and access and ideally ends with data re-use. 
+
+In order for data to be re-used it needs to meet the criteria of the FAIR principles. This is where the largest drawback of physical laboratory notebooks lies. Data in a physical notebook cannot be found, accessed, or reused by other researchers. Data in an ELN can be extracted, downloaded, shared, and stored in a FAIR capacity. This data can also be described with metadata which gives more context needed to make sense of the data and ensure it can be reused.
+
+Unfortunately, the major drawback to the wide use of ELNs in all areas of research appears to be data security risks, specifically when used in medical research. There is still an ongoing discussion on how to best securely manage patient research data in an ELN. However, according to Guerrero the best solutions involve using private servers on site or private institutionally based cloud services {% cite Guerrero2016 %}.
 
 ## Boosting efficiency of everyday tasks
 ELNs increase the efficiency of everyday tasks by providing time-saving features and functions such as search and filtering {% cite vandendorpe_nd %}. ELNs also take advantage of standardisation {% cite rathmann_2021 %}: they have the ability to create templates such as protocols, Standard Operating Procedures (SOPs) and workflows. This facilitates data documentation with metadata {% cite vandendorpe_nd %} and supports clarity and organisation of data and protocols {% cite n4m_wc_elns_2023 %}. ELNs also provide ubiquitous access {% cite vandendorpe_nd %}: protocols, observations, notes and other data can be entered using a computer or mobile device {% cite lma_rdmwg %}.

From 6d08f71322b65c911c905fa8c9aec92e462fb08b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rabea=20M=C3=BCller?=
 <42644523+RabeaMue@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:08:55 +0100
Subject: [PATCH 15/27] Update licence link

---
 docs/_Research-Data-Management/27-data-reuse.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/27-data-reuse.md b/docs/_Research-Data-Management/27-data-reuse.md
index 706e7a41..e1dad947 100644
--- a/docs/_Research-Data-Management/27-data-reuse.md
+++ b/docs/_Research-Data-Management/27-data-reuse.md
@@ -23,7 +23,7 @@ For researchers who publish their data, preparing datasets for reuse is time-con
 For researchers reusing data, there are risks such as unknown quality and denormalisation (i.e. "the same data is stored multiple times in the same database under different names/identifiers"). There is also the challenge of comparing and integrating datasets from different sources {% cite sielemann_2020 %}.
 
 # Relevant licenses and terms of use
-See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/25-licenses).
+See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/26-licenses).
 
 # Criteria for selection trustworthy datasets
 

From 48bdc7d9b8668a2d432cade8422e871af4fc97bc Mon Sep 17 00:00:00 2001
From: Frank Foerster <frank.foerster@computational.bio.uni-giessen.de>
Date: Fri, 16 Feb 2024 10:20:02 +0100
Subject: [PATCH 16/27] Add captions to the structure figures

---
 docs/_Research-Data-Management/24-aruna-object-storage.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/_Research-Data-Management/24-aruna-object-storage.md b/docs/_Research-Data-Management/24-aruna-object-storage.md
index 39b46945..671f6239 100644
--- a/docs/_Research-Data-Management/24-aruna-object-storage.md
+++ b/docs/_Research-Data-Management/24-aruna-object-storage.md
@@ -50,9 +50,13 @@ The main component of AOS is a distributed database system. It synchronizes all
 ## AOS data structure
 AOS organizes data in Version 1.x into Projects, Collections, Object Groups, and Objects, starting with version 2.x the data structure will be even more flexible and are organized into Projects, Collections, Datasets, and Objects with a more flexible relation model.
 
-![Aruna Object Storage Structure V1](/nfdi4microbiota-knowledge-base/assets/img/aruna-1-structure.png "Aruna Object Storage Structure V1"){:width="40%"}
+|![Aruna Object Storage Structure V1](/nfdi4microbiota-knowledge-base/assets/img/aruna-1-structure.png "Aruna Object Storage Structure V1"){:width="50%"} |
+|-|
+| UML diagram of the Aruna Object Storage data structure in Version v1.0.x |
 
-![Aruna Object Storage Structure V2](/nfdi4microbiota-knowledge-base/assets/img/aruna-2-structure.png "Aruna Object Storage Structure V2"){:width="40%"}
+ | ![Aruna Object Storage Structure V2](/nfdi4microbiota-knowledge-base/assets/img/aruna-2-structure.png "Aruna Object Storage Structure V2"){:width="50%"} |
+|-|
+| UML diagram of the Aruna Object Storage data structure starting in Version v2.0. All resources form a directed acyclic graph of belongs to relationships (blue) with Projects as roots and Objects as leaves. Resources can also describe horizontal version relationships (orange), data/metadata relationships (yellow) or even custom user-defined relationships (green). |
 
 # References
 * Dokumentation and Aruna start page: [https://aruna-storage.org](https://aruna-storage.org)

From 1dab31a63fed3d789fd6570c9ace532c59cf1773 Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:24:59 +0100
Subject: [PATCH 17/27] Update 12-eln.md

Turned url reference into hyperlink.
---
 docs/_Research-Data-Management/12-eln.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md
index 31257249..39d015f3 100644
--- a/docs/_Research-Data-Management/12-eln.md
+++ b/docs/_Research-Data-Management/12-eln.md
@@ -22,7 +22,7 @@ ELNs are not data publishing platforms and are not suitable for storing large fi
 # Benefits and drawbacks
 ## Pros & Cons of Physical Lab Notebooks
 
-Historically, documentation of experiments have been done in a physical, paper and pen notebook. For some researchers this is still a preferred method of documentation. It’s easy and inexpensive to use as it does not require computers nor internet access. However, with the technological advancement in data collection and processing there is a greater amount of data produced than ever before and with it there is a need for data to be digitised and managed electronically. 
+Historically, documentation of experiments have been done in a physical, paper and pen notebook. For some researchers this is still a preferred method of documentation. It’s easy and inexpensive to use as it does not require computers nor internet access. However, with the technological advancement in data collection and processing there is a greater amount of data produced than ever before and with it there is a need for data to be digitized and managed electronically. 
 
 Also with advances in communication and travel it is even easier to work collaboratively with researchers at different institutes around the world. This collaboration would be difficult or hindered if scans of physical lab notebooks would need to be shared. Of course, this also does not take into consideration the legibility of the experiment notes or the ability to make general sense of it.
 
@@ -82,7 +82,7 @@ ELNs are sometimes confused with Laboratory Information Management Systems (LIMS
 
 # Implementing an ELN
 ## Changing Culture
-A cultural change is needed in order to transition researchers not only to ELNs from physical notebooks but to adhere to FAIR principles thus working towards open science. According to Nosek, at the Center for Open Science there are “five levels of intervention” which starts at the bottom with infrastructure {% cite nosek_COS %}. 
+A cultural change is needed in order to transition researchers not only to ELNs from physical notebooks but to adhere to FAIR principles thus working towards open science. According to Nosek's [Strategy for Culture Change](https://www.cos.io/blog/strategy-for-culture-change), at the Center for Open Science there are “five levels of intervention” which starts at the bottom with infrastructure. 
 
 Changes to infrastructure would help ease the transition to an ELN by making such it possible to adopt. Covering costs for the use of an ELN at the institutional level, rather than leaving it up to individually funded research projects, would make it possible for groups to justify their use. The next step would be to ensure a good experience with ELNs through a user-friendly interface, training researchers how to use the ELN, and incorporating it into existing workflows.
 

From e912a1e4a1d479518fe0d78e24de24f4c12b7a56 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:28:21 +0100
Subject: [PATCH 18/27] Update 01-rd.md

- added research data types
---
 docs/_Research-Data-Management/01-rd.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/01-rd.md b/docs/_Research-Data-Management/01-rd.md
index 0d5f3ba1..19d1a816 100644
--- a/docs/_Research-Data-Management/01-rd.md
+++ b/docs/_Research-Data-Management/01-rd.md
@@ -25,7 +25,7 @@ Data types in microbiology include the following:
     * Genomic features
     * Genomic organization
   * RNA sequences
-    * 16S ribosomal RNA sequences
+    * 16S, 18S and ITS ribosomal RNA sequences
     * Functional genomics / gene expression data (e.g. ribosome profiling)
     * RNA-protein interactions
     * Small RNA (sRNA)

From 9e6fcb2e190ca0ed2883ff69f213076fd65829e2 Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:30:24 +0100
Subject: [PATCH 19/27] Update references.bib

Removed nosek_COS, reference as it was removed from the text and replaced with a hyperlink.
---
 docs/_bibliography/references.bib | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib
index 13730b72..f411dd21 100644
--- a/docs/_bibliography/references.bib
+++ b/docs/_bibliography/references.bib
@@ -357,12 +357,6 @@ @misc{england_2023_10125224
   url          = {https://doi.org/10.5281/zenodo.10125224}
 }
 
-@misc{nosek_COS,
-  title = {Strategy for Culture Change},
-  howpublished = {\url{https://www.cos.io/blog/strategy-for-culture-change}},
-  note = {Accessed: 2024-02-15}
-}
-
 @article{Guerrero2016,
   title = {Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute},
   volume = {11},

From ac31939eed5fe09de94b75457847044aa6d6cb03 Mon Sep 17 00:00:00 2001
From: catgonzftw1 <120124695+catgonzftw1@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:30:43 +0100
Subject: [PATCH 20/27] Update 03-contributors.md

added myself as a contributor
---
 docs/_Getting-Started/03-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Getting-Started/03-contributors.md b/docs/_Getting-Started/03-contributors.md
index aa9b434e..ca872b1f 100644
--- a/docs/_Getting-Started/03-contributors.md
+++ b/docs/_Getting-Started/03-contributors.md
@@ -20,3 +20,4 @@ docs_css: markdown
 13. Michael Vockenhuber (ORCID ID: [0009-0006-8111-1723](https://orcid.org/0009-0006-8111-1723))
 14. Noriko Cassman (ORCID ID: [0000-0003-1655-0931](https://orcid.org/0000-0003-1655-0931))
 15. Katharina Markus (ORCID ID: [0000-0002-9316-8982](https://orcid.org/0000-0002-9316-8982))
+16. Catherine Gonzalez (ORCID ID: [0000-0002-7585-9990](https://orcid.org/0000-0002-7585-9990))

From 6eca16f72910879e0c0b6711d5a9bb44a06e8e62 Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:48:00 +0100
Subject: [PATCH 21/27] Update and rename 26-data-reuse.md to 27-data-reuse.md

Renamed due to merge conflict.
---
 .../{26-data-reuse.md => 27-data-reuse.md}                       | 1 -
 1 file changed, 1 deletion(-)
 rename docs/_Research-Data-Management/{26-data-reuse.md => 27-data-reuse.md} (99%)

diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/27-data-reuse.md
similarity index 99%
rename from docs/_Research-Data-Management/26-data-reuse.md
rename to docs/_Research-Data-Management/27-data-reuse.md
index 031b4ddc..84a76bbb 100644
--- a/docs/_Research-Data-Management/26-data-reuse.md
+++ b/docs/_Research-Data-Management/27-data-reuse.md
@@ -42,7 +42,6 @@ Below are listed widely used resources in microbiology which facilitate the re-u
 | **Viruses, -omics datasets** 	| [IMG/VR](https://img.jgi.doe.gov/cgi-bin/vr/main.cgi) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.2KIa7T) 	| - 	|
 |  	| Multi-Omics Portal of Virus Infection ([MVIP](https://mvip.whu.edu.cn/)) 	| - | - |
 | **All, Protein sequence search** 	| [InterPro](https://www.ebi.ac.uk/interpro/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.pda11d) 	| [re3data](https://www.re3data.org/repository/r3d100010798) 	|
-{: .table .table-hover}
 
 
 # Relevant licenses and terms of use

From b4c10d4a9b5e73fd95e548405fa99f8a9effc130 Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:52:35 +0100
Subject: [PATCH 22/27] Update 01-rd.md

-added data type
---
 docs/_Research-Data-Management/01-rd.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/_Research-Data-Management/01-rd.md b/docs/_Research-Data-Management/01-rd.md
index 19d1a816..708effe0 100644
--- a/docs/_Research-Data-Management/01-rd.md
+++ b/docs/_Research-Data-Management/01-rd.md
@@ -34,6 +34,7 @@ Data types in microbiology include the following:
   * Protein-protein interactions
   * Proteomes
 * Quantitative and predictive food microbiology
+* Sample and project (meta)data
 * Scientific texts
 * Semantic data
 * Species interaction data (e.g. physical microbial interaction data)

From 77ef91f606b9199af30ec53e12c4c7f2d4abb57d Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:55:20 +0100
Subject: [PATCH 23/27] Update 22-data-repositories.md

PDBj->PDBe
---
 docs/_Research-Data-Management/22-data-repositories.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/22-data-repositories.md b/docs/_Research-Data-Management/22-data-repositories.md
index 55275dfb..9fc0d3bb 100644
--- a/docs/_Research-Data-Management/22-data-repositories.md
+++ b/docs/_Research-Data-Management/22-data-repositories.md
@@ -47,7 +47,7 @@ Below are listed well-established repositories in microbiology. For each reposit
 | **Macromolecular structures** 	| Worldwide Protein Data Bank ([wwPDB](http://www.wwpdb.org/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.mckkb4) 	| [re3data](https://www.re3data.org/repository/r3d100011104) 	|
 |     | RCSB Protein Data Bank ([RCSB PDB](https://www.rcsb.org))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.2t35ja) 	| [re3data](https://www.re3data.org/repository/r3d100010327) 	|
 |     | Protein Data Bank of Japan ([PDBj](https://pdbj.org))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.rs2815) 	| [re3data](https://www.re3data.org/repository/r3d100010910) 	|
-|     | Protein Data Bank of Europe ([PDBj](https://www.ebi.ac.uk/pdbe/))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.26ek1v) 	| [re3data](https://www.re3data.org/repository/r3d100010538) 	|
+|     | Protein Data Bank of Europe ([PDBe](https://www.ebi.ac.uk/pdbe/))     | [FAIRsharing](https://fairsharing.org/FAIRsharing.26ek1v) 	| [re3data](https://www.re3data.org/repository/r3d100010538) 	|
 |  	| Biological Magnetic Resonance Data Bank ([BMRB](https://bmrb.io/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.p06nme) 	| [re3data](https://www.re3data.org/repository/r3d100010191) 	|
 | **Electron microscopy data** 	| Electron Microscopy Data Bank ([EMDB](https://www.ebi.ac.uk/emdb/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.651n9j) 	| [re3data](https://www.re3data.org/repository/r3d100010562) 	|
 |  	| Electron Microscopy Public Image Archive ([EMPIAR](https://www.ebi.ac.uk/empiar/)) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.dff3ef) 	| [re3data](https://www.re3data.org/repository/r3d100012356) 	|

From e23ca2f745e072950da23b5550325b4f6e79650c Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 10:56:51 +0100
Subject: [PATCH 24/27] Update 02-rdm.md

-fixed typo
---
 docs/_Research-Data-Management/02-rdm.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md
index 6aada043..dc3b8cba 100644
--- a/docs/_Research-Data-Management/02-rdm.md
+++ b/docs/_Research-Data-Management/02-rdm.md
@@ -28,7 +28,7 @@ Benefits of RDM are numerous, some of them are listed below {% cite assmann_2022
     * Helps keep track of the project
     * Helps meet formal and legal requirements
     * Enhances teamwork and collaborations
-    * Guaranteeing transparency, verifiability and reproducibility
+    * Guarantees transparency, verifiability and reproducibility
 
 ## Consequences of poor RDM
 Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)).

From 1d5ece6348ca2d11dc8f7f85fad0fd0413c203e9 Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 11:01:55 +0100
Subject: [PATCH 25/27] Update 27-data-reuse.md

Fixing table
---
 docs/_Research-Data-Management/27-data-reuse.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/27-data-reuse.md b/docs/_Research-Data-Management/27-data-reuse.md
index 98e13a47..7c88e7da 100644
--- a/docs/_Research-Data-Management/27-data-reuse.md
+++ b/docs/_Research-Data-Management/27-data-reuse.md
@@ -41,7 +41,7 @@ Below are listed widely used resources in microbiology which facilitate the re-u
 | **Viruses, -omics datasets** 	| [IMG/VR](https://img.jgi.doe.gov/cgi-bin/vr/main.cgi) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.2KIa7T) 	| - 	|
 |  	| Multi-Omics Portal of Virus Infection ([MVIP](https://mvip.whu.edu.cn/)) 	| - | - |
 | **All, Protein sequence search** 	| [InterPro](https://www.ebi.ac.uk/interpro/) 	| [FAIRsharing](https://fairsharing.org/FAIRsharing.pda11d) 	| [re3data](https://www.re3data.org/repository/r3d100010798) 	|
-
+{: .table .table-hover}
 
 # Relevant licenses and terms of use
 See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/26-licenses).

From 9dc58728bcfb27aef5d0ea3b17995264f1e26a8e Mon Sep 17 00:00:00 2001
From: nacnoriko <105923845+nacnoriko@users.noreply.github.com>
Date: Fri, 16 Feb 2024 11:13:06 +0100
Subject: [PATCH 26/27] Update 02-rdm.md

- added research mgmt platforms to list
---
 docs/_Research-Data-Management/02-rdm.md | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md
index dc3b8cba..deccef22 100644
--- a/docs/_Research-Data-Management/02-rdm.md
+++ b/docs/_Research-Data-Management/02-rdm.md
@@ -28,7 +28,7 @@ Benefits of RDM are numerous, some of them are listed below {% cite assmann_2022
     * Helps keep track of the project
     * Helps meet formal and legal requirements
     * Enhances teamwork and collaborations
-    * Guarantees transparency, verifiability and reproducibility
+    * Guaranteeing transparency, verifiability and reproducibility
 
 ## Consequences of poor RDM
 Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)).
@@ -36,7 +36,14 @@ Consequences of poor RDM include paper retraction (e.g. [González Amorós & de
 ## Further resources
 * Brief Guide - Research Data Management: [Training Expert Group 2020](https://doi.org/10.5281/zenodo.4000989)
 * Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences: [bio.tools](https://bio.tools/)
-* Research data management platform: [Coscine](https://coscine.de/)
+  
+* Research data management platforms:
+- [Coscine](https://coscine.de/) by [RWTH Aachen](https://www.rwth-aachen.de)
+- [BEXIS2](https://demo.bexis2.uni-jena.de) by [NFDI4Biodiversity](https://www.nfdi4biodiversity.org/en/) at [FSU Jena](https://www.uni-jena.de)
+- [GfBio](https://www.gfbio.org) consortium services
+  
+* General reources:
+- The Research Data Management toolkit for Life Sciences [RDMkit](https://rdmkit.elixir-europe.org) by [ELIXIR](https://elixir-europe.org)
 
 ## References
 {% bibliography --cited_in_order %}

From 87fcafc5f76e4fa9a24a5879215c11b05801b91e Mon Sep 17 00:00:00 2001
From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com>
Date: Fri, 16 Feb 2024 11:24:16 +0100
Subject: [PATCH 27/27] Update 02-rdm.md

fix merge conflict
---
 docs/_Research-Data-Management/02-rdm.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md
index deccef22..2718b154 100644
--- a/docs/_Research-Data-Management/02-rdm.md
+++ b/docs/_Research-Data-Management/02-rdm.md
@@ -28,7 +28,7 @@ Benefits of RDM are numerous, some of them are listed below {% cite assmann_2022
     * Helps keep track of the project
     * Helps meet formal and legal requirements
     * Enhances teamwork and collaborations
-    * Guaranteeing transparency, verifiability and reproducibility
+    * Guarantees transparency, verifiability and reproducibility
 
 ## Consequences of poor RDM
 Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)).