Merge pull request #136 from nacnoriko/main

Update 26-data-reuse.md

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)
@@ -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)

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 ([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) 	|
@@ -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)

docs/_Research-Data-Management/27-data-reuse.md

@@ -22,6 +22,27 @@ 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](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) 	|
+
+
 # Relevant licenses and terms of use
 See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/26-licenses).
 
@@ -83,6 +104,7 @@ Below is a list of criteria for selecting trustworthy datasets {% cite bres_2022
     * [TerrestrialMetagenomeDB](https://webapp.ufz.de/tmdb/)
 * [Mendeley Data](https://data.mendeley.com/)
 
+
 ### (Meta)data aggregators
 * [B2FIND](https://b2find.eudat.eu/)
 * [data.europa.eu](https://data.europa.eu/en)