first draft for SSI session

FAIR-publishing.qmd

@@ -2,6 +2,11 @@
 title: "How to publish FAIR research outputs"
 author: "Eirini Zormpa"
 institute: "The Alan Turing Institute"
+title-slide-attributes:
+    data-background-image: images/RSC_STACKED-LOGO-WHITE.png, images/SSI_SUBMARK-LOGO-WHITE.png,  images/rsf-logo-white.png
+    data-background-size: 50px  50px
+    data-background-position: top 20px left 50px, top 20px left 120px, top 20px left 190px
+    data-background-opacity: "0.8"
 format:
   revealjs:
     theme: [moon, custom.scss]
@@ -11,12 +16,25 @@ from: markdown+emoji
 ---
 
 
-## Introductions :wave:
+## Hi, I'm Eirini :wave:
 
 ![](https://www.turing.ac.uk/sites/default/files/styles/people/public/2022-06/eirini-zormpa.jpg?itok=Cx2rNcHY){.absolute top=100 right=50 width="320" height="384"}
 
 ::: {.column width="60%"}
-**Eirini Zormpa**, Community Manager Open Collaboration
+**Eirini Zormpa**, Community Manager Open Collaboration @ AIM RSF
+:::
+
+## AI for Multiple Long-term Conditions Research Support Facility (AIM RSF)
+
+![](images/AIM-RSF_explanatory-image.jpg){fig-align="center"}
+
+
+## Hi, I'm Eirini :wave:
+
+![](https://www.turing.ac.uk/sites/default/files/styles/people/public/2022-06/eirini-zormpa.jpg?itok=Cx2rNcHY){.absolute top=100 right=50 width="320" height="384"}
+
+::: {.column width="60%"}
+**Eirini Zormpa**, Community Manager Open Collaboration @ AIM RSF
 
 <br>
 
@@ -27,17 +45,7 @@ Previously:
 :::
 
 
-## Learning objectives
-
-- :white_check_mark: To expand the definition of "research outputs"
-- :white_check_mark: To define the FAIR principles
-- :white_check_mark: To explain how to choose a repository
-- :white_check_mark: To demonstrate how to use a repository for archiving research outputs
-
-<br>
-<br>
-
-**By the end of the workshop, you will be able to use a repository to archive research output in a FAIR manner**.
+# Why and what to share{background-color="#F26B5E"}
 
 ## Advertising scholarship
 
@@ -61,22 +69,24 @@ The actual outputs created during a research project will differ but some exampl
 - Datasets
 - Protocols and workflows
 - Code (analysis scripts and software packages)
-- Outputs related to other aspects of your work, e.g. educational materials
+- Other outputs, e.g. educational materials
 
-## What to share?
-
-The more you can share the better, [**within reason**]{style="color:#F2B705"}.
+## The actual scholarship
 
-- At a minimum, you should share the data and code needed to confirm your findings.
-- Additionally, a lot of work goes into creating those datasets and scripts, e.g. code lists, experimental protocols, consent forms.
+The actual outputs created during a research project will differ but some examples include:
 
-<br>
+- Preregistrations
+- Presentations and posters on your findings
+- **[Datasets]{style="color:#F2B705"}**
+- Protocols and workflows
+- **[Code (analysis scripts and software packages)]{style="color:#F2B705"}**
+- Other outputs, e.g. educational materials
 
-<br>
+. . .
 
-**Don't worry that your outputs aren't important! [You never know what will end up being useful for others!]{style="color:#F2B705"}**
+**You don't know what will be useful for others!**
 
-## Evelina's example
+## Example
 
 ![](https://www.turing.ac.uk/sites/default/files/styles/people/public/2018-06/evelina-gabasova_1000x921_jpg.jpg?itok=SUNC-Irv){.absolute top=100 right=50 width="320" height="384"}
 
@@ -101,11 +111,7 @@ The more you can share the better, [**within reason**]{style="color:#F2B705"}.
 
 ## What (not) to share
 
-- Anything that you found online that isn't licensed for reuse - *more on licences later*!
-
-. . . 
-
-- An obvious issue is personal data, especially sensitive personal data - *more on this later*!
+- Personal data is tricky - some data can be shared with proper consent and (pseudo)anonymisation.
 
 . . . 
 
@@ -115,7 +121,14 @@ The more you can share the better, [**within reason**]{style="color:#F2B705"}.
 
 - Really big data (e.g. in quantum computing, cosmology) - think about what data is **necessary** and whether the data can be recreated.
 
-## How to share?
+. . .
+
+- Anything that you found online that isn't licensed for reuse - *more on licences later*!
+
+
+# How to share{background-color="#F26B5E"}
+
+## The FAIR principles
 
 ![](images/FAIRPrinciples.jpg){fig-align="center"}
 
@@ -129,6 +142,19 @@ First people need to be able to find your outputs!
 For outputs to be findable, they need to be described with **rich metadata**.
 These metadata can be generic (e.g. title, author name, keywords) or discipline-specific.
 
+<br>
+
+. . .
+
+### Resources
+- [FAIRsharing.org](https://fairsharing.org/): a curated resource to help you find (among others) metadata standards
+
+. . .
+
+- [CodeMeta generator](https://codemeta.github.io/codemeta-generator/): a tool to create a minimal metadata file for software
+
+
+
 ## Findable: Persistent identifiers :mag:
 
 Outputs should also be assigned a **unique and persistent identifier**, e.g. a Digital Object Identifier (DOI).
@@ -148,10 +174,10 @@ Persistent identifiers for researchers help if you have a common name or if you
 
 ```{r}
 library(countdown)
-countdown(minutes = 5)
+countdown(minutes = 3)
 ```
 
-:alarm_clock: **5 minutes**
+:alarm_clock: **3 minutes**
 
 1. Navigate to [https://orcid.org/](https://orcid.org/) on your browser
 2. Select Sign in/Register and then Register as a new user
@@ -161,21 +187,16 @@ countdown(minutes = 5)
 ## Accessible: Define processes :door:
 
 After people have found your outputs they need to be able to access them!
-This could mean that they are publicly available in a **repository**.
-
-. . .
-
-<br>
 
-### :warning: Sensitive information
-
-Most of you will be working with sensitive personal information that need to stay restricted :lock:
+- :unlock: This could mean that they are openly and freely available in a **repository**.
 
 . . .
 
-<br>
+- :lock: Sensitive information may not allow for research outputs to be freely shared; in those cases the **access method should be clearly and transparently described** and the metadata should still be shared.
 
-In those cases, the **access method should be described** and the **metadata should still be accessible**.
+. . . 
+
+- :x: If the output is no longer usable, the **metadata should still be accessible**.
 
 
 ## Interoperable :gear:
@@ -404,12 +425,38 @@ Usage licences are different for data and for code:
 Source: [How to attribute Creative Commons photos by Foter](https://foter.com/blog/how-to-attribute-creative-commons-photos/)
 :::
 
-## Where to share?
+## OSI-approved licences for code
 
-```{mermaid}
-flowchart LR
-  A(Supplementary materials) --> B(Specialised or generic repository) --> C(Data or software article) 
-```
+::: {.r-stack}
+![](images/tldrlegal1.png){.fragment}
+
+![](images/tldrlegal2.png){.fragment}
+
+:::
+
+::: aside
+[tl;drLegal](https://www.tldrlegal.com/license-tags/osi-approved)
+:::
+
+## How to apply licences?
+
+:warning: **Check whether your university has a policy on sharing and licensing your research outputs.** :warning:
+
+<br>
+
+. . .
+
+1. Provide the full text of the licence in your repository.
+
+. . .
+
+2. State under what licence your work is shared in the README file.
+
+. . .
+
+3. Ideally, include a [CITATION.cff file](https://citation-file-format.github.io/) in your repository and state in your README how you would like to be cited.
+
+# Where to share?{background-color="#F26B5E"}
 
 ## Where to share: Supplementary materials
 
@@ -495,10 +542,21 @@ Where possible, it's a good idea to use a disclipline-specific repository, usual
 
 ## Data
 
-![](images/uk-data-service.png)
+::: {.r-stack}
+
+![](images/gwas.png){.fragment}
+
+![](images/earthchem.png){.fragment}
+
+![](images/idr.png){.fragment}
+
+![](images/uk-data-service.png){.fragment}
+
+:::
+
 
 ::: aside
-[UK Data Service](https://ukdataservice.ac.uk/)
+[GWAS Catalog](https://www.ebi.ac.uk/gwas/), [EarthChem](https://www.earthchem.org/), [Image Data Resource](http://idr.openmicroscopy.org/about/), [UK Data Service](https://ukdataservice.ac.uk/)
 :::
 
 ## Protocols
@@ -520,12 +578,12 @@ In that case there are generic repositories that are domain-agnostic and which a
 [Zenodo](https://zenodo.org/) is an open repository that accepts most research outputs.
 
 - :white_check_mark: Funded by CERN, OpenAIRE, and the European Commission.
-- :white_check_mark: Built on open source infrastructure
-- :warning: Most resources are Open Access, though embargo and restricted options exist.
+- :white_check_mark: Built on open source infrastructure.
+- :white_check_mark: Offers integration with GitHub to archive code.
 
 ![](images/zenodo.png)
 
-## Demo of data upload {background-color="#F2B705"}
+## Demo of syncing a GitHub and Zenodo repository {background-color="#F2B705"}
 
 Just watch me for now :computer::eyes:
 
@@ -606,11 +664,16 @@ For data or software of special importance, you may consider writing a data or s
 ![](images/thank-you.jpg){fig-align="center"}
 
 ## References {.smaller}
+- AIM RSF, & Scriberia. (2023). Illustrations for AI for multiple long-term conditions: Research Support Facility. Zenodo. [https://doi.org/10.5281/zenodo.8042780](https://doi.org/10.5281/zenodo.8042780)
 - Buckheit, J.B., Donoho, D.L. (1995). WaveLab and Reproducible Research. In: Antoniadis, A., Oppenheim, G. (eds) Wavelets and Statistics. Lecture Notes in Statistics, vol 103. Springer, New York, NY. [https://doi.org/10.1007/978-1-4612-2544-7_5](https://doi.org/10.1007/978-1-4612-2544-7_5)
+- Chue Hong, Neil P., Katz, Daniel S., Barker, Michelle, Lamprecht, Anna-Lena, Martinez, Carlos, Psomopoulos, Fotis E., Harrow, Jen, Castro, Leyla Jael, Gruenpeter, Morane, Martinez, Paula Andrea, Honeyman, Tom, Struck, Alessandra, Lee, Allen, Loewe, Axel, van Werkhoven, Ben, Jones, Catherine, Garijo, Daniel, Plomp, Esther, Genova, Francoise, … RDA FAIR4RS WG. (2022). FAIR Principles for Research Software (1.0). [https://doi.org/10.15497/RDA00068](https://doi.org/10.15497/RDA00068)
 - Ding, K., Zhou, M., Wang, H. et al. A Large-scale Synthetic Pathological Dataset for Deep Learning-enabled Segmentation of Breast Cancer. Sci Data 10, 231 (2023). [https://doi.org/10.1038/s41597-023-02125-y](https://doi.org/10.1038/s41597-023-02125-y)
 - Evelina Gabasova. (2016). Star Wars social network (1.0.1) [Data set]. Zenodo. [https://doi.org/10.5281/zenodo.1411479](https://doi.org/10.5281/zenodo.1411479).
 - Hansen et al., (2023). TextDescriptives: A Python package for calculating a large variety of metrics from text. Journal of Open Source Software, 8(84), 5153, [https://doi.org/10.21105/joss.05153](https://doi.org/10.21105/joss.05153).
+
+## References (continued){.smaller}
 - Lin, D., Crabtree, J., Dillo, I. et al. The TRUST Principles for digital repositories. Sci Data 7, 144 (2020). [https://doi.org/10.1038/s41597-020-0486-7](https://doi.org/10.1038/s41597-020-0486-7).
 - Silvester, N., B. Alako, C. Amid, et al. (2015). Content discovery and retrieval services at the European Nucleotide Archive. Vol. 43 , pp. D23-D29. [DOI: 10.1093/nar/gku1129](https://doi.org/10.1093/nar/gku1129).
 - The Turing Way Community, & Scriberia. (2023). Illustrations from The Turing Way: Shared under CC-BY 4.0 for reuse. Zenodo. [https://doi.org/10.5281/zenodo.7587336](https://doi.org/10.5281/zenodo.7587336).
+- Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). [https://doi.org/10.1038/sdata.2016.18](https://doi.org/10.1038/sdata.2016.18)