moved these items to issues

Author: lwjohnst86

index.Rmd

@@ -580,71 +580,3 @@ test or use this data to advance their own work. This would lead to substantial
 scientific and medical advancements, which will ultimately lead to
 individualised treatment and improved human health in individuals with type 2
 diabetes, and very likely the population overall.
-
-# References
-
-# Questions to discuss (before or after submission)
-
-1. What is DD2's current Research Data Management Plan? 
-3. Thoughts on converting this into an
-article/implementation piece? It’s a fair amount of work we’ve put into it and
-(I believe) would have a considerable benefit to publishing and having people
-read about it. 
- 6. When we get funding, how to limit new personnel from the
-struggles of dealing with the Region’s IT setup? And not have them be given a
-Region computer, which will *for sure* reduce their productivity.
-
-# TODO
-
-## After submission
-
-- TODO: Will eventually need to build a more detailed use case description.
-- IDEA: Some way of generating a DOI for the DD2 itself/for the underlying database, without actually making the data public? Maybe the code or framework, along with the version? Need people to cite it somehow.
-- IDEA: Use this as the basis for a paper on the implementation details of the framework, to show we’re serious about it, and as a way to make this proposal itself a scientific output.
-- TODO: Reference to Data Package/Frictionless Data as Common Data Model: [https://frictionlessdata.io/](https://frictionlessdata.io/) ? Need to decide on exact Data Model.
-- TODO: Basic overview of strengths and weaknesses?
-- TODO: Add notes about licensing and copyright. For software, usually copyright resides with the employer (e.g. for SDCA that would be Region Midt). We’d need to discuss this with the employer before we can move too much forward. License should be permissible, e.g. by using MIT License.
-- TODO: Will need to include a list of “prerequisites” that potential users of this framework would need access to (or similar enough free resources) in order to either minimally or optimally make use the framework
-
-# Misc useful information
-
-- Access to data through “forskermaskine” requires a valid authorization, usually given to only one person (often the head of department) per approved institution. Importantly, if even one researcher working under the institution's authorization breaches data confidentiality (through transferring microdata outside the “forskermaskine”), the access is closed for the entire institution, and in the worst case permanently. Therefore, the authorized institutions (and corresponding persons) are reluctant to give access to researchers outside their own institutions or close collaborators. Thus, DD2 is presently working on establishing legal procedures for data access for researchers from different institutions (national and international).
-- File size of SNP/Genotyping/GWAS data: 0.000072MB per SNP per individual. So for 6,000 individuals and 1 mio genotyped SNPs: 0.4 TB. Also, approx 20 mio SNPs will probably be imputed, so times that by 20, and you get about 8 TB. This is for the planned GWAS 2. GWAS 1 is already available (first 3,000 participants and 500,000 genotyped SNPs, several mio. imputed) is maybe half that size, or smaller, so approx. additional 2-4 TB. Some references [here](https://www.ncbi.nlm.nih.gov/pubmed/29734293) and [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795954/).
-- [https://www.ohdsi.org/data-standardization/the-common-data-model/](https://www.ohdsi.org/data-standardization/the-common-data-model/)
-
-# Minutes
-
-## 2021-04-21
-
-- Organization diagram:
-    - DD2 Project management group: At KEA? At Odense? At Biobank?
-    - Called Research Advisory Board
-        - Two persons from each region of Denmark?
-            - One from Steno Center and another from GPs?
-    - Link: [https://dd2.dk/om-dd2/fagligt-raadgivningsforum](https://dd2.dk/om-dd2/fagligt-raadgivningsforum)
-    - Strategy is approved by DD2 Board
-    - Attach us to the Research Advisory Board?
-        - To highlight we are part of research
-        - To make sure we are “online” with other budget decisions
-- Funding… Update DST data into research engine.
-    - Update where data is stored
-- Data managers at KEA will need access
-
-## 2021-04-28
-
-- Need to include data storage and merging data?
-    - Merging data as in from Core DD2, from DST/SDS, and from the HPC for the larger data
-        - KEA has only additional data from DST/SDS
-            - They are working on ways to streamlining linking and merging.
-        - GWAS (might be) on Computerome2?
-            - Because it is so large (...size?), so can’t really be put on DST/SDS
-            - GWAS also require HPC for its processing
-            - Need two solutions for storage, because one for the large stuff and one for the DST
-    - Data storage at maybe three locations
-        - Data from Forskinemaskiner (?) on DST
-            - Have a shared authorization for sharing DST maskiner
-    - Describe these as key issues to deal with, rather than a key component of this framework.
-        - Data management position should be considered.
-    - SDCA could take lead over the legal stuff? But then it would not be at Odense… but doesn’t mean we take data ownership.
-        - Since we need to work within rules of DST
-        - And get a shared DST server in SDCA?