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Merge pull request #48 from GenomicDataInfrastructure/add-references
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Add references
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M-casado authored Dec 9, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [``GDI-SOP_github-introduction-for-maintainers.md``](docs/GDI-SOP_github-introduction-for-maintainers.md) - Introductory guide for GDI SOP Repository maintainers.

### Modified
- [``GDI-SOP_github-management.md``](docs/GDI-SOP_github-management.md) - Added reference to recorded session
- [``GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md``](sops/european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) - Updated references to _[Data Governance for Research](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit)_ document.

### Fixed

## [1.0.0](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/releases/tag/v1.0.0) - 2024-10-28
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2 changes: 2 additions & 0 deletions docs/GDI-SOP_github-management.md
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# Copying GDI SOP repository
The GDI SOP repository ([**GenomicDataInfrastructure/standard-operating-procedures**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures)) contains both European-level SOP _instances_ and Node-specific SOP _templates_. In order to adapt the Node-specific SOP templates, GDI nodes are expected to make a copy of this GitHub repository and modify them to suit them to their needs.

If you are a member of GDI, you are welcome to go through the [**recorded session**](https://drive.google.com/file/d/1DMbFP1xwu48aOPARTK2y_IVjFYt1bz10/view?usp=drive_link) where we covered this introduction.

Given that the base repository is public, forks of this repository cannot be private. Therefore, making a node's copy of the repository can be done in different ways, explained in this document, depending on the level of privacy that each node may require:
- **Public node's repository**. If the node does not require a private repository, copying the source repository is straightforward. See section _[1. Public repository](#1-public-repository)_.
- **Private node's repository**. On the contrary, if nodes need their SOP instances to be private (e.g. for security reasons), an alternative route is taken. See section _[2. Private repository](#2-private-repository)_.
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2 changes: 1 addition & 1 deletion sops/README.md
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Expand Up @@ -3,5 +3,5 @@ Below you can find the full list of SOPs in this repository.
| Name | Identifier | Template version | Topic | Type | GDI Node | Instance version | Nº steps | Last modified |
|:----------------------------------------------------------------------------------------------------------------------------|:-------------|:-------------------|:---------------------------|:-------------------|:-----------|:-------------------|-----------:|:----------------|
| [GDI-SOP0002_NCPs-veto-EDIC-decision.md](./node-specific/GDI-SOP0002_NCPs-veto-EDIC-decision.md) | GDI-SOP0002 | v1 | Helpdesk & operations | Node-specific SOP | | | 7 | 2024.09.27 |
| [GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md](./european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) | GDI-SOP0003 | v1 | Data & metadata management | European-Level SOP | | | 10 | 2024.10.24 |
| [GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md](./european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) | GDI-SOP0003 | v1 | Data & metadata management | European-Level SOP | | | 10 | 2024.11.11 |
| [GDI-SOP0007_SOP-template-creation.md](./european-level/GDI-SOP0007_SOP-template-creation.md) | GDI-SOP0007 | v1 | Helpdesk & operations | European-Level SOP | | | 7 | 2024.07.08 |
12 changes: 7 additions & 5 deletions sops/european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md
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| Template Version | Instance version | Author(s) | Description of changes | Date |
|------------------|------------------|-------------------|----------------------------------|------------|
| ``v1.0.2`` | | Marcos Casado Barbero | Update references to Data Governance for Research document | ``2024.11.11`` |
| ``v1.0.1`` | | Marcos Casado Barbero | Transform document to markdown and complete version | ``2024.10.24`` |
| ``v1`` | | Marcos Casado Barbero | Transform document to markdown and complete version | ``2024.10.04`` |
| ``v0`` | | Dylan Spalding | First version of SOP drafted | ``2024.04.11`` |
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|-----------------|--------------------------------------------|--------------|
| 1 | On receipt of notification of a new data access application | 1+MG DAC |

As the 1+MG DAC, **check the requester's application**, based on the criteria in the [**Data Access Review**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=kix.9o5agsar78sq) section of the Data Governance document. The application form, which is used to help the data requester enter valid and complete information for the application, must be checked to ensure that:
As the 1+MG DAC, **check the requester's application**, based on the criteria in the _**Data Access Review**_ section of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``). The application form, which is used to help the data requester enter valid and complete information for the application, must be checked to ensure that:
- The research has [institutional sign-off](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth), if applicable.
- The **data analysis plan** is present and suitable for the proposed research.
- The **data minimisation principle** is met.
- **Algorithms** (such as artificial intelligence) **are suitable** for the proposed purpose and transparent.
- The **ethical approval** has been obtained for the proposed research, where applicable, and that the approval is applicable for the proposed research and conclusions of the ethics review are followed.
- The **funding mechanisms** for the proposed research are in place (if required).
- The **project description** corresponds with the data analysis plan, and the **ethical approval and legal requirements** exist with respect to the requested data.
- Any **peer review** of the scientific validity of the proposed research exists. In case it does not, follow [**section II.3**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=id.utnaek5ua0aa) of the Data Governance document.
- Any **peer review** of the scientific validity of the proposed research exists. In case it does not, follow section _**II.3**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``).

You must **finish this initial assessment within 5 working days** (review [**agreed timelines**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=kix.9o5agsar78sq) if needed). After this period,you shall **transmit the outcome of the review and a decision recommendation** to the 1+MG NCPs who can channel it to relevant bodies on the national level.
You must **finish this initial assessment within 5 working days** (review **agreed timelines** at section _**III. DATA ACCESS REVIEW**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``) if needed). After this period, you shall **transmit the outcome of the review and a decision recommendation** to the 1+MG NCPs who can channel it to relevant bodies on the national level.

Be mindful that **this timeline may be affected** where the planned research affects vulnerable subjects or groups, as specified in [**section III.2**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=id.xez4tqfoy9hq) of the Data Governance document.
Be mindful that **this timeline may be affected** where the planned research affects vulnerable subjects or groups, as specified in section _**III.2**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``).

Depending on the outcome of this initial evaluation:
- If all steps are correct, move to **[step 2](#82-recommend-application-for-approval)**.
Expand Down Expand Up @@ -224,4 +225,5 @@ This concludes the process resulting in rejection of the data request.
| [3](../node-specific/GDI-SOP0002_NCPs-veto-EDIC-decision.md) | European GDI SOP - NCPs veto EDIC Decision |
| [4](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU) | 1+MG Data Access Governance for Research |
| [5](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/issues/33) | European GDI - NCP review process of disagreement with 1+MG DAC recommendation |
| [6](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth) | European GDI - Obtain Institutional Sign-off |
| [6](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth) | European GDI - Obtain Institutional Sign-off |
| [7](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) | Data Governance document (``v1.0``) |

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