Welcome to the GDI Standard Operating Procedures (SOPs) repository! ☀️ This repository is the central hub for the creation, management, and dissemination of SOPs for the European Genomic Data Infrastructure (GDI) project. We aim to standardize and harmonize operational procedures across GDI nodes to ensure interoperability and compliance.
This repository is publicly accessible, but GDI nodes may also maintain their own forks or cloned versions with node-specific SOP implementations.
All SOP documents are stored in the sops/ folder. The SOPs are categorized as:
- European-level SOPs: SOPs that can be implemented across all GDI nodes.
- Node-specific SOP templates: SOP Templates that can be adapted by individual nodes based on their specific needs.
An up-to-date index of all released SOPs, along with their metadata, can be found in the index table.
The main branch of this repository always contains the latest version of released SOPs. Furthermore, if you require access to a snapshot of previous SOP releases, you have the following at your disposal:
- GitHub Releases: Static versions of the SOP repository are tagged and available through GitHub releases.
- Zenodo Submissions: Each GitHub release is automatically submitted to the GDI Zenodo community, where a DOI (i.e., a permanent identifier) is assigned for the SOP bundle. You can explore the releases via Zenodo GDI community.
For more information on the release process and DOI minting, please refer to the SOP Accessioning Documentation.
We welcome contributions from all GDI members and the wider community. If you want to request changes, propose new SOPs, or directly contribute to the repository, please check out our CONTRIBUTING guide.
More documentation is available within the docs directory. For detailed information about the SOP framework, processes, and roles within the GDI project, please refer to the Charter, the Information Security Management (ISM) and Organisational Roles and Responsibilities (ORR).
If you encounter any issues or have suggestions for improvements to existing SOPs, feel free to open an issue on GitHub. Simply go to the Issues section and use the appropriate template to describe the problem.
Below is a detailed overview of the SOP development and management process:
flowchart TB
%% Colors
classDef SOP fill:#FFD700,stroke:#000000,stroke-width:2px;
classDef Template fill:#87CEEB,stroke:#000000,stroke-width:2px;
classDef start fill:#e8daef,stroke:#c0392b,stroke-width:2px;
%% Nodes
subgraph Diagram-Legend
subgraph Colour-coding
l_sopTemplate[SOP Template]
l_sopInstance[SOP Instance]
l_start[Diagram start]
end
subgraph Abbreviations
l_oc[**OC**: Operations Committee]
l_spdc[**SDPC**: Security and Data Protection Committee]
l_GDI[**GDI**: European Genomic Data Infrastructure]
l_SOP[**SOP**: Standard Operating Procedure]
end
end
B[GDI project partners]
B -..->|Write SOP proposal| B2
checkValid{Valid request?}
B2 -->|Request<br>is evaluated| checkValid
sopPreparation(Document Preparation)
checkValid -->|Yes|sopPreparation
checkValid -->|No|B2
Repository-maintainers -..->|Maintains| Main-GitHub-repository
F -..->|Is used by| sopPreparation
sopPreparation -->|Outputs| G
G[SOP Template]
G -->|Is taken by| I
%% Boxes
subgraph European-level SOPs
S[SOP Instance draft]
V[Finished European-level<br>SOP Instance]
ZA[Released European-level<br>SOP Instance]
end
ZA -->|Enters| review_e
subgraph European-Review-cycle
review_e[Periodic SOP<br> content review]
review_e -->|Determines| revision_e
revision_e{Is revision<br>required?}
end
revision_e -->|No| review_e
revision_e -->|Yes| SOP-development-cycle
subgraph Node-specific SOPs
Q[SOP Template draft]
W[Finished Node-specific<br>SOP Template]
Z[Released Node-specific<br>SOP Template]
nodeRep[OC/SDPC Representatives<br>from each node]
Z -->|is used by| nodeRep
subgraph Node's-GitHub
nodeTem[Node-specific<br>SOP Template]
nodeSOP[Node-specific<br>SOP Instance]
end
nodeRep -->|Copy SOP Template| Node's-GitHub
subgraph Node's-Roles
nodeRep[Node's OC/SDPC <br> representative]
nodeRep --> |Nominate| nodeExp
nodeExp[Nominated<br>experts]
end
subgraph Node's-SOP-development-process
nodeDev(Template gets adapted<br> with the node's needs)
nodeDev --> nodeRev
nodeRev(Review)
nodeRev --> nodeApp
nodeApp(Approval)
end
Node's-Roles -..->|Responsible for| Node's-SOP-development-process
nodeTem --> nodeDev
nodeApp --> |Produces| nodeSOP
nodeSOP -->|Enters| review_n
subgraph Node's-Review-cycle
review_n[Periodic SOP<br> content review]
review_n -->|Determines| revision_n
revision_n{Is revision<br>required?}
end
revision_n -->|No| review_n
revision_n -->|Yes| nodeDev
end
nodeRep -..->|Approves <br> changes| nodeApp
I --> |Start development process| R
Authors -..-> |Fill in SOP content| L
Reviewers -..->|Review SOP| M
Approvers -..->|Approve SOP|N
Authorizers -..->|Authorize SOP| O
R{Type of SOP?}
R -->|Node-specific| Q
R -->|European-level| S
Q -->|Enters cycle|SOP-development-cycle
S -->|Enters cycle|SOP-development-cycle
subgraph SOP-development-cycle
L(Fill in content)
L --> M
M(Review)
M --> N
N(Approval)
N --> O
O(Authorization)
end
O --> aos-accessioning
aos-merge -->|Produces| V
aos-merge -->|Produces| W
subgraph Main-GitHub-repository
B2[GitHub Issue]
F[General GDI SOP Template]
aos-accessioning(SOP accessioning<br> and formatting)
aos-merge(PR against <br> 'dev' branch)
subgraph SOP-release-process
git1(Pull Request<br>to 'main' branch)
git1 -->|Branch is<br>used for| git2
git2(GitHub release)
end
end
git3(Zenodo release)
git2 -->|Automatically <br> triggers| git3
aos-accessioning --> aos-merge
subgraph ORR-roles
Authors
Reviewers
Authorizers
Approvers
Trainers
Node-maintainers
Repository-maintainers
end
subgraph Authors
I[OC/SDPC]
I -->|Nominate|J
J[Nominated experts]
end
subgraph Reviewers
reviewers1[GDI members]
end
subgraph Approvers
approvers1[OC/SDPC]
end
subgraph Trainers
t_authors[SOP Authors]
t_experts[Nominated<br>experts]
end
subgraph Node-maintainers
n_maintainers[Node's OC/SDPC<br>representative]
n_experts[Nominated<br>experts]
end
Node-maintainers -..->|Are| Node's-Roles
subgraph Repository-maintainers
ocsdpc[OC/SDPC]
end
subgraph Authorizers
authorizers1[Management Board]
authorizers2[1+MG Working Group]
end
V -->|Enters process| SOP-release-process
W -->|Enters process| SOP-release-process
SOP-release-process -->|Produces| ZA
SOP-release-process -->|Produces| Z
SOPtraining[SOP Training]
nodeSOP --> SOPtraining
ZA --> SOPtraining
Trainers -..-> |Provides|SOPtraining
revision[Revision is due]
%% Styles
class S,V,ZA,nodeSOP,l_sopInstance SOP
class G,F,Q,W,Z,nodeTem,l_sopTemplate Template
class B2,l_start start