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Add SOP0014 Add datasets metadata to node beacon #75

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619351e
adding new SOP0014 add datasets medatada to node beacon
costero-e Jun 10, 2026
eaf56c0
modifying chapter, changelog and readme
costero-e Jun 10, 2026
76c2f44
fixing errors
costero-e Jun 10, 2026
769cef3
fixing errors for SOP0009
costero-e Jun 10, 2026
546d7df
fixing errors for SOP0009 involving AF beacon SOP0012
costero-e Jun 10, 2026
41d4cce
fixing table and flowchart
costero-e Jun 22, 2026
37d7d39
changing reference deleting for inserting in section 8.4
costero-e Jun 22, 2026
06f24db
some rewording, adding missing links and extra step for verifier
costero-e Jun 26, 2026
abffcc0
fixing when for steps 8.5 and 8.6
costero-e Jun 26, 2026
cbf7aa1
rephrasing step 8.1
costero-e Jun 26, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [``GDI-SOP0008_node-helpdesk-ticket-classification.md``](sops/node-specific/GDI-SOP0008_node-helpdesk-ticket-classification.md) - GDI Node Helpdesk Ticket Classification SOP.
- [``GDI-SOP0009_dataset-withdrawal.md``](sops/european-level/GDI-SOP0009_dataset-withdrawal.md) - Withdrawal request GDI SOP.
- [``.gitignore``](.gitignore) - File to ignore certain files in git commits.
- [``GDI-SOP0014_add-datasets-metadata-to-node-beacon.md``](sops/node-specific/GDI-SOP0014_add-datasets-metadata-to-node-beacon.md) - Add dataset’s metadata to Node beacon.

### Modified
- [``GDI-SOP_github-management.md``](docs/GDI-SOP_github-management.md) - Added reference to recorded session
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11 changes: 9 additions & 2 deletions docs/GDI-SOP_charter.md
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Expand Up @@ -25,14 +25,17 @@ The following table defines the abbreviations and terms relevant to GDI SOPs.
| 1+MG DAC | 1+MG Data Access Committee |
| AAI | Authentication and Authorization Infrastructure |
| AE | Associated Entity |
| AF | Allele Frequency |
| AI | Action Item |
| AF | Application Form |
| API | Application Programming Interface |
| BEN | Beneficiary |
| CC | Carbon Copy (used in communications to send a copy to others) |
| CRG | Centre for Genomic Regulation |
| CSC | Finnish IT Center for Science |
| DAA | Data Access Agreement |
| DAC | Data Access Committee |
| DKFZ | Deutsches Krebsforschungszentrum |
| DMP | Data Management Plan |
| DO | Data Object |
| DP | Data Protection |
Expand All @@ -56,7 +59,8 @@ The following table defines the abbreviations and terms relevant to GDI SOPs.
| GH | GitHub |
| HD | Helpdesk |
| HRI | Health Research Infrastructure |
| ID | Identity Document |
| HTTPS | Hypertext Transfer Protocol Secure |
| ID | Identifier |
| IdP | Identity Provider |
| INSERM | L'Institut national de la santé et de la recherche médicale (France) |
| ISM | Information Service Management |
Expand Down Expand Up @@ -97,6 +101,7 @@ The following table defines the abbreviations and terms relevant to GDI SOPs.
| UX | User experience |
| VHD | Virtual Helpdesk |
| VPN | Virtual Private Network |
| UM | University of Maribor |
| UP | User portal |
| WG | Working Group |
| WP | Work Package |
Expand All @@ -107,11 +112,13 @@ The following table defines the abbreviations and terms relevant to GDI SOPs.
|------------------|-------------------------------------------------------------------------|
| API | Application Programming Interface is a connection between computers or between computer programs. It is a type of software interface, offering a service to other pieces of software. |
| Beacon |A web-accessible service implementing the GA4GH Beacon specification, enabling federated discovery (and sometimes retrieval) of genomic variant and related biomedical data across distributed resources|
| Beacon Query | HTTPS request to an endpoint of the node’s Allele Frequency beacon. |
| CHANGELOG | Log or record of all notable changes made to a project |
| Data controller |The legal owner or organisation that determines the purposes and means of processing the dataset and can authorise its withdrawal|
| Dataset permissions | All the information related to the dataset grants and its security level configuration. |
| Dataset version |A specific released state of a dataset identified by a version label/number, used to distinguish minor or major changes between releases|
| FitSM | Standards for lightweight IT Services Management; developed initially through The FedSM Project, funded by the European Commission, now maintained by ITEMO (<https://www.fitsm.eu/>) |
| Hard-deletion |Complete, irreversible erasure of the data from all storage media so it cannot be recovered|
| Hard-deletion | Complete, irreversible erasure of the data from all storage media so it cannot be recovered|
| JIRA | Software product developed by Atlassian that allows bug tracking, issue tracking and agile project management. |
| JSON | JavaScript Object Notation is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of name–value pairs and arrays (or other serializable values).|
| Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. |
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3 changes: 2 additions & 1 deletion sops/README.md
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Expand Up @@ -7,4 +7,5 @@ Below you can find the full list of SOPs in this repository.
| [GDI-SOP0003_1+mg-dac-recommendation-approval.md](./european-level/GDI-SOP0003_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 | 2024.10.29 |
| [GDI-SOP0008_node-helpdesk-ticket-classification.md](./node-specific/GDI-SOP0008_node-helpdesk-ticket-classification.md) | GDI-SOP0008 | v1.0.0 | Helpdesk & operations | Node-specific SOP | | | 4 | 2026.03.10 |
| [GDI-SOP0009_dataset-withdrawal.md](./european-level/GDI-SOP0009_dataset-withdrawal.md) | GDI-SOP0009 | v1 | Data & metadata management | European-level SOP | | | 9 | 2026.03.10 |
| [GDI-SOP0009_dataset-withdrawal.md](./european-level/GDI-SOP0009_dataset-withdrawal.md) | GDI-SOP0009 | v1 | Data & metadata management | European-level SOP | | | 9 | 2026.03.10 |
| [GDI-SOP0014_add-datasets-metadata-to-node-beacon.md](./node-specific/GDI-SOP0014_add-datasets-metadata-to-node-beacon.md) | GDI-SOP0014 | v1 | Technical infrastructure & software development | Node-specific SOP | | | 6 | 2026.06.09 |
8 changes: 3 additions & 5 deletions sops/european-level/GDI-SOP0009_dataset-withdrawal.md
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Expand Up @@ -312,7 +312,7 @@ Request details:
- Deadline requested: <Deadline of withdrawal if applicable>

ACTIONS NEEDED [Within 5 working days]:
1. Please follow through with the dataset withdrawal request as per [Step 5](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#85-assign-withdrawal-response-team).
1. Please follow through with the dataset withdrawal request as per [Step 5](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/dev/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#85-assign-withdrawal-response-team).
2. Update the VHD ticket with assigned leads and expected completion timeline.

Once withdrawal is confirmed, the VHD will resume control to verify, notify the requester, and close the ticket.
Expand Down Expand Up @@ -385,10 +385,10 @@ You are appointed **Technical Lead** (TL) for the dataset-withdrawal request det
ACTIONS NEEDED:
1. Acknowledge receipt of this email **within 3 working days**.
2. Determine whether any (meta)data of the dataset resides in the specified GDI system.
3. If present, remove it (within the given scope) as per system SOP (see [Step 7](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#87-per-system-dataset-withdrawal)).
3. If present, remove it (within the given scope) as per system SOP (see [Step 7](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/dev/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#87-per-system-dataset-withdrawal)).
4. Report dataset withdrawal status in the ticket or directly contacting GDI's VHD.

You can find more details about how these tasks have been fulfilled previously at [Step 7](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#87-per-system-dataset-withdrawal).
You can find more details about how these tasks have been fulfilled previously at [Step 7](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/dev/sops/european-level/GDI-SOP0009_dataset-withdrawal.md#87-per-system-dataset-withdrawal).

If you need additional context or support, contact the OC/SDPC (gdi-sdpc [at] elixir-europe.org, gdi-oc [at] elixir-europe.org) or the VHD Officer (<VHD_OFFICER_CONTACT_DETAILS>).
Thank you for your prompt attention.
Expand Down Expand Up @@ -435,8 +435,6 @@ To accomplish these tasks, **follow the appropriate SOP** for your specified sys
- Nodes' Beacons (_#! SOP TBD, see https://github.com/GenomicDataInfrastructure/standard-operating-procedures/issues/64 #!_).
- Dataset Browser (_#! SOP TBD_).
- Nodes' FAIR Data Points (FDP) (_#! SOP TBD, see https://github.com/GenomicDataInfrastructure/standard-operating-procedures/issues/63 #!_).
- Allele Frequency Browser (_#! SOP TBD_).
- Nodes' Allele Frequency Beacons (_#! SOP TBD, see https://github.com/GenomicDataInfrastructure/standard-operating-procedures/issues/65 #!_).
- **Nodes' Secure Processing Environment** (SPE) (_#! SOP TBD_).

Once you have completed the relevant withdrawal SOP for the specified GDI System:
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