From ea43f10379315e27d2e8f8e41b22f45060db0c10 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda Date: Wed, 2 Sep 2026 11:24:14 +0200 Subject: [PATCH 01/11] draft of data reception procedure --- .../GDI-SOP0010_data-reception-procedure.md | 174 ++++++++++++++++++ 1 file changed, 174 insertions(+) create mode 100644 sops/node-specific/GDI-SOP0010_data-reception-procedure.md diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md new file mode 100644 index 00000000..fe626941 --- /dev/null +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -0,0 +1,174 @@ +# European GDI - Data Reception Procedure + +| Metadata | Value | +|----------|-------| +| Template SOP number | GDI-SOP0010 | +| Template SOP version | v1 | +| Topic | Data & Metadata Management | +| Template SOP Type | Node-specific SOP | +| GDI Node | - | +| Instance version | - | + +## Index + +1. [Document History](#1-document-history) +2. [Glossary](#2-glossary) +3. [Roles and Responsibilities](#3-roles-and-responsibilities) +4. [Purpose](#4-purpose) +5. [Scope](#5-scope) +6. [Introduction and Background Information](#6-introduction-and-background-information) +7. [Summary or Context Diagram](#7-summary-or-context-diagram) +8. [Procedure](#8-procedure) +9. [References](#9-references) + +### 1. Document History + +| Template Version | Instance version | Author(s) | Description of changes | Date | +|---------|-----------|-----------|------------------------------|------------| +| `v1` | `v1.0.2` | Jorge Oliveira, Aleksandar Kmetov, Jacek Lebioda | Converting to SOP template and futher refinement | 2026.08.31 | +| `v1` | `v1.0.1` | Jorge Oliveira, Miguel Cisneiros | Further development of the first version of the SOP | 2025.08.22 | +| `v1` | `v1.0.0` | Jorge Oliveira, Pedro Ferreira | Created first version of the SOP | 2024.09.10 | + + +### 2. Glossary +Find GDI SOPs common Glossary at the [**charter document**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_charter.md). + +| Abbreviation | Description | +|---------------|-----------------| +| ELSI | Ethical, Legal, and Social Issues | + +| Term | Definition | +|---------------|-----------------| +| Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. | +| Ticket | Incoming issues from the GDI Virtual Helpdesk, are to be processed within the Node Helpdesk and, after that, returned to the Virtual Helpdesk | +| Data Reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | +| Data Submission | The process of registering, publishing, and making data assets discoverable and accessible | +| Data Preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | +| Data Inclusion | Systematic integration of data into structured and machine-readable datasets | + + +### 3. Roles and Responsibilities +See qualifications and responsabilities of the roles at the [**Organisational Roles and Responsibilities**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_organisational-roles-and-responsibilities.md) document. + +| Role | Full name | GDI/node role | Organisation | +|------------|-----------------|-----------------|--------------| +| Author | Jorge Oliveira | Node technical coordinator | BioData.pt | +| Reviewer | | | | +| Approver | | | | +| Authorizer | | | | + + +### 4. Purpose +This SOP is an overarching procedure on how the data submissions made by the data suppliers will be handled. The purpose is to provide a clear, step-by-step guide for handling data submissions to the European Genomic Data Infrastructure, ensuring that helpdesk members can efficiently and accurately receive and process the submitted data and store it properly. Following, this SOP will streamline data management, maintain consistency, and ensure compliance with relevant protocols. + + +### 5. Scope +This SOP covers the process from receiving a data submission to the proper storage and acknowledgment of the submission. It defines how helpdesk members handle incoming submissions, ensuring they are stored accurately and appropriately for further use. + +### 6. Introduction and Background Information +This is a node-specific SOP template: each node can use this template as a basis and adapt it to their specific needs and procedures in their instances. + +Data Reception in GDI covers two steps of the Data Journey: Data Preparation and Data Inclusion. + + +### 7. Summary or Context Diagram + +```mermaid +graph TB + start( ) + input1[Submission request] + step1.1{Assessment of submission request - Data types verification} + step1.2{Assessment of submission request - ELSI compliance verification} + step2{Storage capacity check} + step3{Complete metadata} + step4(Review submission) + step5(Release datasets) + ending(" ") + + start -..- input1 + input1 -..->|Received by Role 1| step1.1 + step1.1 -->|Assessment OK| step1.2 + step1.1 -->|Assessment not OK| ending + step1.2 -->|Assessment OK| step2 + step1.2 -->|Assessment not OK| ending + step2 -->|Check OK| step3 + step2 -->|Check not OK| ending + step3 -->step4 + step4 -->step5 + step5 -..- ending +``` + +### 8. Procedure + + +#### 1.1 Assessment of submission request - data types evaluation + + +| Step identifier | When | Who | +|:------------------|:------|:----| +| 1.1 | When data is submitted | Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +Check if the submitted data types are in a standardized format - SAM, BAM, CRAM, VCF, FASTA, FASTQ: + * Yes, continue the process + * No, contact the submitter and request appropriate changes. + +#### 1.2 Assessment of submission request - ELSI compliance verification + +| Step identifier | When | Who | +|:------------------|:----|:----| +| 1.2 | After data types verification | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +Make compliance checks, i.e. make sure you have necessary ELSI documents (e.g. informed consent, ethical permits) and ELSI metadata (e.g. data controller). + * Yes, continue the process + * No, there is missing/incomplete/incorrect ELSI documentation or metadata: contact the submitter and request appropriate changes. + + +#### 2. Storage capacity check +| Step identifier | When | Who | +|:---------------------------|:-----------------|:----| +| 2.1 | After ticket assessment successful completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +After evaluating the submission, determine the data size and verify if sufficient storage is available to accommodate it. + * If yes, continue the process + * If not, (TBD) + + +#### 3. Storage capacity check +| Step identifier | When | Who | +|:---------------------------|:-----------------|:----| +| 3 | After completing the request evaluation and all related considerations. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +TBD + + +#### 4. Review submission +| Step identifier | When | Who | +|:---------------------------|:-----------------|:----| +| 4 | After metadata completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +After all, review the full submission: + * Data integrity check + - Validate checksums. + - For BAM/CRAM: samtools quickcheck and header validation. + - For VCF: bcftools view -h and vcftools/bcftools consistency checks. + - For FASTQ: basic read counts, header sanity checks. + * Metadata check + + + +#### 5. Release datasets +| Step identifier | When | Who | +|:---------------------------|:-----------------|:----| +| 5 | After submission review | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | + +TBD + + +### 9. References + +| Reference | Description | +|-----------|------------------------------------------------------| +| [1](#) | European GDI - SOP Charter (including Glossary) | +| [2](#) | European GDI - Procedures for Information Service Management (ISM) for SOPs | +| [3](#) | European GDI - Organisational Roles and Responsibilities (ORR) | +| [4](#) | ... | From 0fd5d5237b8be025b85f8b042464d0e14145b7f0 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 09:44:19 +0200 Subject: [PATCH 02/11] Update index in README.md --- sops/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sops/README.md b/sops/README.md index e06b3844..1d200124 100644 --- a/sops/README.md +++ b/sops/README.md @@ -4,4 +4,5 @@ Below you can find the full list of SOPs in this repository. |:--------------------------------------------------------------------------------------------------------------------|:-------------|:-------------------|:---------------------------|:-------------------|:-----------|:-------------------|-----------:|:----------------| | [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 | 2024.10.29 | | [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 | \ No newline at end of file +| [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-SOP0010_data-reception-procedure.md](./node-specific/GDI-SOP0010_data-reception-procedure.md) | GDI-SOP0010 | v1 | Data & metadata management | Node-specific SOP | | | 5 | 2026.09.02 | From fa1aff4b7dd07d1f1b5d4b13e6771d55793328f0 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 09:49:53 +0200 Subject: [PATCH 03/11] Update GDI-SOP0010_data-reception-procedure.md --- sops/node-specific/GDI-SOP0010_data-reception-procedure.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index fe626941..0d3110ac 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -4,10 +4,10 @@ |----------|-------| | Template SOP number | GDI-SOP0010 | | Template SOP version | v1 | -| Topic | Data & Metadata Management | +| Topic | Data & metadata Management | | Template SOP Type | Node-specific SOP | -| GDI Node | - | -| Instance version | - | +| GDI Node | | +| Instance version | | ## Index From b504d9d4bdd05b45df00514881a9321a97750d10 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 09:50:17 +0200 Subject: [PATCH 04/11] Update README.md --- sops/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sops/README.md b/sops/README.md index a4061938..6735d408 100644 --- a/sops/README.md +++ b/sops/README.md @@ -7,5 +7,5 @@ Below you can find the full list of SOPs in this repository. | [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-SOP0010_data-reception-procedure.md](./node-specific/GDI-SOP0010_data-reception-procedure.md) | GDI-SOP0010 | v1 | Data & metadata management | Node-specific SOP | | | 5 | 2026.09.02 | +| [GDI-SOP0010_data-reception-procedure.md](./node-specific/GDI-SOP0010_data-reception-procedure.md) | GDI-SOP0010 | v1 | Data & metadata management | Node-specific SOP | | | 6 | 2026.08.31 | | [GDI-SOP0011_withdraw-dataset-from-node-fair-data-point.md](./node-specific/GDI-SOP0011_withdraw-dataset-from-node-fair-data-point.md) | GDI-SOP0011 | v1 | Technical infrastructure & software development | Node-specific SOP | | | 5 | 2026.05.20 | From f1745578b14d176014db0498aa6e42b533f5ab32 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 10:07:00 +0200 Subject: [PATCH 05/11] Update GDI-SOP0010_data-reception-procedure.md Fixing some issues found while linting --- .../GDI-SOP0010_data-reception-procedure.md | 63 ++++++++++--------- 1 file changed, 32 insertions(+), 31 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index 0d3110ac..1e9711ca 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -33,14 +33,14 @@ ### 2. Glossary Find GDI SOPs common Glossary at the [**charter document**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_charter.md). -| Abbreviation | Description | +| Abbreviation | Description | |---------------|-----------------| | ELSI | Ethical, Legal, and Social Issues | -| Term | Definition | -|---------------|-----------------| -| Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. | -| Ticket | Incoming issues from the GDI Virtual Helpdesk, are to be processed within the Node Helpdesk and, after that, returned to the Virtual Helpdesk | +| Term | Definition | +|------------------|-----------------| +| Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. | +| Ticket | Incoming issues from the GDI Virtual Helpdesk, are to be processed within the Node Helpdesk and, after that, returned to the Virtual Helpdesk | | Data Reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | | Data Submission | The process of registering, publishing, and making data assets discoverable and accessible | | Data Preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | @@ -52,10 +52,11 @@ See qualifications and responsabilities of the roles at the [**Organisational Ro | Role | Full name | GDI/node role | Organisation | |------------|-----------------|-----------------|--------------| -| Author | Jorge Oliveira | Node technical coordinator | BioData.pt | -| Reviewer | | | | -| Approver | | | | -| Authorizer | | | | +| Author | Jorge Oliveira | Node technical coordinator | BioData.pt | +| Author | Jacek Lebioda | DevOps Engineer | LNDS | +| Reviewer | TBD | TBD | TBD | +| Approver | TBD | TBD | TBD | +| Authorizer | TBD | TBD | TBD | ### 4. Purpose @@ -86,65 +87,65 @@ graph TB ending(" ") start -..- input1 - input1 -..->|Received by Role 1| step1.1 - step1.1 -->|Assessment OK| step1.2 - step1.1 -->|Assessment not OK| ending - step1.2 -->|Assessment OK| step2 - step1.2 -->|Assessment not OK| ending - step2 -->|Check OK| step3 - step2 -->|Check not OK| ending - step3 -->step4 - step4 -->step5 - step5 -..- ending + input1 -..->|Received by Role 1| step8.1 + step8.1 -->|Assessment OK| step8.2 + step8.1 -->|Assessment not OK| ending + step8.2 -->|Assessment OK| step8.3 + step8.2 -->|Assessment not OK| ending + step8.3 -->|Check OK| step8.4 + step8.3 -->|Check not OK| ending + step8.4 -->step8.5 + step8.5 -->step8.6 + step8.6 -..- ending ``` ### 8. Procedure -#### 1.1 Assessment of submission request - data types evaluation +#### 8.1 Assessment of submission request - data types evaluation | Step identifier | When | Who | |:------------------|:------|:----| -| 1.1 | When data is submitted | Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.1 | When data is submitted | Helpdesk member assigned to the ticket (responsible for handling the submission request) | Check if the submitted data types are in a standardized format - SAM, BAM, CRAM, VCF, FASTA, FASTQ: * Yes, continue the process * No, contact the submitter and request appropriate changes. -#### 1.2 Assessment of submission request - ELSI compliance verification +#### 8.2 Assessment of submission request - ELSI compliance verification | Step identifier | When | Who | |:------------------|:----|:----| -| 1.2 | After data types verification | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.2 | After data types verification | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | Make compliance checks, i.e. make sure you have necessary ELSI documents (e.g. informed consent, ethical permits) and ELSI metadata (e.g. data controller). * Yes, continue the process * No, there is missing/incomplete/incorrect ELSI documentation or metadata: contact the submitter and request appropriate changes. -#### 2. Storage capacity check +#### 8.3. Storage capacity check | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 2.1 | After ticket assessment successful completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.3 | After ticket assessment successful completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | After evaluating the submission, determine the data size and verify if sufficient storage is available to accommodate it. * If yes, continue the process * If not, (TBD) -#### 3. Storage capacity check +#### 8.4. Storage capacity check | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 3 | After completing the request evaluation and all related considerations. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.4 | After completing the request evaluation and all related considerations. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | TBD -#### 4. Review submission +#### 8.5. Review submission | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 4 | After metadata completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.5 | After metadata completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | After all, review the full submission: * Data integrity check @@ -156,10 +157,10 @@ After all, review the full submission: -#### 5. Release datasets +#### 8.6. Release datasets | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 5 | After submission review | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 8.6 | After submission review | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | TBD From 4ebb90f7e1f21eec5f12c115ad719632e62814c5 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 10:11:59 +0200 Subject: [PATCH 06/11] Update GDI-SOP0010_data-reception-procedure.md Fixing linting issues --- .../GDI-SOP0010_data-reception-procedure.md | 48 +++++++++---------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index 1e9711ca..1b36dd87 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -1,13 +1,13 @@ # European GDI - Data Reception Procedure -| Metadata | Value | -|----------|-------| -| Template SOP number | GDI-SOP0010 | -| Template SOP version | v1 | -| Topic | Data & metadata Management | -| Template SOP Type | Node-specific SOP | -| GDI Node | | -| Instance version | | +| Metadata | Value | +|----------------------|-------------------| +| Template SOP number | GDI-SOP0010 | +| Template SOP version | v1 | +| Topic | Data & metadata management | +| Template SOP Type | Node-specific SOP | +| GDI Node | | +| Instance version | | ## Index @@ -87,16 +87,16 @@ graph TB ending(" ") start -..- input1 - input1 -..->|Received by Role 1| step8.1 - step8.1 -->|Assessment OK| step8.2 - step8.1 -->|Assessment not OK| ending - step8.2 -->|Assessment OK| step8.3 - step8.2 -->|Assessment not OK| ending - step8.3 -->|Check OK| step8.4 - step8.3 -->|Check not OK| ending - step8.4 -->step8.5 - step8.5 -->step8.6 - step8.6 -..- ending + input1 -..->|Received by Role 1| step1 + step1 -->|Assessment OK| step2 + step1 -->|Assessment not OK| ending + step2 -->|Assessment OK| step3 + step2 -->|Assessment not OK| ending + step3 -->|Check OK| step4 + step3 -->|Check not OK| ending + step4 -->step5 + step5 -->step6 + step6 -..- ending ``` ### 8. Procedure @@ -107,7 +107,7 @@ graph TB | Step identifier | When | Who | |:------------------|:------|:----| -| 8.1 | When data is submitted | Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 1 | When data is submitted | Helpdesk member assigned to the ticket (responsible for handling the submission request) | Check if the submitted data types are in a standardized format - SAM, BAM, CRAM, VCF, FASTA, FASTQ: * Yes, continue the process @@ -117,7 +117,7 @@ Check if the submitted data types are in a standardized format - SAM, BAM, CRAM, | Step identifier | When | Who | |:------------------|:----|:----| -| 8.2 | After data types verification | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 2 | After data types verification | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | Make compliance checks, i.e. make sure you have necessary ELSI documents (e.g. informed consent, ethical permits) and ELSI metadata (e.g. data controller). * Yes, continue the process @@ -127,7 +127,7 @@ Make compliance checks, i.e. make sure you have necessary ELSI documents (e.g. i #### 8.3. Storage capacity check | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 8.3 | After ticket assessment successful completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 3 | After ticket assessment successful completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | After evaluating the submission, determine the data size and verify if sufficient storage is available to accommodate it. * If yes, continue the process @@ -137,7 +137,7 @@ After evaluating the submission, determine the data size and verify if sufficien #### 8.4. Storage capacity check | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 8.4 | After completing the request evaluation and all related considerations. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 4 | After completing the request evaluation and all related considerations. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | TBD @@ -145,7 +145,7 @@ TBD #### 8.5. Review submission | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 8.5 | After metadata completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 5 | After metadata completion. | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | After all, review the full submission: * Data integrity check @@ -160,7 +160,7 @@ After all, review the full submission: #### 8.6. Release datasets | Step identifier | When | Who | |:---------------------------|:-----------------|:----| -| 8.6 | After submission review | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | +| 6 | After submission review | The Helpdesk member assigned to the ticket (responsible for handling the submission request) | TBD From 499595947ab285ac1825641b3ec5eb765867a9cb Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 10:15:01 +0200 Subject: [PATCH 07/11] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3aa4fa45..70b5f8a8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [``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-SOP0011_withdraw-dataset-from-node-fair-data-point.md``](sops/node-specific/GDI-SOP0011_withdraw-dataset-from-node-fair-data-point.md) - Node-specific SOP template describing how a node FAIR Data Point should process soft withdrawal of a dataset or linked distributions. +- [``GDI-SOP0010_data-reception-procedure.md``](sops/node-specific/GDI-SOP0010_data-reception-procedure.md) - Node-specific SOP describing Data Reception. ### Modified - [``GDI-SOP_github-management.md``](docs/GDI-SOP_github-management.md) - Added reference to recorded session From 20212fc125c13002ae93d736f728349db97b4c0c Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 10:25:36 +0200 Subject: [PATCH 08/11] Update GDI-SOP0010_data-reception-procedure.md glossary updates --- .../GDI-SOP0010_data-reception-procedure.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index 1b36dd87..2fd87bf9 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -35,7 +35,12 @@ Find GDI SOPs common Glossary at the [**charter document**](https://github.com/G | Abbreviation | Description | |---------------|-----------------| +| BAM | Binary Alignment Map, file format for aligned sequencing reads mapped to a reference genome | +| CRAM | Compressed Reference-oriented Alignment Map, a space-saving alternative to BAM | | ELSI | Ethical, Legal, and Social Issues | +| FASTA | Fast-A, file format for raw data output directly from DNA/RNA sequencing machines | +| FASTQ | FASTA with Quality, file format for raw data output directly from DNA/RNA sequencing machines | +| VCF | Variant Call Format, file format used to store genetic variations | | Term | Definition | |------------------|-----------------| @@ -170,6 +175,4 @@ TBD | Reference | Description | |-----------|------------------------------------------------------| | [1](#) | European GDI - SOP Charter (including Glossary) | -| [2](#) | European GDI - Procedures for Information Service Management (ISM) for SOPs | -| [3](#) | European GDI - Organisational Roles and Responsibilities (ORR) | -| [4](#) | ... | +| [2](#) | European GDI - Procedures for Information Service Management for SOPs | From 955ae10bdae6b43fe9644e977a7942f4f53dc369 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 11:06:57 +0200 Subject: [PATCH 09/11] Update GDI-SOP0010_data-reception-procedure.md --- .../GDI-SOP0010_data-reception-procedure.md | 25 +++++++++++-------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index 2fd87bf9..66d02b72 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -31,26 +31,31 @@ ### 2. Glossary -Find GDI SOPs common Glossary at the [**charter document**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_charter.md). +Find GDI SOP common Glossary at the [**charter document**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_charter.md). | Abbreviation | Description | |---------------|-----------------| | BAM | Binary Alignment Map, file format for aligned sequencing reads mapped to a reference genome | -| CRAM | Compressed Reference-oriented Alignment Map, a space-saving alternative to BAM | -| ELSI | Ethical, Legal, and Social Issues | -| FASTA | Fast-A, file format for raw data output directly from DNA/RNA sequencing machines | -| FASTQ | FASTA with Quality, file format for raw data output directly from DNA/RNA sequencing machines | -| VCF | Variant Call Format, file format used to store genetic variations | +| CRAM | Compressed Reference-oriented Alignment Map, a space-saving alternative to BAM | +| ELSI | Ethical, Legal, and Social Issues | +| FASTA | Fast-A, file format for raw data output from sequencing machines | +| FASTQ | FASTA with Quality, file format for raw data output from sequencing machines | +| LNDS | Luxembourg National Data Service | +| OK | All correct | +| SAM | Sequence Alignment/Map text file used in bioinformatics | +| SOP | Standard Operating Procedure | +| TB | Top to Bottom | +| TBD | To Be Determined | +| VCF | Variant Call Format, file format used to store genetic variations | | Term | Definition | |------------------|-----------------| | Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. | | Ticket | Incoming issues from the GDI Virtual Helpdesk, are to be processed within the Node Helpdesk and, after that, returned to the Virtual Helpdesk | +| Data Inclusion | Systematic integration of data into structured and machine-readable datasets | +| Data Preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | | Data Reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | | Data Submission | The process of registering, publishing, and making data assets discoverable and accessible | -| Data Preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | -| Data Inclusion | Systematic integration of data into structured and machine-readable datasets | - ### 3. Roles and Responsibilities See qualifications and responsabilities of the roles at the [**Organisational Roles and Responsibilities**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_organisational-roles-and-responsibilities.md) document. @@ -175,4 +180,4 @@ TBD | Reference | Description | |-----------|------------------------------------------------------| | [1](#) | European GDI - SOP Charter (including Glossary) | -| [2](#) | European GDI - Procedures for Information Service Management for SOPs | +| [2](#) | European GDI - Procedures for Information Service Management for SOP | From 137889b42cdf3a3073ed3865f2fbdf276734267c Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 11:07:16 +0200 Subject: [PATCH 10/11] Update GDI-SOP_charter.md --- docs/GDI-SOP_charter.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/GDI-SOP_charter.md b/docs/GDI-SOP_charter.md index 2c086a2a..5dc59149 100644 --- a/docs/GDI-SOP_charter.md +++ b/docs/GDI-SOP_charter.md @@ -28,8 +28,10 @@ The following table defines the abbreviations and terms relevant to GDI SOPs. | AI | Action Item | | AF | Application Form | | API | Application Programming Interface | +| BAM | Binary Alignment Map, file format for aligned sequencing reads mapped to a reference genome | | BEN | Beneficiary | | CC | Carbon Copy (used in communications to send a copy to others) | +| CRAM | Compressed Reference-oriented Alignment Map, a space-saving alternative to BAM | | CSC | Finnish IT Center for Science | | DAA | Data Access Agreement | | DAC | Data Access Committee | @@ -46,6 +48,8 @@ The following table defines the abbreviations and terms relevant to GDI SOPs. | ELSI | Ethical, Legal, and Social Implications | | EMBL | European Molecular Biology Laboratory | | FAIR | Findability, Accessibility, Interoperability and Reusability | +| FASTA | Fast-A, file format for raw data output from sequencing machines | +| FASTQ | FASTA with Quality, file format for raw data output from sequencing machines | | FDP | FAIR Data Point | | FEGA | Federated EGA | | FTP | File Transfer Protocol | @@ -82,6 +86,7 @@ The following table defines the abbreviations and terms relevant to GDI SOPs. | REMS | Resource Entitlement Management System | | RFC | Request For Comments | | RI | Research Infrastructure | +| SAM | Sequence Alignment/Map text file used in bioinformatics | | SDPC | Security and Data Protection Committee | | SLA | Service Level Agreement | | SP | Submitter Portal | @@ -95,6 +100,7 @@ The following table defines the abbreviations and terms relevant to GDI SOPs. | URL | Uniform Resource Locator | | UU | University of Uppsala | | UX | User experience | +| VCF | Variant Call Format, file format used to store genetic variations | | VHD | Virtual Helpdesk | | VPN | Virtual Private Network | | UP | User portal | @@ -109,6 +115,10 @@ The following table defines the abbreviations and terms relevant to GDI SOPs. | 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| | 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| +| Data inclusion | Systematic integration of data into structured and machine-readable datasets | +| Data preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | +| Data reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | +| Data submission | The process of registering, publishing, and making data assets discoverable and accessible | | 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 () | | Hard-deletion |Complete, irreversible erasure of the data from all storage media so it cannot be recovered| From dc244c6b1757531616d8e565c728700594886085 Mon Sep 17 00:00:00 2001 From: Jacek Lebioda <32834948+jLebioda@users.noreply.github.com> Date: Wed, 21 Oct 2026 11:14:32 +0200 Subject: [PATCH 11/11] chore: updated glossary --- .../GDI-SOP0010_data-reception-procedure.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md index 66d02b72..8ae05184 100644 --- a/sops/node-specific/GDI-SOP0010_data-reception-procedure.md +++ b/sops/node-specific/GDI-SOP0010_data-reception-procedure.md @@ -40,6 +40,7 @@ Find GDI SOP common Glossary at the [**charter document**](https://github.com/Ge | ELSI | Ethical, Legal, and Social Issues | | FASTA | Fast-A, file format for raw data output from sequencing machines | | FASTQ | FASTA with Quality, file format for raw data output from sequencing machines | +| GDI | GDI European Genomic Data Infrastructure | | LNDS | Luxembourg National Data Service | | OK | All correct | | SAM | Sequence Alignment/Map text file used in bioinformatics | @@ -50,12 +51,12 @@ Find GDI SOP common Glossary at the [**charter document**](https://github.com/Ge | Term | Definition | |------------------|-----------------| +| Data inclusion | Systematic integration of data into structured and machine-readable datasets | +| Data preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | +| Data reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | +| Data submission | The process of registering, publishing, and making data assets discoverable and accessible | | Node Helpdesk | The support team is responsible for handling tickets related to data management issues associated with the node in the GDI Project. | | Ticket | Incoming issues from the GDI Virtual Helpdesk, are to be processed within the Node Helpdesk and, after that, returned to the Virtual Helpdesk | -| Data Inclusion | Systematic integration of data into structured and machine-readable datasets | -| Data Preparation | The process of structuring, annotating, and formatting data so that systems and users can discover, access and reuse it | -| Data Reception | The process where GDI node securely acquires, ingests, and validates data supplied by a data provider | -| Data Submission | The process of registering, publishing, and making data assets discoverable and accessible | ### 3. Roles and Responsibilities See qualifications and responsabilities of the roles at the [**Organisational Roles and Responsibilities**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_organisational-roles-and-responsibilities.md) document.