diff --git a/docs/index.md b/docs/index.md index a072d2b..fe8707b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -39,10 +39,10 @@ Summary of responsibilities of Central EGA nodes (EMBL-EBI & CRG) and Federated ## How do I start? -The [ELIXIR Federated Human Data (FHD) Community](https://elixir-europe.org/communities/human-data) provides a framework for the secure submission, archival, dissemination, and analysis of sensitive human data across Europe, and wider. All Federated EGA communications are currently sent through the ELIXIR FHD open channels. Welcome to join us! +The ELIXIR Federated Human Data (FHD) Community provides a framework for the secure submission, archival, dissemination, and analysis of sensitive human data across Europe, and wider. All Federated EGA communications are currently sent through the ELIXIR FHD open channels. Welcome to join us! -1. **Join the [ELIXIR FHD Mailing List](https://elixir-europe.org/intranet/join-groups)** (select "Human Data") to hear about the latest updates and events from the FHD community. -1. **Attend the [ELIXIR FHD Community Calls](https://docs.google.com/document/d/10OwVvHbJ7i1gI1Iw4zmVsOs8kDrG077Y52juehiFcmU/edit)** to engage with the FEGA community. Meetings are the 1st Tuesday of the month @ 2pm CEST. +1. **Join the ELIXIR FHD Mailing List** (select "Human Data") to hear about the latest updates and events from the FHD community. +1. **Attend the ELIXIR FHD Community Calls** to engage with the FEGA community. Meetings are the 1st Tuesday of the month @ 2pm CEST. Now that you are connected to the Federated Human Data community, you can learn more about Federated EGA specifically. **Read about the areas that interest you the most** (in no particular order): @@ -62,17 +62,17 @@ Displayed below are the steps a node must take to become a full member of the Fe The materials on this website guide you through onboarding information from the experiences of other nodes. Explore the topics using the navigation panel on the left. Take what you find useful to apply to your own node development. -You can also use the [Federated EGA Maturity Model](https://inab.github.io/fega-mm/) to plan and drive your own node's development. The Maturity Model is divided into different domains, sub-domains, and maturity indicators which closely align with the topics outlined in these materials. [**Here**](https://ega-archive.github.io/FEGA-onboarding/topics/maturity-model/) you can read more about the FEGA Maturity Model. +You can use the Federated EGA Maturity Model to plan and drive your own node's development. The Maturity Model is divided into different domains, sub-domains, and maturity indicators which closely align with the topics outlined in these materials. You can [read more about how to interpret and use the FEGA Maturity Model](topics/maturity-model/). There is no time limit on establishing a Federated EGA Node. Onboarding will take more or less time depending on existing infrastructure and governance models, availability of funding and resources, user needs, and other factors. ## Acknowledgements -We would like to thank all contributors, especially those mentioned in the [Contributors list](https://github.com/EGA-archive/FEGA-onboarding/blob/main/CONTRIBUTORS.yaml), the Federated EGA community for their support, and our funding partners. +We would like to thank all contributors, especially those mentioned in the Contributors list, the Federated EGA community for their support, and our funding partners. -Please see our [contributing guide](https://github.com/EGA-archive/FEGA-onboarding/blob/main/CONTRIBUTING.md) for information on how to contribute to the generation and maintenance of these materials. Thank you in advance for your contributions! +Please see our contributing guide for information on how to contribute to the generation and maintenance of these materials. Thank you in advance for your contributions! ## License -The content of the FEGA onboarding materials and website are licensed under the [Creative Commons Attribution Share Alike 4.0 International License](https://creativecommons.org/licenses/by-sa/4.0/). +The content of the FEGA onboarding materials and website are licensed under the Creative Commons Attribution Share Alike 4.0 International License. diff --git a/docs/topics/data-metadata-management/index.md b/docs/topics/data-metadata-management/index.md index 35b0635..0469de6 100644 --- a/docs/topics/data-metadata-management/index.md +++ b/docs/topics/data-metadata-management/index.md @@ -19,52 +19,54 @@ Welcome! If you are involved in data or metadata standards aspects of establishi **By exploring these materials, you will be able to:** - Define data security and access management best practices - Understand the EGA metadata standard and it's minimal requirements -- Identify data models specific to a domain (e.g. COVID-19) and apply them when needed +- Identify data models specific to a domain (*e.g.* COVID-19) and apply them when needed - Comprehend the (meta)data flow within the Federated EGA Network ## 1. Learn about data security best practices -Central EGA has a [Security Strategy](https://ega-archive.org/files/European_Genome_phenome_Archive_Security_Overview.pdf) which defines best practices in ensuring data are stored securely. The EGA has helped develop the recommendations outlined the [GA4GH Security Technology Infrastructure document](https://www.ga4gh.org/docs/ga4ghtoolkit/data-security/2016May10_REV_SecInfrastructure.pdf), which defines guidelines, best practices, and standards for building and operating an infrastructure that promotes responsible data sharing in accordance with the [GA4GH Privacy and Security Policy](https://www.ga4gh.org/docs/ga4ghtoolkit/data-security/Privacy-and-Security-Policy.pdf). +Central EGA has a Security Strategy which defines best practices in ensuring data are stored securely. The EGA has helped develop the recommendations outlined the GA4GH Security Technology Infrastructure document, which defines guidelines, best practices, and standards for building and operating an infrastructure that promotes responsible data sharing in accordance with the GA4GH Privacy and Security Policy. Summary of best practices recommended for Federated EGA nodes: | Item | Description | Examples/Templates | |:---|:---|:---| -| Breach response protocol | A protocol for addressing potential security breaches, including consideration of other FEGA nodes, CEGA, key contacts, and institutional/organisational policies. | TBD | -| Risk register | A risk management tool used to track identified risks including information such as the nature of the risk, reference and owner, and mitigation measures. | TBD | +| Breach response protocol | A protocol for addressing potential security breaches, including consideration of other FEGA nodes, Central EGA, key contacts, and institutional/organisational policies. | Coming soon! | +| Risk register | A risk management tool used to track identified risks including information such as the nature of the risk, reference and owner, and mitigation measures. | Coming soon! |

## 2. Explore implemented standards -Central EGA largely adhere to [GA4GH standards](https://ega-archive.org/ga4gh). Specific standards already implemented are summarised below: +Central EGA largely adhere to GA4GH standards. Specific standards already implemented are summarised below: | Standard | Purpose | Specification Version | Supported Version | Implementation | Publication/Preprint | |:---|:---|:---|:---|:---|:---| -| Beacon | Supports discovery of genomic variants, individuals, and individuals | v1.0.1 | v0.3 | [Specification](https://github.com/ga4gh-beacon/specification-v2), [Documentation](https://ega-archive.org/beacon/#/), [Endpoint](https://ega-archive.org/beacon-api/) | N/A | -| Crypt4GH | Enables direct byte-level compatible random access to encrypted genetic data stored in community standards (e.g. CRAM, VCF) | v1.0 | v1.0 | [Specification](http://samtools.github.io/hts-specs/crypt4gh.pdf), [Documentation](https://github.com/EGA-archive/crypt4gh), [Endpoints](https://ega-archive.org/federated#) | [DOI](https://doi.org/10.1093/bioinformatics/btab087) | -| Data Use Ontology (DUO) | Allows users to semantically tag datasets with usage restrictions so datasets can be automatically discoverable based on a researcher's authorization level or intended use. | 2021-02-23 | 2021-02-23 | [Specification](https://github.com/EBISPOT/DUO), [Documentation](https://ega-archive.org/data-use-conditions), [Endpoint](https://www.ebi.ac.uk/ols/api/ontologies) | [DOI](https://doi.org/10.1016/j.xgen.2021.100028) | -| htsget | Enables secure, efficient, and reliable access to sequencing read and variation data. | v1.3.0 | v1.0.0 | [Specification](http://samtools.github.io/hts-specs/htsget.html), [Documentation](https://github.com/EGA-archive/ega-download-client), [Endpoint](https://ega.ebi.ac.uk:8052/elixir/tickets/tickets) | [DOI](https://doi.org/10.1093/bioinformatics/bty492)| -| refget | Enables access to reference sequences using an identifier derived from the sequence itself. | v1.2.6 | N/A | [Specification](http://samtools.github.io/hts-specs/refget.html), Documentation, Endpoint | [DOI](https://doi.org/10.1093/bioinformatics/btab524) | -| Researcher IDs (passport, visa) | Specifies the collection of researchers that may access a dataset at any given time, and the credentials they must supply. | v1.0.1 | v1.0.1 | [Specification](https://github.com/ga4gh-duri/ga4gh-duri.github.io/blob/master/researcher_ids/ga4gh_passport_v1.md), [Documentation](https://docs.google.com/document/d/1FTzUYAfV5d2a0zoDkbY9Iy_L5NbSAnHeWnmY2NIrY8M/edit), [Endpoint](https://ega.ebi.ac.uk:8443/ega-permissions/swagger-ui/index.html) | [DOI](https://doi.org/10.1016/j.xgen.2021.100030) | +| Beacon | Supports discovery of genomic variants and individuals. | v1.0.1 | v0.3 | Specification, Documentation, Endpoint | N/A | +| Crypt4GH | Enables direct byte-level compatible random access to encrypted genetic data stored in community standards (*e.g.* CRAM, VCF). | v1.0 | v1.0 | Specification, Documentation, Endpoint | DOI | +| Data Use Ontology (DUO) | Allows users to semantically tag datasets with usage restrictions so datasets can be automatically discoverable based on a researcher's authorization level or intended use. | 2021-02-23 | 2021-02-23 | Specification, Documentation, Endpoint | DOI | +| htsget | Enables secure, efficient, and reliable access to sequencing read and variation data including specific genomic regions. | v1.3.0 | v1.0.0 | Specification, Documentation, Endpoint | DOI | +| refget | Enables access to reference sequences using an identifier derived from the sequence itself. | v1.2.6 | N/A | Specification, Documentation, Endpoint | DOI | +| Researcher IDs (Passports and visas) | Specifies the collection of researchers that may access a dataset at any given time, and the credentials they must supply. | v1.0.1 | v1.0.1 | Specification, Documentation, Endpoint | DOI |

### Data file standards Recommended file formats for: -- Sequencing data (unaligned or aligned reads): [CRAM](http://samtools.github.io/hts-specs/CRAMv3.pdf), [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) -- Variant data: [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) -- Phenotype data: [Phenopackets](https://doi.org/10.1101/2021.11.27.21266944) +- Sequencing data (unaligned or aligned reads): CRAM, BAM +- Variant data: VCF +- Phenotype/clinical data: Phenopackets ### Metadata standards The following resources represent EGA and community guidelines for submitted metadata: -- [EGA metadata model](https://ega-archive.org/submission/sequence/programmatic_submissions/prepare_xml) -- Ontologies: [Experimental Factor Ontology](https://www.ebi.ac.uk/efo/), [Data Use Ontology](https://github.com/EBISPOT/DUO) +- EGA metadata model +- Ontologies: + - Experimental Factor Ontology + - Data Use Ontology - Community-specific standards: - - [COVID-19 metadata mapping model across COVID-19 studies in Federated EGA (ELIXIR-CONVERGE)](https://zenodo.org/record/4893222) - - [COVID-19 Host Genetics Initiative data dictionary](https://docs.google.com/spreadsheets/d/1RXrJIzHKkyB8qx5tHLQjcBioiDAOrQ3odAuqMS3pUUI/edit#gid=549383528) + - COVID-19 metadata mapping model across COVID-19 studies in Federated EGA (ELIXIR-CONVERGE) + - COVID-19 Host Genetics Initiative data dictionary ### Quality control @@ -79,7 +81,7 @@ As defined in the Federated EGA Collaboration Agreement, and in alignment with d - **Personal Metadata**. Information that describes or annotates research data to facilitate its interpretation or to describe the relationship between data elements that has the potential to identify a data subject. For example, demographic or ancestry information that can be used to identify individuals. Personal metadata are not made available through a public metadata catalogue and are not shared between EGA Central and the Node. - **Research Data**. Omics or other forms of genetic (according to Art. 4 Nr. 13 GDPR) and health data (according to Art. 4 Nr. 15 GDPR) that are used for scientific research purposes. This is considered to be special category personal data under Art. 9(1) in conjunction with Art. 4 Nr. 1 GDPR. -Here you can view how the different types of [data flow within the Federated EGA network](https://docs.google.com/presentation/d/1IrU5jPJpGQ7n-WH-7WvJZjjH03ww9LfFMLK1kTBeAco/edit#slide=id.gcf2c0c3039_0_126). +Here you can view how the different types of data flow within the Federated EGA network. ## 4. What's next? diff --git a/docs/topics/governance-legal/index.md b/docs/topics/governance-legal/index.md index f47d5ee..0662262 100644 --- a/docs/topics/governance-legal/index.md +++ b/docs/topics/governance-legal/index.md @@ -35,15 +35,15 @@ Genetic data generated in a healthcare context is subject to more stringent info ### Use cases -Understand more about the current [use cases and architecture for the Federated EGA](https://zenodo.org/record/4893063). Here you can read about the requirements and national use cases of early engaged Federated EGA Nodes which aim to be addressed by joining the Federated EGA. The report also describes how specific use cases can be supported by Federated EGA, for example by a governance structure made up of permanent committees and ad hoc working groups, the use of global and community standards, and guidelines for how data/metadata can be shared within the network. +Understand more about the current use cases and architecture for Federated EGA. Here you can read about the requirements and national use cases of early engaged Federated EGA Nodes which aim to be addressed by joining the Federated EGA. The report also describes how specific use cases can be supported by Federated EGA, for example by a governance structure made up of permanent committees and ad hoc working groups, the use of global and community standards, and guidelines for how data/metadata can be shared within the network. ### Organisation -Here is described the [Federated EGA Structure and Organization](https://ega-archive.org/files/EGA-Federation-Structure-v1.1.pdf). Federated EGA is broadly organised into two main types of nodes: Central EGA nodes (maintained by EMBL-EBI and CRG) and Federated EGA nodes (maintained at national or regional levels). Read the document linked above to learn more about the roles and responsibilities of each type of node. +Here is described the Federated EGA Structure and Organisation. Federated EGA is broadly organised into two main types of nodes: Central EGA nodes (maintained by EMBL-EBI and CRG) and Federated EGA nodes (maintained at national or regional levels). Read the document linked above to learn more about the roles and responsibilities of each type of node. Federated EGA is governed by two permanent committees: -- The **Federated EGA Strategic Committee** [(Terms of Reference)](https://ega-archive.org/files/ToR-Federated-EGA-Strategic-Committee-v1.1.pdf) provides direction and strategic planning for the Federated EGA. The Committee receives input from the Central EGA Strategic Committee and provides feedback for the EGA strategic roadmap. -- The **Federated EGA Operations Committee** [(Terms of Reference)](https://ega-archive.org/files/ToR-Federated-EGA-Operations-Committee-v1.1.pdf) reviews operational performance and coordinates technical implementation roadmaps of the Federated EGA. The Committee receives advice from and provides operational reporting to the Federated EGA Strategic Committee. +- The **Federated EGA Strategic Committee** (Terms of Reference) provides direction and strategic planning for the Federated EGA. The Committee receives input from the Central EGA Strategic Committee and provides feedback for the EGA strategic roadmap. +- The **Federated EGA Operations Committee** (Terms of Reference) reviews operational performance and coordinates technical implementation roadmaps of the Federated EGA. The Committee receives advice from and provides operational reporting to the Federated EGA Strategic Committee. Additional **Federated EGA Working Groups** are established, as needed. Working groups can be initiated from either of the Committee. @@ -53,11 +53,11 @@ Additional **Federated EGA Working Groups** are established, as needed. Working ### FEGA Collaboration Agreement -Inclusion in the Federated EGA is codified by signing of the [Federated EGA Collaboration Agreement](TBD) between Central EGA (represented by the European Molecular Biology Laboratory and Fundació Centre De Regulació Genòmica) and the Federated EGA node. +Inclusion in the Federated EGA is codified by signing of the **Federated EGA Collaboration Agreement** (link coming soon!) between Central EGA (represented by the European Molecular Biology Laboratory and Fundació Centre De Regulació Genòmica) and the Federated EGA node. ### Data Processing Agreement (DPA) -As Central EGA is a Data Processor under GDPR definitions, all data submitters are required to agree to and sign the [EGA Data Processing Agreement](https://ega-archive.org/files/EGA_Data_Processing_Agreement_v1.1.pdf). Federated EGA nodes also acting as Data Processors will require a similar agreement outline the roles and responsibilities of Data Processors, Data Controllers, and Data Requestors. +As Central EGA is a Data Processor under GDPR definitions, all data submitters are required to agree to and sign the EGA Data Processing Agreement. Federated EGA nodes also acting as Data Processors will require a similar agreement outline the roles and responsibilities of Data Processors, Data Controllers, and Data Requestors. ### Data Protection and Impact Analysis (DPIA) @@ -69,23 +69,23 @@ The pathway to becoming a Federated EGA node includes governance/legal steps (re Colored diagram with icons and descriptions of technical and governance steps an interested Federated EGA node needs to complete to join the Network. -* **Contact FEGA with intent to join**. This step can be accomplished by engaging in the ELIXIR FHD Community ("[How do I start?](https://ega-archive.github.io/FEGA-onboarding/#how-do-i-start)") or by contacting Mallory Freeberg or Amy Curwin. +* **Contact FEGA with intent to join**. This step can be accomplished by engaging in the ELIXIR FHD Community ("[How do I start?](../../#how-do-i-start)") or by contacting Mallory Freeberg or Amy Curwin. * **Present use cases to ELIXIR FHD Community; Complete FEGA Use Case Survey**. Nodes are encouraged to present at an ELIXIR FHD Community Call on topics related to: 1) national use cases for managing sensitive human omics, phenotype, and clinical data; 2) current challenges for managing sensitive human data; 3) solutions/initiatives planned or in progress to meet these challenges; and 4) how Federated EGA fits in to the node's overall goals. Some examples of previous presentations from nodes: - * [Canada](https://drive.google.com/file/d/1qZ4YqlKwCuerIcjSfijUGhvaVQy8iMWf/view?usp=sharing) - * [Germany](https://docs.google.com/presentation/d/1mpTQhBt69reQz3Viju3EWPSi50sdfFy6rBO__gyznK8/edit?usp=sharing) - * [Norway](https://drive.google.com/file/d/1Zl6KrKefo2bxV6czTmct7XJYMSX2PP7j/view?usp=sharing) - * [Portugal](https://docs.google.com/presentation/d/1GC65umfBmeNH2T6eFGlJwsPe4JajBKIpirAtkEXj2Fc/edit?invite=CLT52HQ#slide=id.p1) - * [Romania](https://docs.google.com/presentation/d/1f9OcWKrOeYbkk-zLjhsAR6A13gH1_Ao9hEimXWO49vc/edit?usp=sharing) - * [Slovenia](https://docs.google.com/presentation/d/10ykS6GO5P4VprVIPiE95ze00qLrjv6BwsvWFsPom_CA/edit?usp=sharing) - * [Switzerland](https://drive.google.com/file/d/1QPqO_4-5utYt6G761KdPSMT7uOzMllxn/view?usp=sharing) - * [Sweden](https://drive.google.com/file/d/1PzcC--fCTJ75sPVjOfemxwN2PkWisGIZ/view?usp=sharing) -* **Perform FEGA Maturity Model self-assessment**. This step can be accomplished by [evaluating your node against the Maturity Model](https://ega-archive.github.io/FEGA-onboarding/topics/maturity-model/#2-evaluate-against-the-fega-maturity-model). + * Canada + * Germany + * Norway + * Portugal + * Romania + * Slovenia + * Switzerland + * Sweden +* **Perform FEGA Maturity Model self-assessment**. This step can be accomplished by [evaluating your node against the Maturity Model](../maturity-model/#2-evaluate-against-the-fega-maturity-model). * **Sign FEGA Legal Agreement**. Also called the "FEGA Collaboration Agreement", this is the final step to official join the Federated EGA. ## 4. Explore additional resources -- More about [EU GDPR](https://gdpr-info.eu/). -- Training materials developed by ELIXIR-Luxembourg on [data protection in biomedical research](https://zenodo.org/record/5078280#.YrxoEOxKjjD) +- More about EU GDPR +- Training materials developed by ELIXIR-Luxembourg on data protection in biomedical research ## 5. What's next? diff --git a/docs/topics/maturity-model/index.md b/docs/topics/maturity-model/index.md index f5d7733..bb6d9ea 100644 --- a/docs/topics/maturity-model/index.md +++ b/docs/topics/maturity-model/index.md @@ -43,22 +43,24 @@ Each indicator outlines stages of maturity with a 5-level maturation scale:

-Explore details of the indicators and levels of the FEGA Maturity Model on a dedicated **[website](https://inab.github.io/fega-mm/)** or on **[GitHub](https://github.com/inab/fega-mm)**. +Explore details of the indicators and levels of the FEGA Maturity Model on a dedicated website or on GitHub. ## 2. Evaluate against the FEGA Maturity Model -Perform a self-assessment of your node against the Maturity Model (link TBD). +Perform a self-assessment of your node against the Maturity Model (link coming soon!). -Explore aggregated results of the [first node self-assessments](https://docs.google.com/presentation/d/1asFVR4a-luoh7jdQJcp3A2RP0-druX1LaXPk-r7FVsY/edit#slide=id.g121731fd043_2_86) (slides, 8 June 2022). +Explore aggregated results of the first node self-assessments. -Hear about first-hand experiences [costing a FEGA node](https://drive.google.com/file/d/1XjPH3sI69Hqcz7fXO1B_ThWYTayien8l/view?usp=sharing) (audio recording, 1 March 2022) and read about [resource considerations for establishing and operating a federated human data node](https://doi.org/10.7490/f1000research.1118967.1) (poster, 1 June 2022). +Hear about first-hand experiences costing a FEGA node. + +Read about resource considerations for establishing and operating a federated human data node. ## 3. Explore related maturity models -1. Beyond One Million Genomes (B1MG) [Maturity Level Model (MLM)](https://zenodo.org/record/6587561#.YtB4huzMLt0) and [project website](https://b1mg-project.eu/) -1. [ELIXIR Human Data Infrastructure Maturation Model](https://elixir-europe.github.io/human-data-maturity-model/) -1. FAIRplus [Dataset Maturity Model](https://fairplus.github.io/Data-Maturity/) and [project website](https://faircookbook.elixir-europe.org/content/recipes/maturity.html) -1. [European 1+ Million Genomes Initiative (1+MG)](https://digital-strategy.ec.europa.eu/en/policies/1-million-genomes#:~:text=The%20'1%2B%20Million%20Genomes',healthcare%20and%20health%20policy%20making.) +1. Beyond One Million Genomes (B1MG) Maturity Level Model (MLM) and project website +1. ELIXIR Human Data Infrastructure Maturation Model +1. FAIRplus Dataset Maturity Model and project website +1. European 1+ Million Genomes Initiative (1+MG) ## 4. What's next? diff --git a/docs/topics/outreach-training/index.md b/docs/topics/outreach-training/index.md index 789b94f..a280ac4 100644 --- a/docs/topics/outreach-training/index.md +++ b/docs/topics/outreach-training/index.md @@ -24,28 +24,28 @@ Welcome! If you are involved in outreach, communications, or training aspects of ## 1. Engage communication channels ### Internal channels -- The [ELIXIR Federated Human Data Community](https://elixir-europe.org/communities/human-data) is the entry-point for a Node interested in joining the FEGA Network: - - Join the ELIXIR Federated Human Data Community mailing list ([here](https://elixir-europe.org/intranet/join-groups), select "Human Data") - - Attend the ELIXIR Federated Human Data Community Calls ([agenda](https://docs.google.com/document/d/10OwVvHbJ7i1gI1Iw4zmVsOs8kDrG077Y52juehiFcmU/edit)) +- The ELIXIR Federated Human Data (FHD) Community is the main entry-point for a Node interested in joining the FEGA Network: + - Join the ELIXIR FHD Mailing List (select "Human Data") to hear about the latest updates and events from the FHD community. + - Attend the ELIXIR FHD Community Calls to engage with the FEGA community. - Federated EGA has mailing lists for various communications: - FEGA Strategic Committee mailing list (invitation-only): For discussing strategic planning and direction of FEGA - FEGA Operations Committee mailing list (invitation-only): For reviewing operational performance and coordinating technical roadmaps ### External channels -- Follow the [EGA Twitter account](https://twitter.com/EGAarchive) +- Follow the EGA Twitter account - Mention Federated EGA by using: - the hashtag #FederatedEGA - - a combination of hashatg and mention #Federated @EGAarchive + - a combination of hashtag and mention #Federated @EGAarchive ## 2. Incorporate communication materials -- FEGA logo (svg format) Federated EGA logo, colored logo of storage disk with human figure emerging from behind and the text Federated European Genome-phenome Archive on the right. +- FEGA logo (svg format) Federated EGA logo, colored logo of storage disk with human figure emerging from behind and the text Federated European Genome-phenome Archive on the right.

## 3. Follow news and updates -- ["Federated EGA Updates in 2022" (ELIXIR AHM 2022)](https://doi.org/10.7490/f1000research.1118988.1) (slides, 8 June 2022) -- ["Working together towards a Federated European Genome-phenome Archive for Publishing and re-using sensitive research data"](https://www.csc.fi/-/working-together-towards-a-federated-european-genome-phenome-archive) (blog post, 15 March 2022) -- ["Federated EGA: where are we now?" (ELIXIR AHM 2021)](https://doi.org/10.7490/f1000research.1119006.1) (slides, 11 June 2021) -- [FEGA page on EGA website](https://ega-archive.org/federated) +- "Federated EGA Updates in 2022" (ELIXIR AHM 2022) (8 June 2022) +- "Working together towards a Federated European Genome-phenome Archive for Publishing and re-using sensitive research data" (15 March 2022) +- "Federated EGA: where are we now?" (ELIXIR AHM 2021) (11 June 2021) +- FEGA page on EGA website ## 4. What's next? diff --git a/docs/topics/technical-operational/index.md b/docs/topics/technical-operational/index.md index 50e1524..9f71457 100644 --- a/docs/topics/technical-operational/index.md +++ b/docs/topics/technical-operational/index.md @@ -28,19 +28,19 @@ Welcome! If you are involved in technical or operational aspects of establishing ### Standards -- The [FEGA Node Operations Guidelines](https://ega-archive.org/files/EGA-Node-Operations-v2.pdf) document gives an overview of the operational areas which require resources in order to establish and operate a Federated EGA node. The document is based on more than 10 years experience of establishing and operating the EMBL-EBI and CRG Central EGA nodes. It provides a breakdown of the operational areas of responsibility into Helpdesk Services, Technical Operations, Software Development, and IT Infrastructure. -- Federated EGA was established on the principle of implementing global, community standards, including those developed as part of [GA4GH](https://www.ga4gh.org/) and [ELIXIR](https://elixir-europe.org/). -- [Overview of local EGA services and architecture](https://www.youtube.com/watch?v=k9R8W3V3ugU) (video, 19 June 2020) +- The FEGA Node Operations Guidelines document gives an overview of the operational areas which require resources in order to establish and operate a Federated EGA node. The document is based on more than 10 years experience of establishing and operating the EMBL-EBI and CRG Central EGA nodes. It provides a breakdown of the operational areas of responsibility into Helpdesk Services, Technical Operations, Software Development, and IT Infrastructure. +- Federated EGA was established on the principle of implementing global, community standards, including those developed as part of GA4GH and ELIXIR. +- Overview of local EGA services and architecture (19 June 2020) ### Software -A minimal Federated EGA node can be set up on your local infrastructure using the [localEGA software (GitHub repository)](https://github.com/EGA-archive/LocalEGA) and the associated [Readthedocs](https://localega.readthedocs.io/) webpages. It is not required to use the local EGA software suite, but it is a great option compared to developing your own Federated EGA node software from scratch. +A minimal Federated EGA node can be set up on your local infrastructure using the localEGA software (GitHub repository) and the associated Readthedocs webpages. It is not required to use the local EGA software suite, but it is a great option compared to developing your own Federated EGA node software from scratch. -More information about the local EGA software and its implementation can be found in this report for [ELIXIR-CONVERGE: Implementation and documentation to create an operational EGA node (D7.2)](https://zenodo.org/record/4893191) (report, 2 June 2021). +More information about the local EGA software and its implementation can be found in this report on implementation and documentation to create an operational EGA node (2 June 2021). ### Standard Operating Procedures (SOPs) -It is useful to establish SOPs for common node operational tasks to enable consistent service delivery and streamline internal processes. Use this **[template to develop SOPs for your own node](https://docs.google.com/document/d/1BWPL9I9PlWiea6k-vcDDwaMu3rM5FSdV_0n8u7hAQpg/edit?usp=sharing)**. +It is useful to establish SOPs for common node operational tasks to enable consistent service delivery and streamline internal processes. Use this template to develop SOPs for your own node. Standard interactions between Central EGA and Federated EGA node Helpdesk staff have been developed into a set of SOPs. Follow these SOPs below. @@ -48,47 +48,45 @@ Standard interactions between Central EGA and Federated EGA node Helpdesk staff The following SOPs must be followed as part of current FEGA ↔ CEGA node interactions during the submission process: -- [Federated EGA Request from submitter to submit to FEGA node](https://docs.google.com/document/d/1c5YfLqGjCmRlG0NF9lsuU6IWUrCq4u8Ug3Ye5xMrxtI/edit?usp=sharing) -- [Federated EGA Metadata Check and Release Protocol](https://docs.google.com/document/d/1v7l_ODdh-yxyhWl8Y8R3IZC2hEy5x8KgjBQmFyEyGgw/edit?usp=sharing) +- Federated EGA Request from submitter to submit to FEGA node +- Federated EGA Metadata Check and Release Protocol -[**Here**](topics/data-metadata-management/#3-understand-data-definitions-and-flow) you can find more information about data/metadata flow within the Federated EGA network. - -Central EGA Helpdesk have developed a set of SOPs to harmonise both user-facing processes and internal processes. Explore some examples of these SOPs below (and organised **[here](https://drive.google.com/drive/folders/14yFvXOxRyGl-ENogIB5TdogIUdL-gmfk?usp=sharing)**). Please note these are example SOPs and will need to be adapted to how your node operates! +Central EGA Helpdesk have developed a set of SOPs to harmonise both user-facing processes and internal processes. Explore some examples of these SOPs below or organised in this shared EGA Helpdesk SOP Google Drive. Please note these are example SOPs and will need to be adapted to how your node operates! #### Example User-facing Process SOPs -- [Handling Incomplete Submissions](https://docs.google.com/document/d/1gze9UW3yBN2TmFNFS3NFsHxPrdWNx-A74lFsxj8Xs_Q/edit?usp=sharing) -- [Handling Unresponsive DACs](https://docs.google.com/document/d/16_5G97hUUyU2-vjHAD-Yb7XNRCE6A_PQWRWERqnDSFY/edit?usp=sharing) -- [Users Sharing Credentials](https://docs.google.com/document/d/1NHNTmhfguAgCKyLuf1tQAdYWLAeCFBUeFYgONdd17bY/edit?usp=sharing) -- [Reporting Unreasonable Users](https://docs.google.com/document/d/1DC_HJaePbaDomNe-99fdAyZ1d4CodBfqU2uavCcpL3g/edit?usp=sharing) -- [Changing User Institution](https://docs.google.com/document/d/1geswkX9Com_Y4bnbLEtTKd0XXG6ByuADlCsLHppf074/edit?usp=sharing) +- Handling Incomplete Submissions +- Handling Unresponsive DACs +- Users Sharing Credentials +- Reporting Unreasonable Users +- Changing User Institution #### Example Internal Node Process SOPs -- [Helpdesk Ticket Management](https://docs.google.com/document/d/1qIURMTn6-cDv9ZxVsVkJSK5SUcK7Wq-jxbFuD_6gT34/edit?usp=sharing) -- [Helpdesk Ticket Assignment](https://docs.google.com/document/d/10GWK-iw12JF_JX0KL2aUTjsZ8G2liw2A-t_PV5Y81FY/edit?usp=sharing) +- Helpdesk Ticket Management +- Helpdesk Ticket Assignment ## 2. Learn from current node implementations Check-out current Federated EGA node implementations from some of the first established nodes: -- [Finnish FEGA Node](https://research.csc.fi/-/fega) -- [German Human Genome-phenome Archive (GHGA)](https://www.ghga.de/) -- [Federated EGA Norway](https://ega.elixir.no/) -- [Spanish FEGA (es-FEGA)](https://fega-test.bsc.es/docs/) -- [Swedish Sensitive Data Archive](https://nbis.se/infrastructure/sensitive-data-archive.html) +- Finnish FEGA Node +- German Human Genome-phenome Archive (GHGA) +- Federated EGA Norway +- Spanish FEGA (es-FEGA) +- Swedish Sensitive Data Archive Hear more details about node implementations: -- [Norway, Sweden, and Finland FEGA node architecture and implementation](https://www.youtube.com/watch?v=eEoKmMKGCc4) (video, 19 June 2020) -- [Further details on the Norwegian node](https://www.youtube.com/watch?v=DSd_UJyqoGU) (video, 19 June 2020) +- Norway, Sweden, and Finland FEGA node architecture and implementations (19 June 2020) +- Further details on the Norwegian node (19 June 2020) -Engage in FEGA discussions happening with existing and interested FEGA nodes within the ELIXIR Federated Human Data Community by joining the [ELIXIR Federated Human Data Community mailing list](https://elixir-europe.org/intranet/join-groups) (select "Human Data") and attending the [ELIXIR Federated Human Data Community Calls](https://docs.google.com/document/d/10OwVvHbJ7i1gI1Iw4zmVsOs8kDrG077Y52juehiFcmU/edit). +Engage in FEGA discussions happening with existing and interested FEGA nodes within the ELIXIR Federated Human Data (FHD) Community by joining the ELIXIR FHD Mailing List (select "Human Data") and attending the ELIXIR FHD Community Calls. ## 3. Evaluate your implementation -- Understand the domains in which a node matures using the [Federated EGA Maturity Model](https://ega-archive.github.io/FEGA-onboarding/topics/maturity-model/) -- Assess the technical and operational maturation of your node by doing a **self-assessment against the Federated EGA Maturity Model** (Coming soon!) -- Demonstrate the full set of node services for users by planning your [Federated EGA end-to-end demonstrator](https://docs.google.com/document/d/1m7WDC112e73Kw79baZcsRsQOkAAGKtp_AiqJRhrgtUk/edit?usp=sharing) -- Determine compliance of services with FEGA specifications by performing **compliance tests** (Coming soon!) -- Evaluate ability to scale services by performing **stress tests** (Coming soon!) +- Understand the domains in which a node matures using the [Federated EGA Maturity Model](../maturity-model/) +- Assess the technical and operational maturation of your node by doing a self-assessment against the Federated EGA Maturity Model (Coming soon!) +- Demonstrate the full set of node services for users by planning your Federated EGA end-to-end demonstrator +- Determine compliance of services with FEGA specifications by performing compliance tests (Coming soon!) +- Evaluate ability to scale services by performing stress tests (Coming soon!) ## 4. What's next? -Coming soon! \ No newline at end of file +Coming soon!