2 |
3 | # Establishing a Federated EGA Node
4 |
5 | Welcome to the GitHub repository that hosts onboarding materials for establishing a Federated EGA Node!
6 |
7 | ## What am I doing here?
8 |
9 | If you are reading this, you are probably looking for information on how to join the Federated EGA Network. Great! There is a lot of information here for you.
10 |
11 | ## How do I start?
12 |
13 | We suggest you explore these materials on the public website here: **https://ega-archive.github.io/FEGA-onboarding**
14 |
15 | These materials provide guidance for establishing a node in the Federated EGA Network. The materials are based on the knowledge and experiences of current nodes and their use cases. Your node's development might differ depending on your use cases and mandates from stakeholders. Please view these materials as suggestions and best practices - not hard requirements!
16 |
17 | ## Usage
18 |
19 | The content of the material is developed collaboratively in shared Google documents and Markdown. A templating system ([Jekyll](http://jekyllrb.com/)) is used to format the onboarding materials and generate a website (https://ega-archive.github.io/FEGA-onboarding). The theme used is [Read-the-docs](https://docs.readthedocs.io/en/stable/index.html) and Github Pages version by [jekyll-theme-rtd](https://github.com/carlosperate/jekyll-theme-rtd).
20 |
21 | If you want to build the website locally, please have a look at this tutorial (**TBD**).
22 |
23 | ## Acknowledgements
24 |
25 | We would like to thank all contributors, especially those mentioned in the [Contributors list](CONTRIBUTORS.yaml), the Federated EGA community for their support, and our funding partners.
26 |
27 | Please see our [contributing guide](CONTRIBUTING.md) for information on how to contribute to the generation and maintenance of these materials. Thank you in advance for your contributions!
28 |
29 | ## License
30 |
31 | 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/).
32 |
33 |
--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/bug_report.yaml:
--------------------------------------------------------------------------------
1 | name: Report a bug
2 | description: 🐛 Form to report bugs in the FEGA onboarding materials
3 | title: "[BUG]: "
4 | labels: ["bug"]
5 | body:
6 | - type: markdown
7 | attributes:
8 | value: |
9 | This form is a template for **reporting bugs in the FEGA onboarding materials** (e.g. wrong URLs, typos, broken formatting). For issues concerning Central EGA (e.g. download client, [ega-archive](https://ega-archive.org/) website) please contact ``helpdesk [at] ega-archive.org``.
10 | Thank you for your support to the Federated European Genome-phenome Archive (FEGA)!
11 | - type: input
12 | id: bug-title
13 | attributes:
14 | label: Bug summary
15 | description: Please provide a summary or title for the bug.
16 | placeholder: e.g. Typo in the maturity model documentation
17 | validations:
18 | required: true
19 | - type: textarea
20 | id: to-reproduce
21 | attributes:
22 | label: To reproduce
23 | description: Please explain in detail what led you to observe the bug to help us reproduce it while we try to fix it.
24 | placeholder: |
25 | e.g. Steps to reproduce:
26 | 1. Go to the maturity model documentation (https://ega-archive.github.io/FEGA-onboarding/topics/maturity-model/)
27 | 2. Observe a typo in the first paragraph of the ``Learn about the FEGA Maturity Model`` section
28 | validations:
29 | required: true
30 | - type: textarea
31 | id: observed-behaviour
32 | attributes:
33 | label: Observed behaviour
34 | description: Please explain the behaviour you observed and considered a bug. Include any error messages or warnings you observed.
35 | placeholder: e.g. The description says "Gobbernance"
36 | validations:
37 | required: true
38 | - type: textarea
39 | id: expected-behaviour
40 | attributes:
41 | label: Expected behaviour
42 | description: Please explain what you expected to happen if there was no bug.
43 | placeholder: e.g. The description says "Governance"
44 | validations:
45 | required: true
46 | - type: textarea
47 | id: additional-context
48 | attributes:
49 | label: Additional context
50 | description: Use this section to add any context, including error messages or screenshots (if applicable), that could aid in the fixing of the bug.
51 | validations:
52 | required: false
53 |
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/.gitignore:
--------------------------------------------------------------------------------
1 | ###########
2 | # Project #
3 | ###########
4 | .vscode/
5 | .vagrant/
6 | .sass-cache
7 | _site/
8 | _site_mkdocs/
9 |
10 | ###########
11 | # Node.js #
12 | ###########
13 | # Logs
14 | logs
15 | *.log
16 | npm-debug.log*
17 | yarn-debug.log*
18 | yarn-error.log*
19 | lerna-debug.log*
20 |
21 | # Diagnostic reports (https://nodejs.org/api/report.html)
22 | report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
23 |
24 | # Runtime data
25 | pids
26 | *.pid
27 | *.seed
28 | *.pid.lock
29 |
30 | # Directory for instrumented libs generated by jscoverage/JSCover
31 | lib-cov
32 |
33 | # Coverage directory used by tools like istanbul
34 | coverage
35 | *.lcov
36 |
37 | # nyc test coverage
38 | .nyc_output
39 |
40 | # Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
41 | .grunt
42 |
43 | # Bower dependency directory (https://bower.io/)
44 | bower_components
45 |
46 | # node-waf configuration
47 | .lock-wscript
48 |
49 | # Compiled binary addons (https://nodejs.org/api/addons.html)
50 | build/Release
51 |
52 | # Dependency directories
53 | node_modules/
54 | jspm_packages/
55 |
56 | # TypeScript v1 declaration files
57 | typings/
58 |
59 | # TypeScript cache
60 | *.tsbuildinfo
61 |
62 | # Optional npm cache directory
63 | .npm
64 |
65 | # Optional eslint cache
66 | .eslintcache
67 |
68 | # Optional REPL history
69 | .node_repl_history
70 |
71 | # Output of 'npm pack'
72 | *.tgz
73 |
74 | # Yarn Integrity file
75 | .yarn-integrity
76 |
77 | # dotenv environment variables file
78 | .env
79 | .env.test
80 |
81 | ########
82 | # Ruby #
83 | ########
84 | *.gem
85 | *.rbc
86 | /.config
87 | /coverage/
88 | /InstalledFiles
89 | /pkg/
90 | /spec/reports/
91 | /spec/examples.txt
92 | /test/tmp/
93 | /test/version_tmp/
94 | /tmp/
95 |
96 | ## Documentation cache and generated files:
97 | /.yardoc/
98 | /_yardoc/
99 | /doc/
100 | /rdoc/
101 |
102 | ## Environment normalization:
103 | /.bundle/
104 | /vendor/bundle
105 | /lib/bundler/man/
106 |
107 | # for a library or gem, you might want to ignore these files since the code is
108 | # intended to run in multiple environments; otherwise, check them in:
109 | Gemfile.lock
110 | .ruby-version
111 | .ruby-gemset
112 |
113 | # unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
114 | .rvmrc
115 |
116 | ######################
117 | # OS generated files #
118 | ######################
119 | # macoOS
120 | .DS_Store
121 | .DS_Store?
122 | .AppleDouble
123 | .LSOverride
124 | ._*
125 | .Spotlight-V100
126 | .Trashes
127 | Icon?
128 |
129 | # Windows
130 | Thumbs.db
131 | ehthumbs.db
132 | ehthumbs_vista.db
133 | *.stackdump
134 | [Dd]esktop.ini
135 | $RECYCLE.BIN/
136 | *.lnk
137 |
138 | # Linux
139 | *~
140 | .fuse_hidden*
141 | .directory
142 | .Trash-*
143 | .nfs*
144 |
--------------------------------------------------------------------------------
/CONTRIBUTORS.yaml:
--------------------------------------------------------------------------------
1 | # List of contributors
2 | #
3 | # tags: name, email, twitter, gitter, orcid, elixir_node
4 |
5 | # example entry
6 |
7 | # contributer-1:
8 | # name: Fake Name
9 | # email: fake.name@ebi.ac.uk
10 | # twitter: fakename
11 | # gitter: fakename
12 | # orcid: 0000-0000-0000-0000
13 | # elixir_node: xx
14 |
15 | # elixir_node cv: [be, ch, cz, de, dk, ee, embl, es, fi, fr, gr, hu, ie, is, it, lu, nl, no, pt, se, si, uk]
16 |
17 | ---
18 | # Please add yourself below in alphabetical order
19 |
20 | ahornos:
21 | name: Albert Hornos Vidal
22 | email: ahornos@bsc.es
23 | orcid: 0000-0002-7330-668X
24 | elixir_node: es
25 |
26 | ainajene:
27 | name: Aina Jené Cortada
28 | email: aina.jene@crg.eu
29 | orcid: 0000-0001-7721-7097
30 | elixir_node: es
31 |
32 | alex-dem:
33 | name: Alexandros Dimopoulos
34 | email: dimopoulos@fleming.gr
35 | orcid: 0000-0002-4602-2040
36 | elixir_node: gr
37 |
38 | amycurwin:
39 | name: Amy Curwin
40 | email: amy.curwin@crg.eu
41 | orcid: 0000-0003-1086-2483
42 | elixir_node: es
43 |
44 | biodataadmin:
45 | name: Jorge dos Santos Oliveira
46 | email: jorge.oliveira@tecnico.ulisboa.pt
47 | orcid: 0000-0001-6425-2176
48 | elixir_node: pt
49 |
50 | blankdots:
51 | name: Stefan Negru
52 | email: stefan.negru@csc.fi
53 | orcid: 0000-0002-6544-5022
54 | elixir_node: fi
55 |
56 | brane007:
57 | name: Brane Leskošek
58 | email: brane.leskosek@mf.uni-lj.si
59 | orcid: 0000-0001-5202-2349
60 | elixir_node: si
61 |
62 | d-salgado:
63 | name: David Salgado
64 | email: david.salgado@france-bioinformatique.fr
65 | orcid: 0000-0002-5905-3591
66 | elixir_node: fr
67 |
68 | ealloza:
69 | name: Eva Alloza Anguiano
70 | email: ealloza@bsc.es
71 | twitter: EvaAlloza
72 | orcid: 0000-0001-8385-9336
73 | elixir_node: es
74 |
75 | fracassandocasualmente:
76 | name: Miguel Conrado Santos
77 | email: miguel.conrado.santos@tecnico.ulisboa.pt
78 | elixir_node: pt
79 |
80 | jmenglund:
81 | name: Markus Englund
82 | email: markus.englund@nbis.se
83 | orcid: 0000-0003-1688-7112
84 | elixir_node: se
85 |
86 | lauportell:
87 | name: Laura Portell Silva
88 | email: laura.portell@bsc.es
89 | orcid: 0000-0003-0390-3208
90 | elixir_node: es
91 |
92 | lilachic:
93 | name: Liisa Lado-Villar
94 | email: liisa.lado-villar@csc.fi
95 | orcid:
96 | elixir_node: fi
97 |
98 | mfreeberg:
99 | name: Mallory Freeberg
100 | email: mfreeberg@ebi.ac.uk
101 | twitter: MalloryFreeberg
102 | gitter: malloryfreeberg
103 | orcid: 0000-0003-2949-3921
104 | elixir_node: embl
105 |
106 | m-casado:
107 | name: Marcos Casado Barbero
108 | email: mcasado@ebi.ac.uk
109 | orcid: 0000-0002-7747-6256
110 | elixir_node: embl
111 |
112 | silviabah:
113 | name: Silvia Bahena Hernandez
114 | email: sbahena@ebi.ac.uk
115 | orcid: 0000-0002-2734-0449
116 | elixir_node: embl
117 |
--------------------------------------------------------------------------------
/docs/topics/outreach-training/index.md:
--------------------------------------------------------------------------------
1 | ---
2 | excerpt: Outreach, communications, and training aspects of establishing a Federated EGA node
3 | layout: default
4 | title: Outreach and Training
5 | nav_order: 3
6 | has_children: false
7 | has_toc: false
8 | ---
9 | # Outreach and Training
10 |
11 | Welcome! If you are involved in outreach, communications, or training aspects of establishing a Federated EGA node, you are in the right place.
12 |
13 | **You might find this page useful if you are:**
14 | - a data steward
15 | - a support officer
16 | - an outreach or communications officer
17 | - coordinating, organising, or providing training
18 |
19 | **By exploring these materials, you will be able to:**
20 | - Interact with FEGA communication channels
21 | - Find FEGA outreach materials
22 | - Share news and updates related to FEGA and its nodes
23 |
24 | ## 1. Engage communication channels
25 |
26 | ### Internal channels
27 | - The 
42 |
67 | {{ content }}
68 |
69 | -
36 |
- 37 | {{ nav_item.title }} 38 | 39 |
{{ section }}
55 | {%- for nav_item in nav %} 56 | {%- assign path_array = nav_item.dir | split: "/" %} 57 | {%- assign page_section = path_array[1] %} 58 | {%- if page_section == section and nav_item.hide != true and nav_item.nav_exclude != true %} 59 | {%- if nav_item.url == page.url %} 60 | {%- include toc.html html=content sanitize=true h_max=4 item_class="toctree-l%level%" %} 61 | {%- if nav_item.url == page.url %} 62 | {%- assign previous_page = last_loop_page %} 63 | {%- assign set_next_page = true %} 64 | {%- endif %} 65 | {%- else %} 66 |-
67 |
- 68 | {{ nav_item.title }} 69 | 70 |
| # | 5 |Component | 6 |Portugal | 7 |
|---|---|---|
| 1 | 12 |URL | 13 |14 | |
| 2 | 17 |Credentials | 18 |19 | |
| 3 | 22 |FEGA Node Encryption key pair | 23 |24 | |
| 4 | 27 |FEGA Node MQ | 28 |29 | |
| 5 | 32 |Submitter Inbox | 33 |SFTP | 34 |
| 6 | 37 |Ingest Pipeline | 38 |39 | |
| 7 | 42 |Archive storage | 43 |44 | |
| 8 | 47 |Archive File Database | 48 |49 | |
| 9 | 52 |Backup Storage | 53 |S3 | 54 |
| 10 | 57 |Main Source Code Repository | 58 |59 | |
| 11 | 62 |Main Programming Language | 63 |Python | 64 |
| 12 | 67 |Deployment Method | 68 |Docker-Compose | 69 |
| 13 | 72 |Helpdesk Management System | 73 |74 | |
| 14 | 77 |Helpdesk Portal Technology | 78 |79 | |
| 15 | 82 |Monitoring Tool | 83 |84 | |
| 16 | 87 |Metadata Submission Method | 88 |Central EGA submitter Portal | 89 |
| 17 | 92 |Download Solution | 93 |SFTP | 94 |
| 18 | 97 |Data Access Tool | 98 |99 | |
| 19 | 102 |General Contact | 103 |Jorge Oliveira <cto@biodata.pt> | 104 |
| # | 5 |Component | 6 |Spain | 7 |
|---|---|---|
| 1 | 12 |URL | 13 |https://fega-test.bsc.es/docs/ | 14 |
| 2 | 17 |Credentials | 18 |19 | |
| 3 | 22 |FEGA Node Encryption key pair | 23 |24 | |
| 4 | 27 |FEGA Node MQ | 28 |29 | |
| 5 | 32 |Submitter Inbox | 33 |SFTP | 34 |
| 6 | 37 |Ingest Pipeline | 38 |39 | |
| 7 | 42 |Archive storage | 43 |GPFS | 44 |
| 8 | 47 |Archive File Database | 48 |49 | |
| 9 | 52 |Backup Storage | 53 |54 | |
| 10 | 57 |Main Source Code Repository | 58 |https://github.com/EGA-archive/LocalEGA | 59 |
| 11 | 62 |Main Programming Language | 63 |Python | 64 |
| 12 | 67 |Deployment Method | 68 |Docker-Compose | 69 |
| 13 | 72 |Helpdesk Management System | 73 |RT - request tracker | 74 |
| 14 | 77 |Helpdesk Portal Technology | 78 |79 | |
| 15 | 82 |Monitoring Tool | 83 |84 | |
| 16 | 87 |Metadata Submission Method | 88 |Central EGA submitter Portal | 89 |
| 17 | 92 |Download Solution | 93 |Nextcloud | 94 |
| 18 | 97 |Data Access Tool | 98 |99 | |
| 19 | 102 |General Contact | 103 |https://fega-test.bsc.es/docs/contact.html | 104 |
45 | 46 | Explore details of the indicators and levels of the FEGA Maturity Model on a dedicated website or on GitHub. 47 | 48 | ## 2. Evaluate against the FEGA Maturity Model 49 | 50 | Perform a self-assessment of your node against the FEGA Maturity Model. Use this link to **create a copy** of the Federated EGA Maturity Model Self-Evaluation Google spreadsheet which is private to you and whoever you share it with. This tool is meant to be an evolving evaluation of your node's progress in each of the FEGA Maturity Model domains and sub-domains. Additionally, it allows you to provide feedback on the model and tool if you choose to share it. 51 | 52 | Explore aggregated results of the first node self-assessments. 53 | 54 | Hear about first-hand experiences costing a FEGA node. 55 | 56 | Read about resource considerations for establishing and operating a federated human data node. 57 | 58 | ## 3. Explore related maturity models 59 | 60 | 1. Beyond One Million Genomes (B1MG) Maturity Level Model (MLM) and project website 61 | 1. ELIXIR Human Data Infrastructure Maturation Model 62 | 1. FAIRplus Dataset Maturity Model and project website 63 | 1. European 1+ Million Genomes Initiative (1+MG) 64 | 65 | ## 4. What's next? 66 | 67 | Coming soon! 68 | -------------------------------------------------------------------------------- /_layouts/base.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | {% if page and page.excerpt %} 9 | {% elsif page and page.path == "index.md" %}{% endif %} 10 | {% if site.site_author %}{% endif %} 11 | {% if page and page.canonical_url %}{% endif %} 12 | 13 | {% if config.site_favicon %} 14 | {% else %}{% endif %} 15 | 16 |
34 |
35 | {%- comment %} SIDE NAV, TOGGLES ON MOBILE {% endcomment %}
36 |
52 |
53 |
54 |
55 | {%- comment %} MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE {% endcomment %}
56 |
60 |
61 | {%- comment %} PAGE CONTENT {% endcomment %}
62 |
75 |
76 |
77 |
78 | {% include versions.html %}
79 |
80 |
81 |
82 |
83 |
84 |
85 |
91 |
92 |
93 |
94 |
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/docs/_layouts/base.html:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | {% if page and page.excerpt %}
9 | {% elsif page and page.path == "index.md" %}{% endif %}
10 | {% if site.site_author %}{% endif %}
11 | {% if page and page.canonical_url %}{% endif %}
12 |
13 | {% if config.site_favicon %}
14 | {% else %}{% endif %}
15 |
16 |
63 |
73 |
74 |
64 | {% include breadcrumbs.html %}
65 |
72 |
66 |
70 | {% include footer.html %}
71 |
34 |
35 | {%- comment %} SIDE NAV, TOGGLES ON MOBILE {% endcomment %}
36 |
52 |
53 |
54 |
55 | {%- comment %} MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE {% endcomment %}
56 |
60 |
61 | {%- comment %} PAGE CONTENT {% endcomment %}
62 |
75 |
76 |
77 |
78 | {% include versions.html %}
79 |
80 |
81 |
82 |
83 |
84 |
85 |
91 |
92 |
93 |
94 |
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/CONTRIBUTING.md:
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1 | # Contributing to this repository
2 |
3 | ## Table of Contents
4 | - [Introduction](#introduction)
5 | - [Requesting changes](#requesting-changes-to-fega-onboarding-materials)
6 | - [Example request for changes](#example-request-for-changes-to-fega-onboarding-materials)
7 | - [Proposing changes](#proposing-changes-to-fega-onboarding-materials)
8 | - [Reporting bugs](#reporting-bugs)
9 | - [Attribution](#attribution)
10 |
11 | ## Introduction
12 |
13 | This document describes how you can contribute to the development of onboarding materials for establishing a Federated European Genome-phenome Archive (FEGA) nodes by suggesting or requesting changes to the materials via GitHub (GH). The goal is for these materials to continue evolving over time while the Federated EGA Network is being established, making use of knowledge and expertise across the FEGA nodes. All contributions are welcome, and we aim to make contributing as easy as possible!
14 |
15 | **What is in this document?**
16 | - Guidelines for requesting changes to FEGA onboarding materials via GH issues
17 | - Guidelines for proposing changes to FEGA onboarding materials via GH pull requests
18 | - Guidelines for reporting bugs
19 |
20 | **Who should be reading this document?**
21 | - Anyone contributing to establishing a FEGA node in their local jurisdiction
22 | - Anyone interested in improving onboarding materials for establishing a FEGA node
23 |
24 | **What *isn't* in this document?**
25 | - Training materials for using FEGA services (e.g. data discovery, data submission, data access). (Coming soon!)
26 | - Onboarding materials for establishing a FEGA node. This information can be found [here](https://ega-archive.github.io/FEGA-onboarding/).
27 |
28 | ## Requesting changes to FEGA onboarding materials
29 |
30 | To request changes to FEGA onboarding materials, follow the steps below:
31 |
32 | 1. **Gather information** for the requested change. There are two main types of requests: (1) for updates to existing materials and (2) for addition of new materials. To request either type of change, the following pieces of information are required:
33 |
34 | 1. The website URL or GitHub repository path of the page where the requested update/new material is to be located
35 | 1. The requested update/new materials, including as much detail as possible
36 | 1. Why the update/new material is being requested, including what the added value is
37 |
38 | 1. **Submit a request** for the change. Anyone can request changes to the onboarding materials by creating a GH issue in this repository using this ["Request change" GH template](https://github.com/EGA-archive/FEGA-onboarding/issues/new/choose). Follow the template to include the information indicated in Step 1. Please add the "requested-change" label to the issue.
39 |
40 | 1. **Track progress** of the request. The request will be reviewed by members of the FEGA community. Clarification may be requested. A proposed change will be made (via a GH pull request) to address the request and will be reviewed by the FEGA community. Once the change is accepted, the pull request will be merged and the related issue will be closed.
41 |
42 | ## Example request for changes to FEGA onboarding materials
43 |
44 | Coming soon!
45 |
46 | ## Proposing changes to FEGA onboarding materials
47 |
48 | To propose changes to FEGA onboarding materials, follow the steps below:
49 |
50 | 1. **Create a fork** of this repo.
51 |
52 | 1. **Create a new branch** in your local fork for the change(s) you would like to propose. We suggest one type of change per branch.
53 |
54 | 1. **Make the changes** you would like to propose.
55 | 1. Coming soon! Guidance and templates for creating new content.
56 |
57 | 1. **Open a pull request** from your local branch to the main branch of this repo. Request reviewers and add labels to the PR.
58 | 1. Coming soon! Template for creating a PR.
59 |
60 | 1. **Track progress** of PR. Once the PR is accepted, a repo maintainer will merge it.
61 | 1. Coming soon! PR acceptance criteria.
62 |
63 | ## Reporting bugs
64 |
65 | Report any bugs by creating an issue using the ["Bug report" GH template](https://github.com/EGA-archive/FEGA-onboarding/issues/new/choose). Please add the "bug" label to the issue. Example bugs that can be reported include:
66 |
67 | - Dead or broken links
68 | - Typos or grammar mistakes
69 | - Missing images
70 |
71 | ## Attribution
72 |
73 | We would like to keep track of who has contributed to these onboarding materials, as we consider this a highly valuable contribution to the FEGA community. If you contribute, please add your name to the [CONTRIBUTORS.yaml](CONTRIBUTORS.yaml) file as part of a PR.
74 |
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/_includes/toc.html:
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1 | {% capture tocWorkspace %}
2 | {% comment %}
3 | Version 1.0.8
4 | https://github.com/allejo/jekyll-toc
5 |
6 | "...like all things liquid - where there's a will, and ~36 hours to spare, there's usually a/some way" ~jaybe
7 |
8 | Usage:
9 | {% include toc.html html=content sanitize=true class="inline_toc" id="my_toc" h_min=2 h_max=3 %}
10 |
11 | Parameters:
12 | * html (string) - the HTML of compiled markdown generated by kramdown in Jekyll
13 |
14 | Optional Parameters:
15 | * sanitize (bool) : false - when set to true, the headers will be stripped of any HTML in the TOC
16 | * class (string) : '' - a CSS class assigned to the TOC
17 | * id (string) : '' - an ID to assigned to the TOC
18 | * h_min (int) : 1 - the minimum TOC header level to use; any header lower than this value will be ignored
19 | * h_max (int) : 6 - the maximum TOC header level to use; any header greater than this value will be ignored
20 | * ordered (bool) : false - when set to true, an ordered list will be outputted instead of an unordered list
21 | * item_class (string) : '' - add custom class(es) for each list item; has support for '%level%' placeholder, which is the current heading level
22 | * baseurl (string) : '' - add a base url to the TOC links for when your TOC is on another page than the actual content
23 | * anchor_class (string) : '' - add custom class(es) for each anchor element
24 |
25 | Output:
26 | An ordered or unordered list representing the table of contents of a markdown block. This snippet will only
27 | generate the table of contents and will NOT output the markdown given to it
28 | {% endcomment %}
29 |
30 | {% capture my_toc %}{% endcapture %}
31 | {% assign orderedList = include.ordered | default: false %}
32 | {% assign minHeader = include.h_min | default: 1 %}
33 | {% assign maxHeader = include.h_max | default: 6 %}
34 | {% assign nodes = include.html | split: '
63 |
73 |
74 |
64 | {% include breadcrumbs.html %}
65 |
72 |
66 |
70 | {% include footer.html %}
71 |
67 | {{ content }}
68 |
69 | | # | 12 |Component | 13 |Description | 14 |Required | 15 |Link to | 16 |
|---|---|---|---|---|
| 1 | 21 |URL | 22 |Official website for documentation | 23 |- | 24 |25 | |
| 2 | 28 |Credentials | 29 |For connecting to Central EGA there are 2 types of credentials required: User API for identifying and validating in Submitter Inbox the cEGA accounts cEGA MQ credentials for connecting FEGA Node MQ |
30 | Y | 31 |32 | |
| 3 | 35 |FEGA Node Encryption key pair | 36 |A Crypt4GH key pair generated by the FEGA Node, and the public is shared with the Submitter so that files are sent encrypted for the FEGA Node | 37 |Y | 38 |39 | |
| 4 | 42 |FEGA Node MQ | 43 |RabbitMQ which is connected in shovel and federation mechanism with the cEGA MQ | 44 |Y | 45 |2 | 46 |
| 5 | 49 |Submitter Inbox | 50 |An Inbox solution for the Researcher to submit files to a specific Node (e.g. SFTP, REST API). The Inbox needs to be accessible by a Researcher via an URL. |
51 | Y | 52 |2, 3 | 53 |
| 6 | 56 |Ingest Pipeline | 57 |Means of interfacing with the cEGA so that the required messages are being sent at relevant steps of the submission process. https://localega.readthedocs.io/en/latest/amqp.html | 58 |Y | 59 |4, 7, 8, 9 | 60 |
| 7 | 63 |Archive storage | 64 |Storage solution for storing archived files. e.g. S3, POSIX etc. | 65 |Y | 66 |6 | 67 |
| 8 | 70 |Archive File Database | 71 |Means of storing information about the archived files and their AccessionIDs and dataset IDs mapping to AccessionIDs (file to dataset mapping). Note: other details can be stored in the database e.g. checksums, timestamps, headers of crypt4gh file etc. |
72 | Y | 73 |6 | 74 |
| 9 | 77 |Backup Storage | 78 |Storage solution for storing a backup of the archived files. e.g. S3, POSIX etc. Note: A file needs to be backed up in a different location than the Archive |
79 | Y | 80 |6 | 81 |
| 10 | 84 |Main Source Code Repository | 85 |Where the source code can be found | 86 |N | 87 |88 | |
| 11 | 91 |Main Programming Language | 92 |Main programming language for the technical stack pipeline | 93 |- | 94 |95 | |
| 12 | 98 |Deployment Method | 99 |Means which technology is used to put in production different components | 100 |- | 101 |102 | |
| 13 | 105 |Helpdesk Management System | 106 |Main tool for user/helpdesk communication | 107 |N | 108 |109 | |
| 14 | 112 |Helpdesk Portal Technology | 113 |Federated EGA node helpedesk will provide means of interacting with submitter, registering DPA, establisng DACs and monitoring submissions. | 114 |N | 115 |15 | 116 |
| 15 | 119 |Monitoring Tool | 120 |Means of providing an overview of the status of submissions. Good also for auditing purposes. |
121 | N | 122 |14 | 123 |
| 16 | 126 |Metadata Submission Method | 127 |Means how the researchers will send the metadata to Central EGA through a cEGA submitter portal, node portal or another solution | 128 |Y | 129 |130 | |
| 17 | 133 |Download Solution | 134 |Means for a Requester to access the data once approval has been granted. | 135 |Y | 136 |7, 8, 18 | 137 |
| 18 | 140 |Data Access Tool | 141 |Means of enabling Requesters to Download the archived data. tool for facilitating DACs |
142 | N | 143 |144 | |
| 19 | 147 |General Contact | 148 |Email or website to contact the team deploying the solution | 149 |Y | 150 |151 | |
8 |
9 | # Establishing a Federated EGA Node
10 |
11 | Welcome to this collection of onboarding materials for establishing a Federated EGA Node!
12 |
13 | ## What am I doing here?
14 |
15 | If you are reading this, you are probably looking for information on how to join the Federated EGA. Great! There is a lot of information here for you.
16 |
17 | These materials provide guidance for establishing a node within the Federated EGA. The materials are based on the knowledge and experiences of current nodes and their use cases. Your node's development might differ depending on your use cases and mandates from stakeholders. Please view these materials as suggestions and best practices - not hard requirements!
18 |
19 | ## What is Federated EGA (FEGA)?
20 |
21 | **The Federated EGA is an ecosystem or network of Federated EGA Nodes. FEGA Nodes constitute the primary global resource for discovery and access of sensitive human omics and associated data, consented for secondary use, through a network of national human data repositories to accelerate disease research and improve human health.**
22 |
23 | Over the last 10 years, most individual-level human omics data have been generated in the context of research consortia and shared via global repositories such as the European Genome-phenome Archive (EGA). Many countries now have emerging personalized medicine programmes which are generating data from national or regional initiatives. Thus, human genomics is undergoing a step change from being a research-driven activity to one funded through healthcare initiatives.
24 |
25 | Genetic data generated in a healthcare context is subject to more stringent information governance than research data and often must comply with national legislation. To address this need, the Federated EGA provides a network of connected resources to enable transnational discovery of and access to human data for research while also respecting jurisdictional data protection regulations. By providing a solution to emerging challenges around secure and efficient management of human omics and associated data, the Federated EGA fosters data reuse, enables reproducibility, and accelerates biomedical research.
26 |
27 | Summary of responsibilities of Central EGA nodes (EMBL-EBI & CRG) and Federated EGA nodes (national/local jurisdictions):
28 |
29 | | Central EGA Node | Federated EGA Node |
30 | | ---------------- | ------------------ |
31 | | Hosts data | Hosts and/or owns data |
32 | | Shares metadata and provides global discovery | Shares metadata to enable global discovery |
33 | | Accepts data from all around the world | Accepts 3rd party data from jurisdiction |
34 | | Has Helpdesk for Central EGA data | Has Helpdesk responsible for own data/jurisdiction |
35 | | Chairs the Federated EGA Committees | Participates actively in the Federated EGA Committees |
36 | | No time commitment for FEGA | Expected to stay in FEGA for at least 4 years |
37 |
38 |
39 | 40 | 41 | 42 | ## What are the benefits of joining Federated EGA? 43 | 44 | * **Globally Accepted Standards**. Federated EGA develops and follows interoperable global standards for human data access accepted by the Global Alliance for Genomics & Health (GA4GH). This commitment makes the whole service trustworthy for the most demanding data submitters, often concerned with data security and privacy. 45 | * **Built with FAIR in mind**. Federated EGA is deeply commited to the FAIR principles. By abbiding to FAIR you ensure that your data has the necessary Findability, Accessibility, Interoperability, and Reuseability to meet requirements of funders. 46 | * **Enhanced Discoverability**. Your (meta)data will be available in a global catalog, maximizing its discoverability. 47 | * **Aligned with most relevant data initiatives**. Many health data related projects are now under way, in particular the Genomic Data Infrastructure (GDI) and the European Health Data Space (EHDS). These projects use FEGA like architectures for data storage and distribution, once again proving the quality of this design. 48 | * **Network of Experts**. By joining Federated EGA, you will be part of a network of experts, making sure to stay up to date with the State-of-Art on Data Sharing. 49 | 50 | ## How do I start? 51 | 52 | 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! 53 | 54 | 1. **Join the ELIXIR FHD Mailing List** (select "Human Data") to hear about the latest updates and events from the FHD community. You will need to log-in into the ELIXIR intranet. 55 | 1. **Attend the ELIXIR FHD Community Calls** to engage with the FEGA community. Meetings are the 1st Tuesday of the month @ 2pm CET/CEST. 56 | 57 | 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): 58 | 59 | * **[Governance and legal aspects](topics/governance-legal/)** of establishing a Federated EGA Node. Typically most useful for data protection officers, data stewards, policy makers, and strategic decision makers. 60 | 61 | * **[Technical and operational aspects](topics/technical-operational/)** of establishing a Federated EGA Node. Typically most useful for data protection officers, data stewards, policy makers, and strategic decision makers. 62 | 63 | * **[Data and metadata management](topics/data-metadata-management/)** for establishing a Federated EGA Node. Typically most useful for bioinformaticians, data stewards, and support officers. 64 | 65 | * **[Outreach and training aspects](topics/outreach-training/)** of establishing a Federated EGA Node. Typically most useful for data stewards, support officers, outreach/communications officers, and training organisers. 66 | 67 | ## What does the journey look like? 68 | 69 | Displayed below are the steps a node must take to become a full member of the Federated EGA. Based on current experiences, governance and legal development of a node (red, top-right path) usually happens in parallel with technical and operational development (yellow, bottom left path). Development converges when a node is ready to present to the Federated EGA Strategic Committee and sign the Federated EGA Legal (Collaboration) Agreement. You may find that your node's path differs slightly for a variety of reasons - that's ok! 70 | 71 |
72 |
73 | 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.
74 |
75 | 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/).
76 |
77 | 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.
78 |
79 | ## Acknowledgements
80 |
81 | 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.
82 |
83 | 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!
84 |
85 | ## License
86 |
87 | The content of the FEGA onboarding materials and website are licensed under the Creative Commons Attribution Share Alike 4.0 International License.
88 |
89 |
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/docs/topics/data-metadata-management/index.md:
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1 | ---
2 | excerpt: Best practices for data security, data access management, (meta)data standards, and data flow
3 | layout: default
4 | title: Data and Metadata Management
5 | nav_order: 3
6 | has_children: false
7 | has_toc: false
8 | ---
9 | # Data and Metadata Management
10 |
11 | Welcome! If you are involved in data or metadata standards aspects of establishing a Federated EGA node, you are in the right place. The information here covers topics related - but not limited - to best practices for data security, data access management, (meta)data standards, and data flow.
12 |
13 | **You might find this page useful if you are:**
14 | - a bioinformatician
15 | - a data steward
16 | - a data protection officer
17 | - a support officer
18 |
19 | **By exploring these materials, you will be able to:**
20 | - Define data security and access management best practices
21 | - Understand the EGA metadata standard and it's minimal requirements
22 | - Identify data models specific to a domain (*e.g.* COVID-19) and apply them when needed
23 | - Comprehend the (meta)data flow within the Federated EGA Network
24 |
25 | ## 1. Learn about data security best practices
26 |
27 | 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.
28 |
29 | Summary of best practices recommended for Federated EGA nodes:
30 |
31 | | Item | Description | Examples/Templates |
32 | |:---|:---|:---|
33 | | 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! |
34 | | 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! |
35 |
36 | 37 | 38 | ## 2. Explore implemented standards 39 | 40 | Central EGA largely adhere to GA4GH standards. Specific standards already implemented are summarised below: 41 | 42 | | Standard | Purpose | Specification Version | Supported Version | Implementation | Publication/Preprint | 43 | |:---|:---|:---|:---|:---|:---| 44 | | Beacon | Supports discovery of genomic variants and individuals. | v1.0.1 | v0.3 | Specification, Documentation, Endpoint | N/A | 45 | | 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 | 46 | | 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 | 47 | | 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 | 48 | | refget | Enables access to reference sequences using an identifier derived from the sequence itself. | v1.2.6 | N/A | Specification, Documentation, Endpoint | DOI | 49 | | 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 | 50 | 51 |
52 | 53 | ### Data file standards 54 | 55 | Recommended file formats for: 56 | - Sequencing data (unaligned or aligned reads): CRAM, BAM 57 | - Variant data: VCF 58 | - Phenotype/clinical data: Phenopackets 59 | 60 | ### Metadata standards 61 | 62 | The following resources represent EGA and community guidelines for submitted metadata: 63 | - EGA metadata model 64 | - Recommended ontologies to search for concepts and terms at the **Ontology Look-up Service** (OLS): 65 | - **Experimental Factor Ontology** (EFO): ontology record at OLS; EFO GitHub repository. 66 | - **Data Use Conditions** (DUO): ontology record at OLS; DUO GitHub repository. 67 | - Community-specific standards: 68 | - COVID-19 metadata mapping model across COVID-19 studies in Federated EGA (ELIXIR-CONVERGE) 69 | - COVID-19 Host Genetics Initiative data dictionary 70 | 71 | ### Quality control 72 | 73 | Coming soon! 74 | 75 | ## 3. Understand data definitions and flow 76 | 77 | As defined in the Federated EGA Collaboration Agreement, and in alignment with definitions outlined in the GDPR, the following data definitions are used in the context of Federated EGA: 78 | 79 | - **Administrative Data**. Data which are generated through the operation of Federated EGA. This may include personal data according to Art. 4 Nr. 1 GDPR which is directly identifying, such as names and email addresses which are used to communicate with, and support, service users. It may also include personal data and business data which are used internally by staff working on behalf of EGA Central or Federated EGA Nodes and exchanged between them. 80 | - **Non-personal Metadata**. Information that describes or annotates research data to facilitate its interpretation or to describe the relationship between data elements that cannot be used to identify a data subject. For example, the name of the instrument used to generate the data. Non-personal metadata generated or processed by the Node will be shared with EGA Central for inclusion in a searchable, online, public metadata catalogue. 81 | - **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. 82 | - **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. 83 | 84 | Here you can view how the different types of data flow within the Federated EGA network. 85 | 86 | ## 4. What's next? 87 | 88 | Coming soon! 89 | -------------------------------------------------------------------------------- /docs/topics/governance-legal/index.md: -------------------------------------------------------------------------------- 1 | --- 2 | excerpt: Federated EGA node governance, strategic planning, sustainability, and legal 3 | layout: default 4 | title: Governance and Legal 5 | nav_order: 5 6 | has_children: false 7 | has_toc: false 8 | --- 9 | # Governance and Legal 10 | 11 | Welcome! If you are involved in governance or legal aspects of establishing a Federated EGA node, you are in the right place. The information here covers topics related - but not limited - to Federated EGA node governance, strategic planning, sustainability, and legal. 12 | 13 | **You might find this page useful if you are:** 14 | - a team or node lead 15 | - a grant writer 16 | - a project manager or coordinator 17 | - a lawyer or legal expert 18 | - a data protection officer (DPO) 19 | 20 | **By exploring these materials, you will be able to:** 21 | - Understand the aims of the Federated EGA 22 | - Understand the role of Committees and Working Groups within the Federated EGA 23 | - Evaluate the roles and responsibilities of your node within the Federated EGA 24 | - Make use of examples and templates to define your node's governance and legal policies 25 | 26 | ## 1. Understand governance structure 27 | 28 | ### Vision 29 | 30 | **The Federated EGA is the primary global resource for discovery and access of sensitive human omics and associated data consented for secondary use, through a network of national human data repositories to accelerate disease research and improve human health.** 31 | 32 | Over the last 10 years, most individual-level human omics data have been generated in the context of research consortia and shared via global repositories such as the European Genome-phenome Archive (EGA). Many countries now have emerging personalized medicine programmes which are generating data from national or regional initiatives. Thus, human genomics is undergoing a step change from being a research-driven activity to one funded through healthcare initiatives. 33 | 34 | Genetic data generated in a healthcare context is subject to more stringent information governance than research data and often must comply with national legislation. To address this need, the Federated EGA provides a network of connected resources to enable transnational discovery of and access to human data for research while also respecting jurisdictional data protection regulations. By providing a solution to emerging challenges around secure and efficient management of human omics and associated data, the Federated EGA fosters data reuse, enables reproducibility, and accelerates biomedical research. 35 | 36 | ### Use cases 37 | 38 | 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. 39 | 40 | ### Organisation 41 | 42 | 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. 43 | 44 | Federated EGA is governed by two permanent committees: 45 | - 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. 46 | - 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. 47 | 48 | Additional **Federated EGA Working Groups** are established, as needed. Working groups can be initiated from either of the Committee. 49 | 50 |
51 |
52 | ## 2. Implement legal frameworks
53 |
54 | ### FEGA Collaboration Agreement
55 |
56 | Inclusion in the Federated EGA is codified by signing of the **Federated EGA Collaboration Agreement** (CA) between Central EGA (represented by the European Molecular Biology Laboratory and Fundació Centre De Regulació Genòmica) and the Federated EGA node. Nodes are welcome to make a copy of this current version of the CA to start its review with their legal teams and understand the responsibilities of joining FEGA. Nevertheless, this version (the one with a watermark) shall not be signed: the official version needs to be obtained from FEGA prior signing through its official channels.
57 |
58 | ### Data Processing Agreement (DPA)
59 |
60 | 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.
61 |
62 | ### Data Protection and Impact Analysis (DPIA)
63 |
64 | Coming soon!
65 |
66 | ### Node Operations Guidelines
67 |
68 | 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.
69 |
70 | ## 3. Complete steps to join Federated EGA
71 |
72 | The pathway to becoming a Federated EGA node includes governance/legal steps (red, top-right path) that must be completed:
73 |
74 | 
75 |
76 | * **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.
77 | * **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:
78 | * Canada
79 | * Germany
80 | * Norway
81 | * Portugal
82 | * Romania
83 | * Slovenia
84 | * Switzerland
85 | * Sweden
86 | * **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).
87 | * **Sign FEGA Legal Agreement**. Also called the "FEGA Collaboration Agreement", this is the final step to official join the Federated EGA.
88 |
89 | ## 4. Explore additional resources
90 |
91 | - More about EU GDPR
92 | - Training materials developed by ELIXIR-Luxembourg on data protection in biomedical research
93 |
94 | ## 5. What's next?
95 |
96 | Coming soon!
97 |
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216 |
217 | {% include_relative countries_tech_stack/component_description.html %}
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222 |
223 | {% include_relative countries_tech_stack/finland_tech_stack.html %}
224 |
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227 |
228 | {% include_relative countries_tech_stack/norway_tech_stack.html %}
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232 |
233 | {% include_relative countries_tech_stack/sweden_tech_stack.html %}
234 |
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237 |
238 | {% include_relative countries_tech_stack/germany_tech_stack.html %}
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242 |
243 | {% include_relative countries_tech_stack/spain_tech_stack.html %}
244 |
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247 |
248 | {% include_relative countries_tech_stack/portugal_tech_stack.html %}
249 |
250 |