diff --git a/.github/workflows/mk-beacon-docs.yml b/.github/workflows/mk-beacon-docs.yml new file mode 100644 index 0000000..84feede --- /dev/null +++ b/.github/workflows/mk-beacon-docs.yml @@ -0,0 +1,19 @@ +name: mk-beacon-docs +on: + push: + branches: + - main +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + with: + python-version: 3.x + - run: pip install mkdocs-material + - run: pip install mkdocs-macros-plugin + - run: pip install mkdocs-mermaid2-plugin + - run: pip install pymdown-extensions + - run: pip install mdx_gh_links + - run: mkdocs gh-deploy --force diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..59311f2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +.DS_Store +site +*.lock diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..4bf6e2c --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2018 ELIXIR Beacon project + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README b/README deleted file mode 100644 index 653dd49..0000000 --- a/README +++ /dev/null @@ -1 +0,0 @@ -This is the placeholder for building the updated Beacon website. diff --git a/README.md b/README.md new file mode 100644 index 0000000..32213a5 --- /dev/null +++ b/README.md @@ -0,0 +1,16 @@ +# ELIXIR Beacon Project website + +The main information site for the ELIXIR Beacon Project - i.e. the formatted content of this repository - can be accessed as [Beacon website](http://genomebeacons.org/). Detailed information about the Beacon technology can be found in the [Beacon v2 code repository](http://github.com/ga4gh-beacon/beacon-v2/) and on the [API documentation site](http://docs.genomebeacons.org). + +For more information about the project you may also consult the corresponding [ELIXIR website](https://www.elixir-europe.org/about-us/implementation-studies/beacons). + +## Website Technology + +The website is built from this repository's Markdown files. After adding or editing a post in the `master` branch, the corresponding website is auto-updated using Github's actions and a mkdocs workflow. + +## Managing posts + +=> The easiest way to create a new post is to copy and modify an old one from the same category. <= + +New web pages are created by adding Markdown pages to the [docs](./docs] directory. + diff --git a/docs/CNAME b/docs/CNAME new file mode 100644 index 0000000..e879539 --- /dev/null +++ b/docs/CNAME @@ -0,0 +1 @@ +genomebeacons.org \ No newline at end of file diff --git a/docs/FAQ.md b/docs/FAQ.md new file mode 100644 index 0000000..6dc2048 --- /dev/null +++ b/docs/FAQ.md @@ -0,0 +1,39 @@ +# Frequently Asked Questions + +!!! Note "Citation" + + **Beacon v2 and Beacon Networks: a "lingua franca" for federated data discovery in biomedical genomics, and beyond.** + Jordi Rambla, Michael Baudis, Tim Beck, Lauren A. Fromont, Arcadi Navarro, Manuel Rueda, Gary Saunders, Babita Singh, J.Dylan Spalding, Juha Tornroos, Claudia Vasallo, Colin D.Veal, Anthony J.Brookes. _Human Mutation_ (2022) [DOI](https://doi.org/10.1002/humu.24369). + +??? faq "Is it `Beacon` or `beacon`?" + + The uppercase `Beacon` is used to label API, framework or protocol and their + components - while lower case `beacons` are instances of these, _i.e._ individual + resources using the protocol. + + ##### last change 2023-03-13 by Michael Baudis [:fontawesome-brands-github:](https://github.com/mbaudis) + + +??? faq "Security: What are the general security principles for Beacon?" + + An implementation of a Beacon must implement the Global Alliance for Genomics and Health ([GA4GH](https://www.ga4gh.org)) Beacon standard. The V2 standard has been approved by both the Regulatory and Ethics, and Data Security foundational workstreams. + + The Beacon uses a [3-tiered access model - anonymous, registered, and controlled access](http://docs.genomebeacons.org/security/): + + * A Beacon that supports anonymous access responds to queries irrespective of the source of the query. + * For a Beacon to respond to a query at the registered tier, the user must identify themselves to the Beacon, for example by using an ELIXIR identity. + * For a Beacon to respond to a controlled access query, the user must have applied for, and been granted access to, the Beacon (or data derived from one or more individuals within the Beacon) before sending the query. + + Note that a Beacon may contain datasets (or collections of individuals) whose data is only accessible at specified tiers within the Beacon. This tiered access model allows the owner or controller of a Beacon to determine which responses are returned to whom depending on the query and the user who is making the request, for example to ensure the response respects the consent under which the data were collected. The ELIXIR Beacon network supports Beacons which respond at different tiers, for example only Beacons which have a response to anonymous queries need respond to an anonymous request. + + As part of the ELIXIR 2019-21 Beacon Network Implementation Study deliverable [D3.3](https://docs.google.com/document/d/1q7XuUB-Z4A_DogWT1AVrvkp_qHWWtbbICxokHup_tts/edit) a document has been written to describe security best practice for users interested in deploying or running a Beacon or users who govern data hosted within a Beacon, and the requirements for adding the Beacon to the ELIXIR Beacon network. As the Beacon standard extends in V2 towards supporting phenotype and range queries, the tiered access model becomes more important to ensure the Beacon response is appropriate to the underlying data. + +??? faq "Security: How is security actually implemented when I deploy a Beacon?" + + Security attributes are part of the Beacon v2 [Framework](https://github.com/ga4gh-beacon/beacon-v2/tree/main/framework). The file [`beaconConfiguration.json`](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/json/configuration/beaconConfigurationSchema.json) defines the schema of the JSON file that includes core aspects of a Beacon instance configuration. Its third section, called **securityAttributes**, defines the security. + + Check out the **securityAttributes** section on the [Beacon Documentation website](http://docs.genomebeacons.org/framework/#the-beacon-configuration-file). + +??? faq "Security: How do I test a Beacon without having to go through complex security matters (yet)?" + + As a Beacon is designed to support data discoverability of controlled access datasets, it is recommended that synthetic or artificial data is used for testing and initial deployment of Beacon instances. The use of synthetic data for testing is important in that it ensures that the full functionality of a Beacon can be tested and / or demonstrated without risk of exposing data from individuals. In addition to testing or demonstrating a deployment, synthetic data should be used for development, for example adding new features. Additionally, these data can also be used to demonstrate the access levels and data governance procedures for loading data to a Beacon to build trust with data controllers or data access committees who may be considering loading data to a Beacon. An example dataset that contains chromosome specific vcf files is hosted at EGA under dataset accession EGAD00001006673. While this dataset requires a user to log in to get access, the EGA test user can access this dataset. \ No newline at end of file diff --git a/docs/css/theme_overrides.css b/docs/css/theme_overrides.css new file mode 100644 index 0000000..f41089f --- /dev/null +++ b/docs/css/theme_overrides.css @@ -0,0 +1,41 @@ +:root { + --md-accent-fg-color: #076d63; +} + +.md-grid { + max-width: 1200px; +} + +.md-header__source { + background-image: url("/img/elixir-white-48x36.png"); + background-repeat: no-repeat; + background-position: right; +} + +h2 { + color: var(--md-accent-fg-color); + border-top: var(--md-accent-fg-color) thin solid; + border-bottom: var(--md-accent-fg-color) thin solid; +} + +div.tabbed-set { + background-color: #fafafa; +} + +.tabbed-content { + padding: 5px; +} + +li li { + list-style-type: circle; +} + +li li li { + list-style-type: "–"; + font-size: 0.9em; +} + +.mermaid { + display: flex; + justify-content: center; +} diff --git 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b/docs/index.md @@ -0,0 +1,93 @@ +# GA4GH Beacon project + +This website provides some general information about the GA4GH Beacon protocol. + +!!! note "Technical Documentation" + + Please visit [docs.geneomebeacons.org](http://docs.genomebeacons.org) for technical and implementation details. + +## Why Beacon? + +![Beaconize hospitals](/img/Beaconizing_hospitals_Webpage.png) +###### A schematic representation of how Beacon works. (A) Beacon API implementation and (B) A Beacon query and aggregated response + +One of the main bottlenecks in human genomics research is lack of data. A Beacon is a genomics discovery tool which allows to aggregate worldwide genomics dataset through a shared query protocol. + +Genomics data _in principle_ may allow the re-dentification of individuals in genomics data repositories which leads to a generally high level of protective measure being applied to such data. However, with the right choice of data sharing protocols, data security infrastructure and good health data practices, the sharing and discovery of genomics and related data can be possible and enable valuable insights into disease related as well as prognostic and lifestyle related genomic variations. + +In order to promote personalised medicine, inclusive diagnostics, prognostic and therapeutic strategies, we cannot afford to keep the data completely "locked in". The Beacon API aims to solve this problem by enabling the search of genomic variants and associated information without jeopardising the privacy of the dataset. Any hospital or research entity can choose to 'beaconize' their omics dataset without compromising the privacy or the ownership of the dataset, thus helping the worldwide community of researchers and assisting science through the power of data. + +The Beacon Project is developed under a Global Alliance for Genomics and Health (GA4GH) Iniciative for the federated discovery of genomic data in biomedical research and clinical applications. + +## What is Beacon? + +The Beacon protocol defines the programming interface ("API") for implementing individual beacon resources. A beacon resource uses the Beacon API (usually extended with a [user interface](https://beacon-giab-test.ega-archive.org)) that allows for data discovery of genomic and phenoclinic data. + +Originally, the Beacon protocol (versions 0 and 1) was limited to information about the presence/absence of a given, specific, genomic mutation in a set of data, from patients of a given disease or the population in general (Figure 2). Examples can be found in the [ELIXIR Beacon network page](https://beacon-network.elixir-europe.org). + +![Beacon v1 principle](/img/Beacon-v1.png){: style="display: block; margin: auto; width: 500px"} +###### Schematic example of "classical" Beacon query (up to version 1) + +!!! Warn "Move to Beacon v2" + + With the release of Beacon v2 implementations of v1 and earlier are not longer supported. + Deployers of Beacon instances or networks are advised to migrate to v2 of the + standard. The functionality of Beacon v1 [can be easily implemented in v2](http://docs.genomebeacons.org/FAQ/#v1-emulation). + +The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022. It includes, among other changes: + +* Query options for biological or technical "meta"data using [**filters**](http://docs.genomebeacons.org/filters/) defined through CURIEs (e.g. phenotypes, disease codes, sex or age). +* An option to trigger the next step in the **data access** process (e.g. who to contact or which are the data use conditions). +* An option to **jump to another system** where the data could be accessed (e.g. if the Beacon is for internal use of the hospital, to provide the Id of the EHR of the patients having the mutation of interest). +* **Annotations** about the variants found, among which the expert/clinician conclusion about the pathogenicity of a given mutation in a given individual or its role in producing a given phenotype. +* Information about **cohorts**. + + + +![Beacon v2 Network Specification](/img/Beacon-graphics-v2-network-960x540.png) +###### Schematic example of a Beacon query + + +## Beacon v2 technology + +The Beacon v2 is based on a two-part concept: + +* The Beacon [Framework](http://docs.genomebeacons.org/framework/). +* The Beacon [Model](http://docs.genomebeacons.org/models/). + +In principle, this concept allows for different Models (in other domains outside of the Beacon v2 realm, e.g. “Imaging Beacon”) to be built using the same Framework. However, in the current context of Beacon v2, we consider the two elements interdependent and likely to be updated together for subsequent major versions (e.g. from v2 to v3). + +For further information please refer to the [Beacon v2 documentation](http://docs.genomebeacons.org). + +## Acknowledgements + +### Beacon partners +In 2020, the GA4GH Beacon group started a set of meetings and interviews with GA4GH Driver Projects and with ELIXIR partners in order to determine the scope of the next generation Beacon. The goal was to be useful without breaking the simplicity that made Beacon version 1 successful. +Interviews were conducted with the following GA4GH Driver Projects: + +* [Autism Speaks](https://www.autismspeaks.org/) +* [BRCA Exchange](https://brcaexchange.org/) +* [CanDIG](https://www.distributedgenomics.ca/) +* [European Genome-phenome Archive](https://ega-archive.org/), [European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/home), [European Vegetation Archive](http://euroveg.org/eva-database) +* [EuCanCancer](https://eucancan.com/) +* [European Joint Programme - Rare Diseases](https://www.ejprarediseases.org/) +* [H3Africa](https://h3africa.org/) +* [GEM Japan](https://www.amed.go.jp/en/aboutus/collaboration/ga4gh_gem_japan.html) +* [Genomics England](https://www.genomicsengland.co.uk/) +* [Matchmaker Exchange](https://www.matchmakerexchange.org/) +* SVIP /SPHN +* VICC + +Some ELIXIR partners were also interviewed, i.e. Café Variome, FPS, RD-Connect, CINECA, and Disgenet. +Among ELIXIR Spain TransBioNet and Bioinformatics in Barcelona members, a set of Catalan hospitals (e.g. Hospital Clinic) are exploring how to use Beacons inside their genomic diagnose teams and how to share the diagnoses between hospitals. + +### Beacon early implementers + +At the time of submission at the end of 2021, five Beacons were already implemented in the Beacon [Service Registry](https://ga4gh-approval-service-registry-demo.ega-archive.org). +The "early implementers" actively participated in refining the Framework as they were responsible for spotting any issue they might encounter with the Framework or Model. + +* European Genome-Phenome Archive [EGA Beacon](https://ga4gh-approval-beacon.ega-archive.org) +* Progenetix' [Beacon+](https://progenetix.org/search/) +* [Cafe Variome](https://beaconv2.cafevariome.org/form) +* Fundación Progreso y Salud's [Beacon v2 API](https://csvs-beacon.clinbioinfosspa.es/csvs/ga4ghbeacon/v2/api/) +* CNAG's [Beacon v2 API](https://playground.rd-connect.eu/beacon2/api) diff --git a/docs/minutes/2021-04-27-documentation-minutes.md b/docs/minutes/2021-04-27-documentation-minutes.md new file mode 100644 index 0000000..8e28d75 --- /dev/null +++ b/docs/minutes/2021-04-27-documentation-minutes.md @@ -0,0 +1,14 @@ +--- +title: 'Beacon Documentation Team' +date: 2021-04-27 +template: post.html +authors: ["@laurenfromont"] +--- + +The Beacon Documentation Scout develops documentation more easily browsable by clinical partners and researchers. + + + +#### 2021-04-27: Beacon Documentation TC + +* [Discussion document](https://docs.google.com/document/d/1-1EF-qwasLT6ads11PwiRBiUvy6Qepj-5wsQeAhJJ1A/edit?usp=sharing) diff --git a/docs/minutes/2021-05-28-genomic-variants-minutes.md b/docs/minutes/2021-05-28-genomic-variants-minutes.md new file mode 100644 index 0000000..f6770af --- /dev/null +++ b/docs/minutes/2021-05-28-genomic-variants-minutes.md @@ -0,0 +1,25 @@ +--- +title: 'Beacon Genomic Variants Team' +date: 2021-05-28 +template: post.html +author: ["@laurenfromont"] +--- + +The Genomic Variants Team evaluates "structural" types of genomic variants +with respect to their representation & query through current & future versions +of the Beacon API. This scope intersects with work being pursued in the +[ELIXIR h-CNV community](https://hcnv.github.io) and considers standards under +development by the GA4GH GKS workstream. + + + +Every three weeks, GV scout members meet to document genomic variants use cases and query examples. + +### Members + +* [Babita Singh](https://beacon-project.io/people/Babita-Singh/) (chair) + +### Genomic Variants TC + +* [Genomic variants: use cases and examples (working document)](https://docs.google.com/document/d/1cwwRQ2PtlN1dBffCugdkbSHWCPmLgLkADd-5mu-rVAw/edit?usp=sharing) +* [Meeting minutes](https://docs.google.com/document/d/198qR-MNPqXUdDySDeOIbBtVRrkG2uxY_MX3KMpnbuE8/edit?usp=sharing) diff --git a/docs/minutes/2021-06-01-beacon-api-minutes.md b/docs/minutes/2021-06-01-beacon-api-minutes.md new file mode 100644 index 0000000..0058144 --- /dev/null +++ b/docs/minutes/2021-06-01-beacon-api-minutes.md @@ -0,0 +1,8 @@ +--- +title: 'Beacon API Technical Team' +date: 2021-05-30 +template: post.html +author: ["@laurenfromont"] +--- + +* [Beacon API technical scout minutes](https://docs.google.com/document/d/1IgHcUK-pX-vThtW1xVA6RzvjCSclCruFn1RWCW1ZACY/edit?usp=sharing) diff --git a/docs/minutes/2021-06-01-beacon-ga4gh.md b/docs/minutes/2021-06-01-beacon-ga4gh.md new file mode 100644 index 0000000..965c99b --- /dev/null +++ b/docs/minutes/2021-06-01-beacon-ga4gh.md @@ -0,0 +1,21 @@ +--- +title: 'Beacon GA4GH API — Discovery work stream' +date: 2021-06-01 +template: post.html +author: ["@laurenfromont"] +--- + +These are the minutes for the Beacon API Sub Group of the GA4GH Discovery Work Stream. For further information, please visit the [GA4GH Work Stream page](https://www.ga4gh.org/how-we-work/workstreams/). +This call happens every second Tuesday of the month. + + + +### Coordinators + +* [Michael Baudis](https://beacon-project.io/people/Michael-Baudis/) (Discovery co-chair) +* [Jordi Rambla](https://beacon-project.io/people/Jordi-Rambla/) (chair) +* [Lauren Fromont](https://beacon-project.io/people/Lauren-Fromont/) (coordinator) + +### GA4GH Beacon API TC + +* [Meeting minutes](https://docs.google.com/document/d/1tHCUhzR-OuzNelgOH2cTlWJ0LjDSkpz99sQAMRlrTSE/edit) diff --git a/docs/minutes/compliance-minutes-2020.md b/docs/minutes/compliance-minutes-2020.md new file mode 100644 index 0000000..092962e --- /dev/null +++ b/docs/minutes/compliance-minutes-2020.md @@ -0,0 +1,32 @@ +--- +title: 'Beacon Compliance Team' +date: 2020-01-13 +template: post.html +author: ["@mbaudis", "@viklund"] +www_links_formatted: + - 'beacon-api-tests Repository' +--- + +The Beacon Compliance Team develops tests & tools for evaluating the query +compliance of Beacon implementations. + + + +### 2020-01-13: Beacon Compliance TC + +##### Johan Viklund, Malin Klang, Andreas Kähäri, Michael Baudis, Marta Ferri + +#### Agenda + +* Current [test suite](https://github.com/NBISweden/beacon-api-tests) status. +* How is test data stored and loaded into a beacon. + +#### Todo + +* Format of test data. + - Define individual call sets (i.e. a variant that is twice should be twice in test data) +* How to interpret the API. Different sites have had different interpretation on how queries and the response should be formatted. We need to go through these and agree. +* Structure tests into different classes. +* How new queries are added to the API and compliance tests - to be discussed in a bigger setting. + + diff --git a/docs/minutes/filters-minutes-2020.md b/docs/minutes/filters-minutes-2020.md new file mode 100644 index 0000000..8f707bd --- /dev/null +++ b/docs/minutes/filters-minutes-2020.md @@ -0,0 +1,19 @@ +--- +title: 'Beacon Filters Team Minutes 2020' +date: 2020-01-13 +template: post.html +author: ["@mbaudis"] +--- + +The Beacon Filters Team develops tests & tools for evaluating the query +compliance of Beacon implementations. + + + +#### Meeting Dial-In + +* [Zoom 296706422](https://zoom.us/j/296706422) + +#### 2020-01-29: Beacon Filters TC + +* [Discussion document](https://docs.google.com/document/d/1261e4k8MAD2C7eM98OmMzmB3yUZXYE5Wztei7C2at_k/edit) \ No newline at end of file diff --git a/docs/minutes/index.md b/docs/minutes/index.md new file mode 100644 index 0000000..06f0238 --- /dev/null +++ b/docs/minutes/index.md @@ -0,0 +1,9 @@ +--- +template: minutes_list.html +--- + +# Protocols and Minutes + +The Beacon project organizes one monthly GA4GH Beacon call (which focuses on the specification), and one monthly ELIXIR Beacon call (which focuses on the implementation). In addition, we put together several working groups (or "scouts") that focus on specific aspects of Beacon. Following the "open & transparent" approach of GA4GH, the meeting minutes and outputcan be accessed either as archives or rolling documents. + +![Teamwork](/img/programming-team.jpg){: style="display: block; margin: auto; width: 560px"} \ No newline at end of file diff --git a/docs/news/2018-03-16-news-beacon-0.4-ELIXIR-press-release.md b/docs/news/2018-03-16-news-beacon-0.4-ELIXIR-press-release.md new file mode 100644 index 0000000..13534e2 --- /dev/null +++ b/docs/news/2018-03-16-news-beacon-0.4-ELIXIR-press-release.md @@ -0,0 +1,20 @@ +--- +title: 'Global network of Beacons - Beacon v0.4' +description: Global network of Beacons lighting up the world of genomic data +template: post.html +author: "@mbaudis" +www_link: https://www.elixir-europe.org/news/beacon-API-website +--- + +The Beacon Project has released new Beacon API v0.4 specifications to provide greater search functions and richer search results. + + + +These API specifications are available through the new Beacon website which will provide up-to-date support and regular updates on the project developments. + +More details can be found here: + +* ELIXIR [press release](https://www.elixir-europe.org/news/beacon-API-website) +* New [Beacon website](http://beacon-project.io) +* [Beacon v0.4 release](https://github.com/ga4gh/beacon-team/releases/tag/v0.4.0) +* [development site](https://github.com/ga4gh-beacon/specification) diff --git a/docs/news/2018-10-18-news-beacon-1.0-ELIXIR-GA4GH-press-release.md b/docs/news/2018-10-18-news-beacon-1.0-ELIXIR-GA4GH-press-release.md new file mode 100644 index 0000000..141d309 --- /dev/null +++ b/docs/news/2018-10-18-news-beacon-1.0-ELIXIR-GA4GH-press-release.md @@ -0,0 +1,19 @@ +--- +title: 'Press Release: GA4GH and ELIXIR Release Beacon API v1' +description: GA4GH and ELIXIR Release Beacon API v1 with increased security measures +template: post.html +author: "@mbaudis" +excerpt_separator: +www_link: https://www.elixir-europe.org/news/beacon-API-release +--- + +ELIXIR and the Global Alliance for Genomics and Health (GA4GH) have announced the release of the first genomic data interoperability standard from the GA4GH 2018 Strategic Roadmap. + + + +More details can be found here: + +* ELIXIR [press release](https://www.elixir-europe.org/news/beacon-API-release) +* [code release](https://github.com/ga4gh-beacon/specification/releases/tag/v1.0.0) +* [development site](https://github.com/ga4gh-beacon/specification) +* GA4GH [press release](https://ga4gh.edit.sanger.ac.uk/news/ga4gh-and-elixir-release-beacon-api-v1-with-increased-security-measures/) diff --git a/docs/news/2019-02-28-beacon-plant-meeting-bordeaux.md b/docs/news/2019-02-28-beacon-plant-meeting-bordeaux.md new file mode 100644 index 0000000..429233e --- /dev/null +++ b/docs/news/2019-02-28-beacon-plant-meeting-bordeaux.md @@ -0,0 +1,20 @@ +--- +title: 'Plant Beacons Hackathon Bordeaux' +date: 2019-02-28 +template: post.html +author: "@mbaudis" +--- + +The hackaton took place the 2019-02-28 in the center of Bordeaux in the room "RE" of the former Law Faculty of the University of Bordeaux. + + + +* Description and history : + - https://www.u-bordeaux.fr/Universite/L-universite-de-Bordeaux/Histoire-et-patrimoine/Bordeaux-Pey-Berland +* Map + - https://goo.gl/maps/ofhzbVi8ptr +* Program + - 9h30 Welcome Coffee break + - 10h00 : Beginning of the meeting + - 15h30 : Coffee break + - 17h : End of the Hackaton diff --git a/docs/news/2019-03-04-news-GA4GH-press-release-Beacon-paper.md b/docs/news/2019-03-04-news-GA4GH-press-release-Beacon-paper.md new file mode 100644 index 0000000..1b64f66 --- /dev/null +++ b/docs/news/2019-03-04-news-GA4GH-press-release-Beacon-paper.md @@ -0,0 +1,14 @@ +--- +title: 'Beacon publication at Nature Biotechnology' +template: post.html +author: "@mbaudis" +www_links_formatted: + - Beacon publication at Nature Biotechnology + - GA4GH Press Release +--- + +#### Federated discovery and sharing of genomic data using Beacons +##### Marc Fiume, Miroslav Cupak, Stephen Keenan, Jordi Rambla, Sabela de la Torre, Stephanie O. M. Dyke, Anthony J. Brookes, Knox Carey, David Lloyd, Peter Goodhand, Maximilian Haeussler, Michael Baudis, Heinz Stockinger, Lena Dolman, Ilkka Lappalainen, Juha Törnroos, Mikael Linden, J. Dylan Spalding, Saif Ur-Rehman, Angela Page, Paul Flicek, Stephen Sherry, David Haussler, Susheel Varma, Gary Saunders and Serena Scollen + + +Today, Nature Biotechnology published the Beacon manuscript "Federated discovery and sharing of genomic data using Beacons". This was accompanied by a GA4GH press release. Enjoy! diff --git a/docs/news/2019-03-07-beacon-hackathon-stockholm.md b/docs/news/2019-03-07-beacon-hackathon-stockholm.md new file mode 100644 index 0000000..0231a3a --- /dev/null +++ b/docs/news/2019-03-07-beacon-hackathon-stockholm.md @@ -0,0 +1,20 @@ +--- +title: 'Beacons Hackathon Stockholm' +date: 2019-03-07 +template: post.html +author: "@mbaudis" +excerpt_separator: +pdf_file_name: +www_link: https://docs.google.com/document/d/1ECcfX4nAJaCKebueaT1r1MZq-keTklcycDhLPE1AUvw/edit# +category: # please adjust + - events +tags: # please adjust + - events +--- + +On March 7, Beacon team members from ELIXIR and DNAstack will meet at the SciLife Center Stockholm for Face-to-face meeting and Hackathon. + + + +* Location:SciLifeLab, Tomtebodavägen 23a, Stockholm, meeting room “Earth” +* Time: 0930-1630 diff --git a/docs/news/2019-06-17-Beacon-at-ELIXIR-All-Hands-Lisbon.md b/docs/news/2019-06-17-Beacon-at-ELIXIR-All-Hands-Lisbon.md new file mode 100644 index 0000000..a4c9204 --- /dev/null +++ b/docs/news/2019-06-17-Beacon-at-ELIXIR-All-Hands-Lisbon.md @@ -0,0 +1,30 @@ +--- +template: post.html +title: ELIXIR Beacons at ELIXIR All Hands 2019 Workshop +start_date: 2019-06-17T16:00:00 +end_date: 2019-06-17T17:30:00 +venue: Marriott Hotel Lisbon +city: Lisbon +country: Portugal +event_type: Meetings and conferences +date: 2019-06-17 +author: "@mbaudis" +www_link: "https://docs.google.com/document/d/1E55l-K8OHi5FQbFutivH3UoO7hkrGoG6qsBjr5rhDlk/edit#" +--- + + +#### Purpose of this workshop: + +* Update on GA4GH Beacon API and Beacon Network developments +* Demonstrate ELIXIR Beacon implementation of new API and Network features +* Present the future vision for Beacons - Beacon 2.0 + +#### Presentations + +* Michael Baudis: [ELIXIR and GA4GH in Beacon development](/pdf/2019-06-17___Michael-Baudis__Beacon-session-ELIXIR-and-GA4GH__ELIXIR-Lisbon-2019.pdf) +* Juha Törnroos: [ELIXIR Beacon Network](/pdf/2019-06-17___Juha-Törnroos__ELIXIR-Beacon-Network__Beacon-WS-slides.pdf) +* Mikael Linden and Dominik F. Bucik: [AAI and Affiliation Assignment](/pdf/2019-06-17___Mikael-Linden__AAI-Manual-assignment-of-affiliation__Beacon-WS-slides.pdf) + + +Please see the link below for more information. + diff --git a/docs/news/2019-07-01-Beacon-workshop-Zurich.md b/docs/news/2019-07-01-Beacon-workshop-Zurich.md new file mode 100644 index 0000000..a5357c7 --- /dev/null +++ b/docs/news/2019-07-01-Beacon-workshop-Zurich.md @@ -0,0 +1,22 @@ +--- +template: post.html +title: Barcelona Goes Zurich - Beacon Code Alignment Workshop +start_date: 2019-07-01T12:00:00 +end_date: 2019-07-02 +venue: University of Zurich, Irchel Campus, Y-13L-11 +street: Winterthurerstrasse 190 +city: Zurich +country: CH +postcode: 8057 +event_type: Meetings and conferences +date: 2019-07-01 +author: "@mbaudis" +www_link: "https://docs.google.com/document/d/1Ym-3gWd5DNUsv4GwMyy9kpHuP0-JICrCSI9jawOZXbY/edit#" +--- + + +The Zurich meeting is intended to align the current development version of the Beacon API and the Beacon+ driver, and to improve the documentation structure of the Beacon project. + +In another part of the 2-days meeting we will explore further the concept and possible implementation of "Evidence Beacons", together with developers from the SVIP project. + +The tentative agenda for the meeting is linked below. diff --git a/docs/news/2019-10-21-beaconv2-ga4ghplenary.md b/docs/news/2019-10-21-beaconv2-ga4ghplenary.md new file mode 100644 index 0000000..1d22fd8 --- /dev/null +++ b/docs/news/2019-10-21-beaconv2-ga4ghplenary.md @@ -0,0 +1,52 @@ +--- +title: 'GA4GH 2019 — Beacon v2: Towards a modular Beacon protocol empowering clinical use' +template: post.html +author: + - "@mbaudis" + - "@laurenfromont" +date: 2019-10-21 +--- + +#### Poster abstract for the GA4GH Plenary, Boston 2019 + +The Beacon Project is a Global Alliance for Genomics and Health (GA4GH) +initiative for the federated discovery of genomic data in biomedical research +and clinical applications. Originally implemented as a tool reporting the +existence of Single Nucleotide Polymorphisms (SNP) in aggregated genomic data +collections, the protocol has evolved towards more complex applications with +increased functionality. Implementations of the current Beacon API enable the +search for structural variants (e.g. deletions and duplications) and return +richer responses (e.g. variant metadata and call counts). + + + +With growing interest from the community in the implementation of the Beacon +protocol into resources and workflows, the next major release 2.0 will introduce +new features which were considered important by the community: +Queries by type: The Beacon will define different sets of attributes for +requests and responses depending on the type of query; e.g. a specific request +and response to return variants within a region in a chromosome +(wildcard/region queries) or to get a list of samples related to a phenotype, +provided the required authentication or authorization (see Access levels below). +Filters: The next major version of Beacon will include a feature to filter the +matched variants by additional conditions on e.g. sample specific or technical information (e.g., associated phenotypes, assay type). Here the utilisation of ontologies will be encouraged, with alternative use of custom vocabularies for local applications. +Schema versions: Given that new query types will return differing responses +(e.g., variant annotations, pointers to data delivery protocols), a mechanism will be implemented to reference internal or external data schemas that describe the content of the Beacon response (e.g., returning variant information using “GA4GH Variant Representation v1”). +Access levels: Beacon administrators will be able to specify the level of access +(public, registered or controlled) for each field in the Beacon response and +even refine this definition by dataset, if these diverge from the default +values. This is applicable also to the query types supported (genomic variants, sample lists, etc...) + +##### Author List: + +* Sabela de la Torre. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. +* Frederic Haziza. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. +* Marta Ferri. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. +* Michael Baudis. Institute of Molecular Life Sciences (IMLS) and Swiss Institute of Bioinformatics (SIB), University of Zurich +* Joaquin Dopazo, Clinical Bioinformatics Area, Fundacion Progreso y Salud, Hospital Virgen del Rocio, Sevilla, Spain +* Niclas Jareborg. National Bioinformatics Infrastructure Sweden / ELIXIR-SE +* Gary Saunders, ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK. +* Dylan Spalding, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK +* Arcadi Navarro. Universitat Pompeu Fabra and Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. +* Juha Tornroos, CSC - IT Center for Science Ltd +* Jordi Rambla. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. diff --git a/docs/news/2019-11-18-biohackathon-europe.md b/docs/news/2019-11-18-biohackathon-europe.md new file mode 100644 index 0000000..fa640b3 --- /dev/null +++ b/docs/news/2019-11-18-biohackathon-europe.md @@ -0,0 +1,64 @@ +--- +title: "CNV Beacon at Biohackathon Europe" +template: post.html +date: 2019-11-18 +author: ["@mbaudis"] +www_link: https://www.biohackathon-europe.org +--- + + +For the Biohackathon Europe (Nov 18-22), the hCNV project submitted a proposal +which was accepted for the event near Paris. + + + +#### PROPOSAL ACCEPTED FOR THE BIOHACKATHON +### Copy Number Variation Beacon + +**Abstract** CNV are major source of genomic variation. However, whilst Next-Generation Sequencing technologies, especially Whole Genome Sequencing, are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect and interpret CNV is still heterogeneous and remains a non trivial process. + +Recently, leading European researches from such areas as rare disease genetics, bioinformatics and cancer genomics have established the ELIXIR h-CNV community with the goal to improve CNV detection and identification of CNV associated to phenotypes, beyond individual resources or research projects. An essential part of the strategy concerns the federated access to clinical and reference CNV datasets, e.g. through the implementation of innovative data APIs. + +The GA4GH Beacon API allows any resource to share the presence or the absence of a particular variation, including since its v0.4 release in 2018 - the support for CNVs. Also, the ELIXIR Beacon Network enables federated searching of multiple Beacons via an a single graphical interface. + +The objective of this project is to set up a reference Beacon instance on top of a CNV dataset. The implementation should support all features of the latest protocol version and provide rich responses (differential observation frequencies, variant & phenotype information in responses or through handover protocols). Additionally, we shall link this Beacon to the ELIXIR Beacon Network, and enable data sharing via at least one of the three levels of access (public, registered, or controlled), which are enabled via ELIXIR AAI. Also, the project is expected to develop tooling for the conversion of CNV storage formats (e.g. VCF files) to Beacon compatible representations. + + +##### Hacking topic title + +Facilitate interpretation of CNV through Beacons + +##### Leads + +* Michael Baudis +* David Salgado +* Gary Saunders + +##### Research Area Alignment + +This project is principally aligned with the ELIXIR h-CNV Community and the ELIXIR Beacon GA4GH Driver Project. Is it also aligned more generally with the ELIXIR Human Data Communities. + +##### Expected Outcomes: + +1. Functional Beacon sharing CNV data +2. Registering this Beacon to the ELIXIR Beacon Network +3 Controlled vocabulary / Common data elements used to describe a CNV +4. Specifications +5. Draft implementation + +##### Expected Audience + +Anyone interested in CNV, Beacon, Interoperability, controlled vocabulary... + +##### Nominated Participant + +* Michael Baudis +* David Salgado +* Gary Saunders +* Bo Gao + +##### Number of expected Hacking day for project + +4 days + + diff --git a/docs/news/2020-09-30-Michael-Baudis__Beaconv2__GA4GH2020-poster.md b/docs/news/2020-09-30-Michael-Baudis__Beaconv2__GA4GH2020-poster.md new file mode 100644 index 0000000..0caa7fc --- /dev/null +++ b/docs/news/2020-09-30-Michael-Baudis__Beaconv2__GA4GH2020-poster.md @@ -0,0 +1,29 @@ +--- +title: "GA4GH Beacon v2 at GA4GH Plenary" +description: Evolving Reference Standard for Genomic Data Exchange +template: post.html +date: 2020-09-30 +excerpt_link: https://info.baudisgroup.org/presentations/2020-09-30-Michael-Baudis__Beaconv2__GA4GH2020-poster/ +authors: + - '@mbaudis' +--- + +#### [GA4GH 8th Plenary](https://broadinstitute.swoogo.com/ga4gh-8th-plenary/455678) +### Gary Saunders, Jordi Rambla de Argila, Anthony Brookes, Juha Törnroos and Michael Baudis +##### For the ELIXIR Beacon project, GA4GH Discovery work stream and the international network of Beacon API developers + +The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. +Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard: +* requests beyond genomic variants ("filters") +* payload responses, secured through open AAI +* aligning w/ GA4GH standards (Phenopackets, VRS, DUO...) through SchemaBlocks [{S}[B]](https://schemablocks.org) +* Working with international partners on deployment of advanced implementations + + + +#### Additional Links + +* [Beacon Website](http://beacon-project.io) +* [SchemaBlocks {S}[B]](https://schemablocks.org) +* [Beacon+ in progenetix-next](https://progenetix.org/beaconplus-instances/beaconplus/) +* [Bycon Project](https://github.com/progenetix/bycon) diff --git a/docs/news/2020-09-30-Michael-Baudis__Progenetix-and-Beacon__GA4GH2020-poster.md b/docs/news/2020-09-30-Michael-Baudis__Progenetix-and-Beacon__GA4GH2020-poster.md new file mode 100644 index 0000000..681a139 --- /dev/null +++ b/docs/news/2020-09-30-Michael-Baudis__Progenetix-and-Beacon__GA4GH2020-poster.md @@ -0,0 +1,28 @@ +--- +title: "Progenetix - A cancer genomics reference resource around GA4GH standards" +template: post.html +date: 2020-09-30 +excerpt_link: https://info.baudisgroup.org/presentations/2020-09-30-Michael-Baudis__Progenetix-and-Beacon__GA4GH2020-poster/ +authors: + - '@mbaudis' +--- + +#### [GA4GH 8th Plenary](https://broadinstitute.swoogo.com/ga4gh-8th-plenary/455678) +### Michael Baudis + +The Progenetix oncogenomics resource provides sample-specific cancer +genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts. + + + +Progenetix has been widely used in research studies, clinical diagnostics and recently in the development of data protocols and standards with the Global Alliance for Genomics and Health (GA4GH) and the European bioinformatics initiative ELIXIR. Specifically, the Beacon+ service, implemented on top of the Progenetix datasets, has been instrumental in developing and testing advanced features of the Beacon protocol such as structural variant queries, "handover" data delivery and the implementation of queries for phenoptypic and diagnostic parameters using CURIE based "filters". During development of GA4GH metadata concepts and schemas - which have influenced emerging standards such as the Phenopackets format - cancer specific annotations from the Progenetix collection have served to identify conceptual requirements and to develop domain-specific mappings (e.g. ICD-O to NCIt translations). The resource's focus on structural genome variants has been instrumental in addressing their specific requirements in GA4GH schema development and the Beacon protocol. + +Here, we will demonstrate how an open genomic reference resource has been built around GA4GH standards and how it is being used to support ongoing and future developments in GA4GH standard development and ELIXIR implementation studies. + +progenetix.org + +#### Additional Links + +* [Beacon Website](http://beacon-project.io) +* [Beacon+ in progenetix-next](https://progenetix.org/beaconplus-instances/beaconplus/) +* [Bycon Project](https://github.com/progenetix/bycon) diff --git a/docs/news/2021-01-15-Beacon-New-Year.md b/docs/news/2021-01-15-Beacon-New-Year.md new file mode 100644 index 0000000..6f539c8 --- /dev/null +++ b/docs/news/2021-01-15-Beacon-New-Year.md @@ -0,0 +1,13 @@ +--- +title: 'Happy 2021 from the Beacon Team' +date: 2021-01-15 +template: post.html +author: + - "@mbaudis" + - "@laurenfromont" +--- + +The Beacon Team wishes everybody a happy and healthy 2021! We're excited about our upcoming Beacon v2, expected to be finalized later this year. + + + diff --git a/docs/news/2021-03-02-ga4gh-connect.md b/docs/news/2021-03-02-ga4gh-connect.md new file mode 100644 index 0000000..a6abcd7 --- /dev/null +++ b/docs/news/2021-03-02-ga4gh-connect.md @@ -0,0 +1,26 @@ +--- +title: "GA4GH Connect - Beacon v2 Structural Variants" +template: post.html +excerpt_separator: +date: 2021-03-02 +authors: + - '@mbaudis' + - '@laurenfromont' +--- + +#### [GA4GH Connect 2021](https://broadinstitute.swoogo.com/ga4gh-connect-2021/?i=sNK7RoeeqhyJE1ueSnn5lz4F9RRfnnIU) +#### Michael Baudis +##### Beacon v2 Structural Variants [[slides]](/pdf/2021-03-02___Michael-Baudis__Beacon-structural-variants-queries.pdf) + +#### Lauren Fromont & Jordi Rambla +##### Beacon v2 Cohort model [[slides]](https://drive.google.com/file/d/1rjpWt_yqNBq-S8ul4blN-onsY1rWHNOh/view?usp=sharing) + + + +#### Additional Links + +* [Beacon Website](http://beacon-project.io) +* [Cohorts in Default Schema](https://beacon-schema-2.readthedocs.io/en/latest/beacon_schema/#cohorts-link-to-cohort-schema-doc) +* [SchemaBlocks {S}[B]](https://schemablocks.org) +* [Beacon+ in progenetix-next](https://progenetix.org/beaconplus-instances/beaconplus/) +* [Bycon Project](https://github.com/progenetix/bycon) diff --git a/docs/news/2021-04-20-Michael-Baudis__ELIXIR-Beacon__RDA.md b/docs/news/2021-04-20-Michael-Baudis__ELIXIR-Beacon__RDA.md new file mode 100644 index 0000000..70a450e --- /dev/null +++ b/docs/news/2021-04-20-Michael-Baudis__ELIXIR-Beacon__RDA.md @@ -0,0 +1,22 @@ +--- +title: "Progenetix, Beacon and GA4GH at RDA" +description: Research Data Alliance - RDA Virtual Plenary 17 +template: post.html +date: 2021-04-20 +authors: + - '@mbaudis' +links: + - '[Presentation slides]' + - '[Beacon Website]' + - '[Beacon Development at Github]' + - '[Beacon+ in Progenetix]' +--- + +#### Concepts | Status | History | Outlook +### Michael Baudis +#### [Research Data Alliance - RDA Virtual Plenary 17](https://rda-idcc.junolive.co/RDAVP17) + +This seminar gives an overview of current state of the Progenetix Beacon project +and the overall connection to the Global Alliance for Genomics and Health (GA4GH). + + diff --git a/docs/news/2021-06-08-Beacon-ELIXIR-AllHands.md b/docs/news/2021-06-08-Beacon-ELIXIR-AllHands.md new file mode 100644 index 0000000..1eb2446 --- /dev/null +++ b/docs/news/2021-06-08-Beacon-ELIXIR-AllHands.md @@ -0,0 +1,26 @@ +--- +template: post.html +title: Beacon Workshop at ELIXIR AllHands +date: 2021-06-08 +author: "@mbaudis" +--- + +#### Chairs: Gary Saunders, Juha Tornroos, Michael Baudis, Dylan Spalding, Lauren Fromont, Jordi Rambla + +Beacon now stands as the ‘default’ data discovery solution in GA4GH and ELIXIR portfolios, and is increasingly adopted by third-party projects. Beacons become particularly successful through their aggregation in Beacon networks, which provide a way to query many genomic variant resources through a central federation node while receiving aggregated responses all at once. Both Beacon and Beacon Network are part of the 1+MG and B1MG service catalogs and represent core discovery solutions in ELIXIR across the Federated Human Data, Rare Diseases, and human Copy Number Variation Communities. + +During this workshop we will discuss: + +1) progress of the fruitful collaboration with the GA4GH Beacon community +2) latest developments of the ELIXIR Beacon project including deployment tested instances in clinical and non-clinical settings (via various H2020 projects, GA4GH Driver projects and ELIXIR partners) +3) extensions to the ELIXIR Services specification in order to manage Beacon v2 instances +4) security features of Beacon v2 according to real world needs +5) an extended and improved ELIXIR Beacon Network service. + +As a result this workshop will describe how Beacons that are integrated in the ELIXIR Beacon Network Infrastructure can further the contribution and implementation of GA4GH standards, and empower nodes to be part of the federated sensitive human data infrastructure. + +Agenda [here](https://docs.google.com/document/d/1ISClkkZZXM0SV1oKLrYrerXoSZ2ydf_tAH_wCc0tlE4/edit#) + +
+All hands 2021 +
diff --git a/docs/news/2021-09-13-Michael-Baudis__Beacon__BC2-2021-GA4GH-Session.md b/docs/news/2021-09-13-Michael-Baudis__Beacon__BC2-2021-GA4GH-Session.md new file mode 100644 index 0000000..64b38e8 --- /dev/null +++ b/docs/news/2021-09-13-Michael-Baudis__Beacon__BC2-2021-GA4GH-Session.md @@ -0,0 +1,18 @@ +--- +title: "A Standardized Format for Federated Genomic Data Exchange" +description: 'The GA4GH Beacon Protocol Presented at BC2 Basel 2021
Session "Federating computational analyses with GA4GH standards"' +template: post.html +date: 2021-09-13 +authors: + - '@mbaudis' +links: + - '[Presentation slides]' + - '[Beacon Website]' + - '[Beacon Development at Github]' + - '[Beacon+ in Progenetix]' +--- + +#### Michael Baudis + +![BC2 logo](http://info.baudisgroup.org/img/logo_bc2.svg){: style="float: right; width: 200px; margin-top: -120px;"}During the "Federating computational analyses with GA4GH standards" workshop at BC2 2021 Michael presented history and the current status of the Beacon project, as well as its integration with specific data resources and analysis initiatives. + diff --git a/docs/news/2021-12-29-Beacon v2 submitted to GA4GH.md b/docs/news/2021-12-29-Beacon v2 submitted to GA4GH.md new file mode 100644 index 0000000..43f3571 --- /dev/null +++ b/docs/news/2021-12-29-Beacon v2 submitted to GA4GH.md @@ -0,0 +1,13 @@ +--- +template: post.html +title: Beacon v2 submitted to GA4GH +date: 2021-12-29 +author: "@laurenfromont" +--- + +Beacon v2 was submitted to the [Global Alliance for Genomics and Health](https://www.ga4gh.org) and is now available for public review! +Our specification is available on [Github](https://github.com/ga4gh-beacon/beacon-v2) and several [implementations](https://ga4gh-approval-service-registry-demo.ega-archive.org) are already available! + +
+beacon-spec-github +
diff --git a/docs/news/2021-12-30-cineca-webinar.md b/docs/news/2021-12-30-cineca-webinar.md new file mode 100644 index 0000000..ff21fa5 --- /dev/null +++ b/docs/news/2021-12-30-cineca-webinar.md @@ -0,0 +1,15 @@ +--- +template: post.html +title: "The Beacon: a data discovery solution in genomics and health" +description: Beacon v2 Webinar at CINECA +date: 2021-12-30 +author: "@laurenfromont" +--- + +#### Presenter: Lauren Fromont + +Personalised medicine is making great progress: facilitating secure access to human data for researchers and clinicians has become key to achieving this. The Beacon aims to promote this by delivering a federated infrastructure for data discovery of human genetic and phenotypic data. + +The Beacon is a protocol for sharing information about the presence or absence of a specific mutation in a given dataset. The latest version (v2) of the Beacon also allows to: filter by variables or interest (e.g. gender or age), trigger the data access process, and consult clinical annotation about the variants found, among others. Further, it inserts a brand new feature that was developed for CINECA’s needs: a cohort model, allowing researchers to find appropriate populations (e.g., a group of patients with a specific disease) to help answer their research questions. + +Watch the public recording of the presentation [here](https://www.cineca-project.eu/news-events-all/the-beacon-a-data-discovery-solution-in-genomics-and-health) diff --git a/docs/news/2022-04-06-Beacon-All-Hands.md b/docs/news/2022-04-06-Beacon-All-Hands.md new file mode 100644 index 0000000..b614f5d --- /dev/null +++ b/docs/news/2022-04-06-Beacon-All-Hands.md @@ -0,0 +1,22 @@ +--- +template: post.html +title: "Beacon implementations: Beaconize your genomics data" +description: Beacon v2 Workshop at ELIXIR All Hands +date: 2022-04-06 +author: "@laurenfromont" +--- + +#### Hosts: Lauren Fromont, Michael Baudis & Jordi Rambla +#### Amsterdam, 7th June 2022 [Link to webpage](https://elixir-europe.org/events/elixir-all-hands-2022) + +One of the main bottlenecks in human genomics research is the lack of tools for federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention since genomics data sees an ever greater application in clinical settings, such as for medical diagnostic or prognostic purposes, in rare diseases or cancer. Currently, most of the molecular analyses generated in hospitals are not utilised for further research due to lack of proper tools for an interoperable and ethical sharing of the data. The Beacon project (ELIXIR, see also the Global Alliance in Health and Genomics for the standard) aims to alleviate the problem of genomics data sharing through enabling the search of genomic variants and associated information without jeopardising the privacy of the dataset. This way, any hospital or research entity can choose to 'beaconize' their dataset without compromising its privacy or ownership. + +With growing interest from the community in the implementation of the Beacon protocol into resources and workflows, the release 2.0 introduces new features considered important by the community: e.g. queries by entity type, filters, schema versions, and access levels. While both the research and the clinical community recognizes the value of these additions, practical implementation of the Beacon could still be a challenging task, especially for institutions with limited IT resources. The ELIXIR implementation studies (2019-2021; 2022-2024) aim to develop a reference implementation so researchers and clinicians can use it as an example to deploy their own Beacon without needing extensive knowledge on how to build an API. + +This workshop has two objectives, to provide participants with: + +1- Demos and insights on Beacon implementations. For this objective we will invite early Beacon v2 implementers who provided valuable feedback to the specification and will share their use-cases and experiences: Michael Baudis (Progenetix), Tim Beck (Café Variome), and Carles Hernandez (CNAG-CRG). + +2- A training session on how to d eploy a Beacon using the reference implementation. For this objective we will invite members of the European Genome-phenome Archive (Manuel Rueda) who support Beacon deployment in hospitals and clinical institutions and will provide a hands-on session. + +Beacon version 2 is a highly expected product in the genomics research and clinical communities. Now that the Beacon community has released a stable version, it is time to provide beacon implementers guidelines and resources to implement or deploy their own Beacons to foster data discovery and data re-use. diff --git a/docs/news/2022-06-07-Michael-Baudis__Progenetix-and-BeaconPlus__ELIXIR-All-Hands.md b/docs/news/2022-06-07-Michael-Baudis__Progenetix-and-BeaconPlus__ELIXIR-All-Hands.md new file mode 100644 index 0000000..9791d66 --- /dev/null +++ b/docs/news/2022-06-07-Michael-Baudis__Progenetix-and-BeaconPlus__ELIXIR-All-Hands.md @@ -0,0 +1,16 @@ +--- +title: "Progenetix & BeaconPlus - An open cancer genomics resource on a stack of Beacon code..." +description: ELIXIR All Hands Amsterdam 2022 +template: post.html +authors: + - '@mbaudis' +date: 2022-06-07 +links: + - '[[slides]](http://info.baudisgroup.org/pdf/2022-06-07___Michael-Baudis__Progenetix-and-BeaconPlus__ELIXIR-All-Hands-Slides.pdf)' +--- + +#### Michael Baudis + +Here Michael provides some overview of the multi-year trajectory of the Beacon API +development, and how BeaconPlus & Progenetix have been utilized for "implementation +driven design". \ No newline at end of file diff --git a/docs/news/2022-08-08-GA4GH-Plenary-2022.md b/docs/news/2022-08-08-GA4GH-Plenary-2022.md new file mode 100644 index 0000000..aba77a2 --- /dev/null +++ b/docs/news/2022-08-08-GA4GH-Plenary-2022.md @@ -0,0 +1,32 @@ +--- +title: 'GA4GH 2022 — Beacon v2 standard highlighted at the GA4GH plenary' +date: 2022-08-02 +template: post.html +author: + - "@AnaT-DCO" +excerpt_separator: +www_links_formatted: +category: + - events + - beaconv2 +tags: + - specification + - development + - events +--- + + +Jordi Rambla, one of the key [Beacon v2](https://beacon-project.io/) leaders, will present the Beacon v2 Specification in Barcelona for the [Global Alliance for Genomics And Health (GA4GH)](https://www.ga4gh.org/) 10th Plenary Meeting. + +
+ +
CosmoCaixa building in Barcelona.
+
+ + + +The 10th Plenary, which will be held from 22 to 23 September 2022 at the [CosmoCaixa](https://cosmocaixa.org/es/cosmocaixa-barcelona), will bring together organizations and stakeholders from the genomics and health community. + +The event will focus on genomic and clinical data sharing issues that pervade a diverse cross-section of industries, disciplines, and communities. + +For more information, please visit the official website of the [Plenary Meeting](https://broadinstitute.swoogo.com/ga4gh-10th-plenary). diff --git a/docs/news/2022-08-11-ECCB-Beacon-workshop.md b/docs/news/2022-08-11-ECCB-Beacon-workshop.md new file mode 100644 index 0000000..a385f9b --- /dev/null +++ b/docs/news/2022-08-11-ECCB-Beacon-workshop.md @@ -0,0 +1,27 @@ +--- +title: 'Beacon v2 will be at the European Conference on Computational Biology with a Workshop on tools and techniques to make sensitive data discoverable' +date: 2022-08-11 +template: post.html +author: + - "@AnaT-DCO" +--- + +The Workshop [**"Tools and techniques to make sensitive data discoverable (Use-cases, hands-on session of Beacon implementation)"**](https://eccb2022.org/ntb-w06/) will take place on September 15th, in the framework of the [21st European Conference on Computational Biology (ECCB)](https://eccb2022.org/). This workshop aims to provide knowledge and hands-on sessions about the discoverability of sensitive genomics and clinical data without jeopardizing the privacy or ownership of such datasets. + +
+ +
+ + + +One of the main bottlenecks in human genomics research is the lack of secure and federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention with the expansion of genomics data in clinical application, such as for medical diagnostic or prognostic purposes in rare diseases or cancer. + +[This workshop](https://eccb2022.org/ntb-w06/) aims to provide knowledge and hands-on sessions about the discoverability of sensitive genomics and clinical data without jeopardizing the privacy or ownership of such datasets. [European Genome-phenome Archive (EGA)](https://ega-archive.org/) along with [ELIXIR](https://elixir-europe.org/) and the [Global Alliance for Genomics and Health (GA4GH)](https://www.ga4gh.org/) has been involved to develop tools and techniques to tackle this challenge. [Beacon](https://beacon-project.io/) recently became an approved GA4GH standard for data sharing. Now, anyone handling sensitive human dataset can choose to ‘Beaconize’ their dataset and add it to Beacon network to make their data discoverable. + +The [workshop](https://eccb2022.org/ntb-w06/) has three objectives with following sessions for the participants: + +- **Session I – Sensitive data challenges**. What makes data, a sensitive data? Introduction to long-term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data. Re-usuablity of datasets, FAIR data principles, public trust and policies on data governance. +- **Session II – Beacon use case: Secure sharing of clinical genomics data by connecting different hospitals of Catalunya**. Bottlenecks of sensitive data sharing and data re-usability challenges, how does it impact in real-life scenarios? Patient’s journey, stories, use-cases and Introduction to Beacon pilot project launched to connect hospitals of Catalunya. +- **Session III – Demo Beacon Implementation (BYOD: Bring your own dataset)**. Participants will learn how to make their sensitive data discoverable without jeopardising the privacy of such dataset through demo/hands-on training on Beacon tool reference implementation ([Documentation](http://docs.genomebeacons.org/)). + +The workshop will be open to ECCB registered participants and its format will be virtual. For more information, please visit the [ECCB website](https://eccb2022.org/ntb-w06/). diff --git a/docs/news/2022-09-22-Michael-Baudis__Feature-rich-Beacon-v2-Implementation__GA4GH-plenary-poster.md b/docs/news/2022-09-22-Michael-Baudis__Feature-rich-Beacon-v2-Implementation__GA4GH-plenary-poster.md new file mode 100644 index 0000000..e8cc25a --- /dev/null +++ b/docs/news/2022-09-22-Michael-Baudis__Feature-rich-Beacon-v2-Implementation__GA4GH-plenary-poster.md @@ -0,0 +1,21 @@ +--- +title: 'Beacon v2 - Feature-rich Implementation of the Genomic Data Discovery Protocol' +description: GA4GH 2022 Plenary Barcelona +template: post.html +authors: + - '@mbaudis' +date: 2022-09-22 +pdf_file_name: 2022-09-22___Michael-Baudis-Beacon-Progenetix__GA4GH-poster.pdf +links: + - "[GA4GH 10th Plenary](https://broadinstitute.swoogo.com/ga4gh-10th-plenary)" + - "[Global Alliance for Genomics and Health](http://ga4gh.org)" + - "[Progenetix Genome Resource](http://progenetix.org)" +--- + +#### Michael Baudis + +The “Beacon” protocol - developed with support from ELIXIR, the European bioinformatics infrastructure organization, as a standard of the Global Alliance for Genomics and Health (GA4GH) - represents an emerging standard for an “Internet for Genomics”. While the initial version of the protocol served as a widely adopted test bed for the sharing of genomic variants over federated query systems connecting hundreds of internationally distributed resources, the version 2 of the protocol provides a framework for extended, metadata-rich query and response options in both public and restricted federated access scenarios. + +With the adoption of Beacon v2 as a GA4GH standard in 2022, a current focus of the Beacon development lies is in the implementation of Beacon networks employing the new query and data delivery options, as well as in supporting the transition of existing Beacon instances to v2. In the context of ELIXIR, these developments are supported through a dedicated Beacon Infrastructure Service project as well as by supporting the utilization of Beacon throughout ELIXIR resources and platforms. As example of the latter, members of the ELIXIR hCNV community work to “beaconize” and network existing resources focussed on genomic copy number variations in the areas of rare diseases and cancer. + +Here we highlight some of the new features of the Beacon v2 protocol and how the Progenetix oncogenomic resource serves as a driver for the Beacon protocol development, as well as to demonstrate extensive use of the Beacon protocol as foundation of a networked genomics resource including tight integration with ELIXIR community projects. \ No newline at end of file diff --git a/docs/news/2022-10-20-Michael-Baudis__Genomics-Data-Federation-through-Global-Alliance-for-Genomics-and-Health-Standards--Development-and-Implementation-of-the-GA4GH-Beacon-Protocol__Korea-genomics-seminar.md b/docs/news/2022-10-20-Michael-Baudis__Genomics-Data-Federation-through-Global-Alliance-for-Genomics-and-Health-Standards--Development-and-Implementation-of-the-GA4GH-Beacon-Protocol__Korea-genomics-seminar.md new file mode 100644 index 0000000..31c34f7 --- /dev/null +++ b/docs/news/2022-10-20-Michael-Baudis__Genomics-Data-Federation-through-Global-Alliance-for-Genomics-and-Health-Standards--Development-and-Implementation-of-the-GA4GH-Beacon-Protocol__Korea-genomics-seminar.md @@ -0,0 +1,20 @@ +--- +title: 'Genomics Data Federation through Global Alliance for Genomics and Health Standards: Development and Implementation of the GA4GH Beacon Protocol' +description: Seminar Yonsei University Medical School Seoul +template: post.html +authors: + - '@mbaudis' +date: 2022-10-20 +pdf_file_name: +links: + - "[Presentation Slides](http://info.baudisgroup.org//pdf/2022-10-20___Michael-Baudis__GA4GH-principles-and-implementation-of-the-Beacon-standard__Korea-genomics-standards.pdf)" + - "[Progenetix cancer genomics resource](http://progenetix.org)" + - "[Meeting Program](http://info.baudisgroup.org//pdf/2022-10-20-Smart-Health-Standards-Forum-Seminar-Program__Korea-genomics-standards.pdf)" + - "[Global Alliance for Genomics and Health](http://ga4gh.org)" +--- + +#### Michael Baudis + +In this Seoul meeting presentation Michael introduces the Global Alliance for Genomics and Healt and its involvement in Genomics standards development, followed by a discussion of the Beacon protocol and the role of the Progenetix resouce in its development. + +![](/img/Yonsei-sign-1024x768.png) diff --git a/docs/news/2022-10-25-Beacon-training-BY-Covid-project.md b/docs/news/2022-10-25-Beacon-training-BY-Covid-project.md new file mode 100644 index 0000000..d7e9544 --- /dev/null +++ b/docs/news/2022-10-25-Beacon-training-BY-Covid-project.md @@ -0,0 +1,35 @@ +--- +title: 'Beacon training course: How to make COVID-19 sensitive data discoverable using Beacons' +date: 2022-10-25 +template: post.html +author: + - "@AnaT-DCO" +excerpt_separator: +www_links_formatted: +category: + - events +tags: + - events +--- + + +The online workshop [**BEACON - How to make sensitive data discoverable**](https://docs.google.com/document/d/1SdWCPhmX4Pb_tF4Pw6AyrGADeWBaBMj6/edit#heading=h.gq5n092lscjf) will take place on November 2 and 3. The [European Genome-phenome Archive (EGA)](https://ega-archive.org/) Beacon Team will provide a special hands-on training session for the [BY-COVID](https://by-covid.org/) partners for "Beaconising" the datasets. + +
+ +
+ + + +One of the main bottlenecks in human data research is the lack of tools for the secure and federated data discovery of such data. Identifiable human data requires tight privacy controls, especially now with the expansion of genomics data in clinical application, such as for medical diagnostic or prognostic purposes in rare diseases or cancer. + +This workshop aims to provide knowledge and hands-on sessions about the discoverability of sensitive genomics and clinical data without jeopardising the privacy or ownership of such datasets. European Genome-phenome Archive (EGA) in collaboration with ELIXIR and the Global Alliance in Health and Genomics (GA4GH) has developed the [Beacon project](https://beacon-project.io/) to tackle this challenge. + +The training will be divided in two sessions: + +- **Session I – Introduction to Beacon: secure sharing of clinical genomics data through Beacons**. This part is oriented towards clinicians or researchers handling human data (mutations, variants, Covid-19 patients etc), genomics data (VCF files) and/or associated phenoclinic metadata and would like to understand the architecture of Beacon and map their data onto the Beacon model. +- **Session II – Implementation or deployment of Beacon on datasets**. This part is oriented towards programmers/bioinformaticians, and some command line knowledge is required. This will be a **hands-on session to deploy Beacon reference implementation (Beacon-RI) on a mock dataset or real dataset generated in session 1**. + +Find out more information about the sessions and the full program [here](https://docs.google.com/document/d/1SdWCPhmX4Pb_tF4Pw6AyrGADeWBaBMj6/edit#heading=h.gq5n092lscjf). + +The Beacon online workshop is free and open to anyone! [Registration](bit.ly/3D7kOOF) will be open until __October 31st__. diff --git a/docs/news/2022-11-16-Michael-Baudis__Beacon-Migration-and-Features__GA4GH-Connect.md b/docs/news/2022-11-16-Michael-Baudis__Beacon-Migration-and-Features__GA4GH-Connect.md new file mode 100644 index 0000000..003b9bf --- /dev/null +++ b/docs/news/2022-11-16-Michael-Baudis__Beacon-Migration-and-Features__GA4GH-Connect.md @@ -0,0 +1,22 @@ +--- +title: 'Beacon v2 - Onboarding Strategies & Feature Examples' +description: Beacon Sessions at GA4GH Connect +template: post.html +authors: + - '@mbaudis' +date: 2022-11-16 +pdf_file_name: +links: + - "[Presentation Slides](http://info.baudisgroup.org/pdf/2022-11-16___Michael-Baudis__Beacon-conversion-and-features__GA4GH-Connect.pdf)" + - "[Progenetix cancer genomics resource](http://progenetix.org)" +--- + +#### Michael Baudis + +The Beacon Sessions at GA4GH Connect November 2022 targeted the migration of existing and +implementation of new **v2** Beacons, with emphasis on the "how to get there easily" rather +than on all Beacon v2 features. + +The slides here represent the introductory and "Michael's view" part of the 2x 90min sessions, +with additional material being presented by other "beaconeers" and a lot of discussions happening. + diff --git a/docs/news/2023-01-24-ICHG-Beacon-Discovery-workshop.md b/docs/news/2023-01-24-ICHG-Beacon-Discovery-workshop.md new file mode 100644 index 0000000..6754287 --- /dev/null +++ b/docs/news/2023-01-24-ICHG-Beacon-Discovery-workshop.md @@ -0,0 +1,33 @@ +--- +title: 'Beacon v2 at the International Congress of Human Genetics with hands-on sessions on Discovery' +date: 2023-01-24 +template: post.html +author: + - "@AnaT-DCO" +--- + + +These Hands-on workshops will take place on February the 26th and 27th, in the framework of the [International Congress of Human Genetics (ICHG)](https://www.ichg2023.com/), that is being held in Cape Town from February 22 – 26. + +
+ +
+ + + +The training courses aim to provide knowledge about what is Beacon, how was it developed and which are the three different scenarios that can be faced by an institution that wants to deploy a Beacon. + +#### 26th February: "How to make sensitive data discoverable", hosted by the CINECA project + +This training course will take place within the framework of the ["Federated data analysis workshop"](https://www.cineca-project.eu/news-events-all/federated-data-analysis-workshop), organised by the CINECA project. +The workshop, provided in this occasion by Mamana Mbiyavanga (H3Africa, UCT, South Africa), Mauricio Moldes (European Genome-phenome Archive, CRG, Barcelona, Spain) and Coline Thomas (European Genome-phenome Archive, EMBL, Hixton, United Kingdom), will share with the participants three queries to try the Beacon potential. You can try one of them from your computer too: +- ["Do we see the variant A > G in position 160500074?"](https://ega-archive.org/beacon-apis/cineca/g_variants/?start=16050074&end=16050075&alternateBases=G&referenceBases=A) + +#### 27th February: “Technical implementation of GA4GH standards for data discoverability. Tools and techniques to make sensitive data discoverable”, in collaboration with the H3ABioNet +This workshop is intended for [H3Africa](https://h3africa.org/) technical members. Organised by Mamana Mbiyavanga (H3Africa, UCT, South Africa), Mauricio Moldes (European Genome-phenome Archive, CRG, Barcelona, Spain), Nicola Mulder (H3Africa, UCT, South Africa) and Sumr Panji (H3Africa, UCT, South Africa), in collaboration with the [Pan African Bioinformatics Network for the H3Africa consortium (H3ABioNet)](https://h3abionet.org/), the session will focus on the technical side of the Beacon deployment. + +#### The current Beacon V2 Reference Implementation (B2RI) +The B2RI is a free opensource software package that includes tools for lighting up a Beacon out-of-the-box. You can read more about in the [Beacon V2 Reference Implementation (B2RI) paper](https://academic.oup.com/bioinformatics/article/38/19/4656/6671215?login=false), as it is now open access to know more about this set of tools that enables federated sharing of genomic and phenotypic data. + +#### About the International Congress of Human Genetics +Hosted by the [African Society of Human Genetics (AfSHG)](https://www.afshg.org/) and the [Southern African Society for Human Genetics (SASHG)](https://sashg.org/), the International Congress of Human Genetics reunite international experts to highlight how genomic technologies are being managed to address challenges generated by the current status of Human Health and Genomics. diff --git a/docs/news/2023-05-17-Beacon-workshop-ga4gh-april-connect.md b/docs/news/2023-05-17-Beacon-workshop-ga4gh-april-connect.md new file mode 100644 index 0000000..c0d49d0 --- /dev/null +++ b/docs/news/2023-05-17-Beacon-workshop-ga4gh-april-connect.md @@ -0,0 +1,19 @@ +--- +title: 'Beacon v2 standard highlighted during the GA4GH April Connect 2023' +date: 2023-05-16 +template: post.html +author: + - "@AnaT-DCO" +--- + + +Last month Beacon was present at the [GA4GH Connect 2023](https://broadinstitute.swoogo.com/ga4ghaprilconnect23/), the working meeting to advance the GA4GH Roadmap and gather feedback on product development and needs. + +
+ +
+ + + +The GA4GH Connect 2023 was held at the Royal Society of London from 19 to 21 April 2023, gathering 188 in-person attendees and more than 200 online. Several members of the Beacon leads attended the event, participating in the session [Beacon, Phenopackets, cohorts — combining standards for discovery and exchange](https://broadinstitute.swoogo.com/ga4ghaprilconnect23/session/1409275/beacon-phenopackets-cohorts-%E2%80%94-combining-standards-for-discovery-and-exchange) that took place on April the 20th. +If you want to explore how to optimise their integration, check the recording of the session [here](https://drive.google.com/file/d/1JHaDG0ahnC1KFwezrwIsragked7Nxqha/view). diff --git a/docs/news/2023-07-17-new-co-lead.md b/docs/news/2023-07-17-new-co-lead.md new file mode 100644 index 0000000..c78e285 --- /dev/null +++ b/docs/news/2023-07-17-new-co-lead.md @@ -0,0 +1,13 @@ +--- +title: Discovery Co-Lead Appointed +description: GA4GH Discovery Work Stream welcomes new Co-Lead Nara Sobreira of Johns Hopkins Medicine +date: 2023-07-17 + +template: post.html +links: + - '[GA4GH Discovery Work Stream welcomes new Co-Lead Nara Sobreira of Johns Hopkins Medicine](https://www.ga4gh.org/news_item/ga4gh-discovery-work-stream-welcomes-new-co-lead-nara-sobreira-of-johns-hopkins-medicine/)' +--- + +Nara Lygia De Macena Sobreira, associate professor of genetic medicine at Johns Hopkins University School of Medicine, joins the GA4GH Standards Steering Committee as Discovery Work Stream Co-Lead. + +More information can be found on the GA4GH page linked below. diff --git a/docs/news/2024-03-20-Michael-GHGA-virtual-seminar.md b/docs/news/2024-03-20-Michael-GHGA-virtual-seminar.md new file mode 100644 index 0000000..8a80954 --- /dev/null +++ b/docs/news/2024-03-20-Michael-GHGA-virtual-seminar.md @@ -0,0 +1,21 @@ +--- +title: 'Federated genomic discoveries: Deploying the GA4GH Beacon protocol' +description: 'Virtual Seminar
GHGA Lecture Series' +template: post.html +authors: + - '@mbaudis' +date: 2024-03-20 +pdf_file_name: +links: +# - '[Seminar slides](/pdf/)' + - "[GHGA Event Page](https://www.ghga.de/events/detail/ghga-lecture-series-michael-baudis-virtual)" + - "[Progenetix cancer genomics resource](http://progenetix.org)" + - '[`bycon` software project](https://github.com/progenetix/bycon/)' + - "[Beacon documentation](http://docs.genomebeacons.org)" +--- + +![GHGA logo](/img/logo-ghga.webp){ style="float: right; margin: 0px 0px 10px 20px;" } +With the ever increasing amount of genomic data produced in the context of research studies, population analyses and medical diagnostics the need for access to genomic information beyond administrative or geographic boundaries has become a matter of eminent importance. +Here, the Beacon standard by the Global Alliance for Genomics an Health (GA4GH) has emerged as the major protocol for federated genomic data discovery with potential for implementation in different environments, from research nodes to international networks. + +Professor Michael Baudis will present the history and trajectory of the Beacon protocol as well as discuss it in the context of GA4GH and ELIXIR standards and potential deployment options for genomics resources, Beacon networks and aggregators. diff --git a/docs/news/2024-04-21-GA4GH-connect-Ascona.md b/docs/news/2024-04-21-GA4GH-connect-Ascona.md new file mode 100644 index 0000000..b93de7f --- /dev/null +++ b/docs/news/2024-04-21-GA4GH-connect-Ascona.md @@ -0,0 +1,22 @@ +--- +template: post.html +title: GA4GH Connect April 2024 in Ascona +description: Spring 2024 GA4GH Connect working meeting co-organized by our group +date: 2024-04-21 +links: + - '[CSF meeting calendar](https://csf.ethz.ch/csf-meetings.html)' + - '[GA4GH events](https://www.ga4gh.org/news-events/events/#)' +--- + +![elixir logo](/img/2024-GA4GH-Connect-Ascona-Logo.png){ style="width: 250px; float: right; margin: 0px 0px 10px 20px;" } +We're proud to host the next Spring GA4GH Connect meeting in April 2024 at the +_Congressi Stefano Franscini_ on the Monte Verità in Ascona. This will provide an +excellent opportunity for Swiss genomics and bioinformatics to, well, connect with +the international "genomics and health" community and projects. + + + +As a working meeting this one is invitation only; if you are a contributor or you +feel that you want to get involved with GA4GH projects please let Michael Baudis know! + + diff --git a/docs/news/index.md b/docs/news/index.md new file mode 100644 index 0000000..987007e --- /dev/null +++ b/docs/news/index.md @@ -0,0 +1,8 @@ +--- +template: post_list.html +title: Beacon News +description: Beacon Project News and Updates +path_element: news +--- + +# Beacon Project News and Updates \ No newline at end of file diff --git a/docs/pdf/2017-12-31-GA4GH-Beacon-Strategic-Meeting-Minutes-2017.pdf b/docs/pdf/2017-12-31-GA4GH-Beacon-Strategic-Meeting-Minutes-2017.pdf new file mode 100644 index 0000000..6729c4a Binary files /dev/null and b/docs/pdf/2017-12-31-GA4GH-Beacon-Strategic-Meeting-Minutes-2017.pdf differ diff --git a/docs/pdf/2018-04-04___Michael-Baudis__Beacon-Range-Matches__documentation.pdf b/docs/pdf/2018-04-04___Michael-Baudis__Beacon-Range-Matches__documentation.pdf new file mode 100644 index 0000000..f489d4d Binary files /dev/null and b/docs/pdf/2018-04-04___Michael-Baudis__Beacon-Range-Matches__documentation.pdf differ diff --git "a/docs/pdf/2019-06-17___Juha-T\303\266rnroos__ELIXIR-Beacon-Network__Beacon-WS-slides.pdf" "b/docs/pdf/2019-06-17___Juha-T\303\266rnroos__ELIXIR-Beacon-Network__Beacon-WS-slides.pdf" new file mode 100644 index 0000000..866cf6c Binary files /dev/null and "b/docs/pdf/2019-06-17___Juha-T\303\266rnroos__ELIXIR-Beacon-Network__Beacon-WS-slides.pdf" differ diff --git a/docs/pdf/2019-06-17___Michael-Baudis__Beacon-session-ELIXIR-and-GA4GH__ELIXIR-Lisbon-2019.pdf b/docs/pdf/2019-06-17___Michael-Baudis__Beacon-session-ELIXIR-and-GA4GH__ELIXIR-Lisbon-2019.pdf new file mode 100644 index 0000000..546b8b9 Binary files /dev/null and b/docs/pdf/2019-06-17___Michael-Baudis__Beacon-session-ELIXIR-and-GA4GH__ELIXIR-Lisbon-2019.pdf differ diff --git a/docs/pdf/2019-06-17___Mikael-Linden__AAI-Manual-assignment-of-affiliation__Beacon-WS-slides.pdf b/docs/pdf/2019-06-17___Mikael-Linden__AAI-Manual-assignment-of-affiliation__Beacon-WS-slides.pdf new file mode 100644 index 0000000..b7c579b Binary files /dev/null and b/docs/pdf/2019-06-17___Mikael-Linden__AAI-Manual-assignment-of-affiliation__Beacon-WS-slides.pdf differ diff --git a/docs/pdf/2020-06-10-ELIXIR-All-Hands-2020-Beacon-WS.pdf b/docs/pdf/2020-06-10-ELIXIR-All-Hands-2020-Beacon-WS.pdf new file mode 100644 index 0000000..a018a86 Binary files /dev/null and b/docs/pdf/2020-06-10-ELIXIR-All-Hands-2020-Beacon-WS.pdf differ diff --git a/docs/pdf/2021-03-02___Michael-Baudis__Beacon-structural-variants-queries.pdf b/docs/pdf/2021-03-02___Michael-Baudis__Beacon-structural-variants-queries.pdf new file mode 100644 index 0000000..4340acc Binary files /dev/null and b/docs/pdf/2021-03-02___Michael-Baudis__Beacon-structural-variants-queries.pdf differ diff --git a/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q1-2018.pdf b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q1-2018.pdf new file mode 100644 index 0000000..22c05be Binary files /dev/null and b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q1-2018.pdf differ diff --git a/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q2-2018.pdf b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q2-2018.pdf new file mode 100644 index 0000000..8c76cbc Binary files /dev/null and b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q2-2018.pdf differ diff --git a/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q3-2018.pdf b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q3-2018.pdf new file mode 100644 index 0000000..8a8e4f8 Binary files /dev/null and b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q3-2018.pdf differ diff --git a/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q4-2018.pdf b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q4-2018.pdf new file mode 100644 index 0000000..76c818e Binary files /dev/null and b/docs/pdf/GA4GH-Beacon-Strategic-Meeting-Minutes-Q4-2018.pdf differ diff --git a/docs/people/Ana-Alonso-Ayuso.md b/docs/people/Ana-Alonso-Ayuso.md new file mode 100644 index 0000000..2c52972 --- /dev/null +++ b/docs/people/Ana-Alonso-Ayuso.md @@ -0,0 +1,8 @@ +--- +title: "Ana Alonso Ayuso" +date: 2022-07-16 +email: ana.alonso@crg.eu +--- + +* Beacon documentation team member +* Centre for Genomic Regulation (CRG) diff --git a/docs/people/Anthony-Brookes.md b/docs/people/Anthony-Brookes.md new file mode 100644 index 0000000..83ca31f --- /dev/null +++ b/docs/people/Anthony-Brookes.md @@ -0,0 +1,15 @@ +--- +title: "Anthony J. Brookes" +description: Professor of Genetics | Beacon Project Co-Lead +date: 2020-01-16 +person_image_file: abrookes.png +person_github_id: antbro +person_email: ajb97@leicester.ac.uk +is_contact: true +--- + +![](/img/people/abrookes.png){: style="float: right; width: 120px; margin-top: -70px;"} + +* Department of Genetics +* University of Leicester +* Co-lead ELIXIR Beacon diff --git a/docs/people/Babita-Singh.md b/docs/people/Babita-Singh.md new file mode 100644 index 0000000..a68cbd1 --- /dev/null +++ b/docs/people/Babita-Singh.md @@ -0,0 +1,13 @@ +--- +title: "Babita Singh" +date: 2020-01-16 +person_image_file: "bsingh.jpg" +person_github_id: babisingh +person_email: babita.singh@crg.eu +--- + +* Structural Variants scout team lead +* Post Doctoral Bioinformatics Researcher +* European Genome-phenome Archive +* Centre for Genomic Regulation (CRG) +* PRBB - Barcelona diff --git a/docs/people/Bo-Gao.md b/docs/people/Bo-Gao.md new file mode 100644 index 0000000..15e9a0f --- /dev/null +++ b/docs/people/Bo-Gao.md @@ -0,0 +1,17 @@ +--- +title: "Bo Gao" +image_file: bgao.png +date: 2020-06-01 +is_gone: True +--- + +* Developer, Beacon project +* PhD in Bioinformatics +* University of Zurich + + + +#### Developer: + +* Beacon +* data compatibility & integration diff --git a/docs/people/David-Salgado.md b/docs/people/David-Salgado.md new file mode 100644 index 0000000..3d9755f --- /dev/null +++ b/docs/people/David-Salgado.md @@ -0,0 +1,9 @@ +--- +title: "David Salgado" # required +date: 2020-01-16 # optional +person_email: david.salgado@univ-amu.fr # recommended +--- + +* Structural Variants scout team +* Bioinformatics Research Engineer +* Marseille Medical Genetics Bioinformatics platform manager diff --git a/docs/people/Gary-Saunders.md b/docs/people/Gary-Saunders.md new file mode 100644 index 0000000..52ca06a --- /dev/null +++ b/docs/people/Gary-Saunders.md @@ -0,0 +1,14 @@ +--- +title: "Gary Saunders" +image_file: "garys.jpg" +date: 2021-12-31 +is_gone: True +--- + +* ELIXIR Beacon Coordinator +* ELIXIR Hub + + + +* email [gary.saunders@elixir-europe.org](mailto:elixir-europe.org) + diff --git a/docs/people/Hangjia-Zhao.md b/docs/people/Hangjia-Zhao.md new file mode 100644 index 0000000..100a16d --- /dev/null +++ b/docs/people/Hangjia-Zhao.md @@ -0,0 +1,12 @@ +--- +title: "Hangjia Zhao" +date: 2022-07-01 +--- + +* Department of Molecular Life Sciences +* University of Zurich +* Swiss Institute of Bioinformatics **SIB** + + + +* web [group](https://info.baudisgroup.org) diff --git a/docs/people/Ilkka-Lappalainen.md b/docs/people/Ilkka-Lappalainen.md new file mode 100644 index 0000000..a0a2d3e --- /dev/null +++ b/docs/people/Ilkka-Lappalainen.md @@ -0,0 +1,12 @@ +--- +title: "Ilkka Lappalainen" +image_file: "ilappalainen.jpg" +date: 2021-12-31 +is_gone: True +--- + +* ELIXIR Human Data +* ELIXIR-GA4GH partnership +* CSC - IT Center for Science +* email [ilkka.lappalainen@csc.fi](mailto:ilkka.lappalainen@csc.fi) + diff --git a/docs/people/Jordi-Rambla.md b/docs/people/Jordi-Rambla.md new file mode 100644 index 0000000..9596a56 --- /dev/null +++ b/docs/people/Jordi-Rambla.md @@ -0,0 +1,19 @@ +--- +title: "Jordi Rambla De Argila" +image_file: "jrambla.jpg" +description: European Genome-Phenome Archive | Beacon Project Co-Lead +date: 2016-01-16 +is_contact: true +--- + +![](/img/people/jrambla.jpg){: style="float: right; width: 120px; margin-top: -70px;"} + +* Champion ELIXIR Beacon Driver project (API lead) +* Center for Genome Regulation Barcelona +* European Genome-Phenome Archive + + + +* email [jordi.rambla@crg.eu](mailto:jordi.rambla@crg.eu) +* web [CRG](https://www.crg.eu/en/programmes-groups/ega-team) +* web [EGA](https://ega-archive.org/about/team) diff --git "a/docs/people/Juha-T\303\266rnroos.md" "b/docs/people/Juha-T\303\266rnroos.md" new file mode 100644 index 0000000..64faa43 --- /dev/null +++ "b/docs/people/Juha-T\303\266rnroos.md" @@ -0,0 +1,15 @@ +--- +title: "Juha Törnroos" +person_image_file: 'jtornroos.jpg' +person_github_id: juhtornr +person_homepage: https://csc.fi +person_email: juha.tornroos@csc.fi +date: 2020-06-01 +is_gone: True +--- + +* Champion ELIXIR Beacon Driver project (Network lead) +* ELIXIR Finland +* CSC + + diff --git a/docs/people/Lauren-Fromont.md b/docs/people/Lauren-Fromont.md new file mode 100644 index 0000000..37442ef --- /dev/null +++ b/docs/people/Lauren-Fromont.md @@ -0,0 +1,19 @@ +--- +title: "Lauren Fromont" +image_file: "lfromont.png" +description: Project Manager Beacon +date: 2020-01-01 +is_contact: true +--- + +![](/img/people/lfromont.png){: style="float: right; width: 120px; margin-top: -70px;"} + +* Beacon API project manager +* Center for Genome Regulation Barcelona +* European Genome-Phenome Archive + + + +* email [lauren.fromont@crg.eu](mailto:lauren.fromont@crg.eu) +* web [CRG](https://www.crg.eu/en/programmes-groups/ega-team) +* web [EGA](https://ega-archive.org/about/team) diff --git a/docs/people/Manuel_Rueda.md b/docs/people/Manuel_Rueda.md new file mode 100644 index 0000000..8e20020 --- /dev/null +++ b/docs/people/Manuel_Rueda.md @@ -0,0 +1,14 @@ +--- +title: "Manuel Rueda" +date: 2020-01-01 +--- + +* Developer - Beacon Reference Implementation +* Center for Genome Regulation Barcelona +* European Genome-Phenome Archive + + + +* email [manuel.rueda@crg.eu](mailto:manuel.rueda@crg.eu) +* web [CRG](https://www.crg.eu/en/programmes-groups/ega-team) +* web [EGA](https://ega-archive.org/about/team) diff --git a/docs/people/Marc-Fiume.md b/docs/people/Marc-Fiume.md new file mode 100644 index 0000000..986dda3 --- /dev/null +++ b/docs/people/Marc-Fiume.md @@ -0,0 +1,13 @@ +--- +title: "Marc Fiume" +date: 2021-12-31 +is_gone: True +--- + +* Developer of the original Beacon network (pre-v1) +* DNAstack + + + +* web [DNAstack](http://dnastack.com) + diff --git a/docs/people/Michael-Baudis.md b/docs/people/Michael-Baudis.md new file mode 100644 index 0000000..b9e9d5a --- /dev/null +++ b/docs/people/Michael-Baudis.md @@ -0,0 +1,21 @@ +--- +title: "Michael Baudis" +description: Professor of Bioinformatics | Beacon Project Co-Lead +date: 2016-01-16 +is_contact: true +--- + +![](/img/people/mbaudis.jpg){: style="float: right; width: 120px; margin-top: -70px;"} + +* Co-chair GA4GH Discovery Work Stream ([Beacon](http://beacon-project.io) & [SchemaBlocks](http://schemablocks.org)) +* Professor of Bioinformatics +* University of Zurich +* Swiss Institute of Bioinformatics + + + +* email [mbaudis@progenetix.org](mailto:mbaudis@progenetix.org) +* web [UZH](https://www.imls.uzh.ch/en/research/baudis.html) +* web [SIB](https://www.sib.swiss/michael-baudis-group) +* web [group](https://info.baudisgroup.org) + diff --git a/docs/people/Miro-Cupak.md b/docs/people/Miro-Cupak.md new file mode 100644 index 0000000..80bc6d4 --- /dev/null +++ b/docs/people/Miro-Cupak.md @@ -0,0 +1,14 @@ +--- +title: "Miro Cupak" +image_file: mcupak.jpg +date: 2021-12-31 +is_gone: True +--- + +* Developer +* DNAstack + + + +* web [DNAstack](http://dnastack.com) + diff --git a/docs/people/Rahel-Paloots.md b/docs/people/Rahel-Paloots.md new file mode 100644 index 0000000..b96fcd8 --- /dev/null +++ b/docs/people/Rahel-Paloots.md @@ -0,0 +1,14 @@ +--- +title: "Rahel Paloots" +date: 2021-03-15 +image_file: 'rahelp.jpg' + +--- + +* Department of Molecular Life Sciences +* University of Zurich +* Swiss Institute of Bioinformatics **SIB** + + + +* web [group](https://info.baudisgroup.org) diff --git a/docs/people/Roberto-Ariosa.md b/docs/people/Roberto-Ariosa.md new file mode 100644 index 0000000..035cea8 --- /dev/null +++ b/docs/people/Roberto-Ariosa.md @@ -0,0 +1,8 @@ +--- +title: "Roberto Ariosa Hernandez" +image_file: "rariosa.png" +date: 2021-12-31 +is_gone: True +--- + +* Former developer in ELIXIR Beacon Project diff --git a/docs/people/Sabela-de-la-Torre.md b/docs/people/Sabela-de-la-Torre.md new file mode 100644 index 0000000..3b4cf01 --- /dev/null +++ b/docs/people/Sabela-de-la-Torre.md @@ -0,0 +1,17 @@ +--- +title: "Sabela de la Torre Pernas" +image_file: "sdelatorre.jpg" +date: 2021-12-31 +is_gone: True +--- + +* Developer in ELIXIR Beacon Project +* Center for Genome Regulation Barcelona +* European Genome-Phenome Archive + + + +* email [sabela.delatorre@crg.eu](mailto:sabela.delatorre@crg.eu) +* web [CRG](https://www.crg.eu/en/programmes-groups/ega-team) +* web [EGA](https://ega-archive.org/about/team) + diff --git a/docs/people/Serena-Scollen.md b/docs/people/Serena-Scollen.md new file mode 100644 index 0000000..b4b432a --- /dev/null +++ b/docs/people/Serena-Scollen.md @@ -0,0 +1,17 @@ +--- +title: "Serena Scollen" +image_file: "sscollen.jpg" +date: 2021-12-31 +is_gone: True +--- + +* Lead, ELIXIR Human Data +* Lead, ELIXIR-GA4GH partnership +* ELIXIR Hub + + + +* email [serena.scollen@elixir-europe.org](mailto:serena.scollen@elixir-europe.org) +* web [ELIXIR](https://www.elixir-europe.org/about-us/who-we-are/hub) + + diff --git a/docs/people/Tim-Beck.md b/docs/people/Tim-Beck.md new file mode 100644 index 0000000..8ab4376 --- /dev/null +++ b/docs/people/Tim-Beck.md @@ -0,0 +1,17 @@ +--- +title: "Tim Beck" # required +date: 2020-02-10 # optional +person_image_file: tbeck.jpg # recommended +--- + + + +* UKRI Innovation Fellow at Health Data Research UK +* University of Leicester +* lead ["Beacon Filters"](https://beacon-project.io/teams/filters.html) scout team + + + +#### Links + +* email [timbeck@leicester.ac.uk](mailto:timbeck@leicester.ac.uk) diff --git a/docs/people/Ziying-Yang.md b/docs/people/Ziying-Yang.md new file mode 100644 index 0000000..f134279 --- /dev/null +++ b/docs/people/Ziying-Yang.md @@ -0,0 +1,10 @@ +--- +title: "Ziying Yang" +date: 2021-07-01 +--- + +* Department of Molecular Life Sciences +* University of Zurich +* Swiss Institute of Bioinformatics **SIB** + +* web [group](https://info.baudisgroup.org) diff --git a/docs/people/index.md b/docs/people/index.md new file mode 100644 index 0000000..34a127e --- /dev/null +++ b/docs/people/index.md @@ -0,0 +1,7 @@ +--- +template: contacts_list.html +authors: + - '@mbaudis' +--- + +# Beacon Project Contacts & Contributors diff --git a/docs/publications/2019-01-23-publication-beacon.md b/docs/publications/2019-01-23-publication-beacon.md new file mode 100644 index 0000000..8f529e1 --- /dev/null +++ b/docs/publications/2019-01-23-publication-beacon.md @@ -0,0 +1,16 @@ +--- +title: "Federated discovery and sharing of genomic data using Beacons" +template: post.html +date: 2019-01-23 +author: "@mbaudis" +links: + - '[PDF](http://info.baudisgroup.org/pdf/2019-03-04___Fiume-et-al.__Federated-discovery-and-sharing-of-genomic-data-using-Beacons__NatBiotech.pdf)' + - '[PubMed]' + - '[Nature Biotechnology]' + - '[GA4GH Press Release]' +--- + +#### Miroslav Cupak , Stephen Keenan , Jordi Rambla , Sabela de la Torre , Stephanie Dyke , Anthony Brookes , Knox Carey , David Lloyd , Peter Goodhand , Maximilian Haeussler , Michael Baudis , Heinz Stockinger , Lena Dolman , Ilkka Lappalainen , Juha Törnroos , Mikael Linden , John Spalding , Saif Ur-Rehman , Angela Page , Paul Flicek , Susheel Varma , Gary Saunders , Serena Scollen , Stephen Sherry , David Haussler , Beacon Project Team +##### Nat Biotechnol (2019), accepted 2019-01-23 + +*Abstract* The Beacon Project (github.com/ga4gh-beacon/) is a GA4GH initiative that is developing an open specification for genetic variation discovery and sharing. The project is demonstrating the willingness of international organizations to work together to define standards for, and actively engage in, genomic data sharing. In the two years since the project’s inception, over 90 Beacons have been lit by 35 organizations serving over 200 datasets. These datasets are searchable individually or in aggregate via the Beacon Network (beacon-network.org), a federated search engine across the world’s public beacons. Beacons serve large, diverse, valuable collections of genomics datasets, showing the viability of a global federated model for genomics data discovery and sharing through a simple and securable technical protocol. With continued adoption, Beacons will produce a large network of searchable genomics datasets whose global representation and accessibility will unlock potential for new genomics-derived discoveries and applications in medicine. \ No newline at end of file diff --git a/docs/publications/2021-06-30-publication-Progenetix-2021.md b/docs/publications/2021-06-30-publication-Progenetix-2021.md new file mode 100644 index 0000000..508192a --- /dev/null +++ b/docs/publications/2021-06-30-publication-Progenetix-2021.md @@ -0,0 +1,31 @@ +--- +title: "The Progenetix oncogenomic resource in 2021" +description: Article describing the current content & technical status of progenetix.org +date: 2021-06-30 +template: post.html +pdf_file_name: 2021-06-30___Huang-et-al.__The-Progenetix-oncogenomic-resource-in-2021__DATABASE.pdf +authors: + - '@mbaudis' + - '@qingyao' +links: + - '[article at OUP DATABASE](https://academic.oup.com/database/article/doi/10.1093/database/baab043/6323245)' + - '[preprint at biorXiv](https://www.biorxiv.org/content/10.1101/2021.02.15.428237v)' +--- + +#### Qingyao Huang, Paula Carrio Cordo, Bo Gao, Rahel Paloots, Michael Baudis +##### Database (Oxford). 2021 Jul 17;2021:baab043. +* doi: 10.1093/database/baab043. +* PMID: 34272855 +* PMCID: PMC8285936. +* bioRxiv. doi: https://doi.org/10.1101/2021.02.15.428237 + +![DATABASE logo](/img/logo-database-journal-300x150.png){: style="float: right; width: 150px; margin-top: -100px;"} + +**Abstract** In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. During the last few years, the fields of genomics and cancer research have seen significant advancement in terms of molecular genetics technology, disease concepts, data standard harmonization as well as data availability, in an increasingly structured and systematic manner. For the Progenetix resource, continuous data integration, curation and maintenance have resulted in the most comprehensive representation of cancer genome CNA profiling data with 138 663 (including 115 357 tumor) copy number variation (CNV) profiles. In this article, we report a 4.5-fold increase in sample number since 2013, improvements in data quality, ontology representation with a CNV landscape summary over 51 distinctive National Cancer Institute Thesaurus cancer terms as well as updates in database schemas, and data access including new web front-end and programmatic data access. + +Database URL: + +#### Notes + +The first version of the article had been posted at biorXiv on 2021-02-15. + diff --git a/docs/publications/2021-11-10-Cell-Genomics-GA4GH-VRS.md b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-VRS.md new file mode 100644 index 0000000..b813bd2 --- /dev/null +++ b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-VRS.md @@ -0,0 +1,27 @@ +--- +title: 'The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation.' +date: 2021-11-10 +template: post.html +authors: + - '@mbaudis' +links: + - [Cell Genomics] + - [bioRxiv] + - [Article PDF] + - [Preprint PDF] +--- + +#### Alex H. Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L. Cameron, Melissa Cline , Malachi Griffith, Obi L. Griffith, ..., Melissa Konopko, Heidi L. Rehm, Andrew D. Yates, Robert R. Freimuth, Reece K. Hart + +##### Wagner, Alex H. et al. Cell Genomics, Volume 1, Issue 2, 100027 [doi:10.1016/j.xgen.2021.100027](https://doi.org/10.1016/j.xgen.2021.100027) +##### bioRxiv. version 20212021.01.15.426843. (2021-01-15) + +#### Note + +![Cell Genomics logo](/img/logo-cell-genomics.png){: style="float: right; width: 150px; margin-top: -50px;"}This article was published as part of a special GA4GH edition of [Cell Genomics](https://www.cell.com/cell-genomics/issue?pii=S2666-979X(21)X0003-1). + +**Abstract** Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced “verse”), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH). + +#### Code and information + +The specification, documentation, examples, and community links are available at https://vrs.ga4gh.org/. diff --git a/docs/publications/2021-11-10-Cell-Genomics-GA4GH-federation-paper.md b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-federation-paper.md new file mode 100644 index 0000000..1eb9d61 --- /dev/null +++ b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-federation-paper.md @@ -0,0 +1,21 @@ +--- +title: "International federation of genomic medicine databases using GA4GH standards" +date: 2021-11-10 +template: post.html +authors: + - '@mbaudis' +pdf_file_name: +links: + - [Cell Genomics] + - [Article PDF] +--- + +#### Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney + +##### Thorogood, Adrian et al. Cell Genomics, Volume 1, Issue 2, 100032 [doi:10.1016/j.xgen.2021.100032](https://doi.org/10.1016/j.xgen.2021.100032) + +#### Note + +![Cell Genomics logo](/img/logo-cell-genomics.png){: style="float: right; width: 150px; margin-top: -50px;"}This article was published as part of a special GA4GH edition of [Cell Genomics](https://www.cell.com/cell-genomics/issue?pii=S2666-979X(21)X0003-1). + +**Abstract** We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach wherein data providers have the mandate and resources to share, but where data cannot move for legal or technical reasons. We recommend a federated approach to connect national genomics initiatives into a global network and precision medicine resource. diff --git a/docs/publications/2021-11-10-Cell-Genomics-GA4GH-marker-paper.md b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-marker-paper.md new file mode 100644 index 0000000..9bb46d8 --- /dev/null +++ b/docs/publications/2021-11-10-Cell-Genomics-GA4GH-marker-paper.md @@ -0,0 +1,20 @@ +--- +title: "GA4GH: International policies and standards for data sharing across genomic research and healthcare" +date: 2021-11-10 +template: post.html +authors: + - '@mbaudis' +links: + - [Cell Genomics] + - [Article PDF] +--- + +#### Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili , Daniel L. Cameron, Robert J. Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P. Chaudhari, Shu Hui Chen, J. Michael Cherry, Justina Chung, Melissa Cline, Hayley L. Clissold, Robert M. Cook-Deegan, Mélanie Courtot, ..., Peter Goodhand, Kathryn North, Ewan Birney + +##### Rehm, Heidi L. et al. Cell Genomics, Volume 1, Issue 2, 100029 [doi:10.1016/j.xgen.2021.100029](https://doi.org/10.1016/j.xgen.2021.100029) + +#### Note + +This article was published as part of a special GA4GH edition of [Cell Genomics](https://www.cell.com/cell-genomics/issue?pii=S2666-979X(21)X0003-1). + +**Abstract** The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits. diff --git a/docs/publications/2022-03-17-Beacon_paper.md b/docs/publications/2022-03-17-Beacon_paper.md new file mode 100644 index 0000000..0628279 --- /dev/null +++ b/docs/publications/2022-03-17-Beacon_paper.md @@ -0,0 +1,16 @@ +--- +title: 'Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond' +template: post.html +authors: + - '@mbaudis' + - "@rahelp" +description: Beacon v2 publication +date: 2022-03-17 +--- + +#### Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD. +##### Human Mutation. 2022 Mar 17. [PMID:35297548](https://onlinelibrary.wiley.com/doi/10.1002/humu.24369) + +**Abstract** Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. + +The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects. diff --git a/docs/publications/2022-06-15-Phenopackets-paper-NatBiotech.md b/docs/publications/2022-06-15-Phenopackets-paper-NatBiotech.md new file mode 100644 index 0000000..0bf72e3 --- /dev/null +++ b/docs/publications/2022-06-15-Phenopackets-paper-NatBiotech.md @@ -0,0 +1,16 @@ +--- +title: The GA4GH Phenopacket schema defines a computable representation of clinical data +template: post.html +authors: + - '@mbaudis' +description: Phenopackets v2 publication +date: 2022-06-15 +--- + +![Cell Genomics logo](/img/nature-biotechnology-logo.svg){: style="float: right; width: 200px; margin-top: -35px;"} +#### Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, ... , Haendel MA, Robinson PN, The GAGHPMC. +##### Nature Biotechnology. 2022;40:817-820. [LINK](https://rdcu.be/cPLaA) | [PMID:35705716](https://pubmed.ncbi.nlm.nih.gov/35705716/) + +**Abstract** Despite great strides made in the development and wide acceptance of standards for exchanging structured information about genomic variants, progress in standards for computational phenotype analysis for translational genomics has lagged behind. Phenotypic features (signs, symptoms, laboratory and imaging findings, results of physiological tests, etc.) are of high clinical importance, yet exchanging them in conjunction with genomic variation information is often overlooked or even neglected. In the clinical domain, substantial work has been dedicated to the development of computational phenotypes. Traditionally, these approaches have largely relied on rule-based methods and large sources of clinical data to identify cohorts of patients with or without a specific disease. However, they were not developed to enable deep phenotyping of abnormalities, to facilitate computational analysis of interpatient phenotypic similarity or to support computational decision support. To address this, the Global Alliance for Genomics and Health6 (GA4GH) has developed the Phenopacket schema, which supports the exchange of computable longitudinal case-level phenotypic information for diagnosis of, and research on, all types of disease, including Mendelian and complex genetic diseases, cancers and infectious diseases. A Phenopacket characterizes an individual person or biosample, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses and treatments. + +The Phenopacket software is available at . \ No newline at end of file diff --git a/docs/publications/2022-08-26-Phenopackets-practical-introduction-AdvGen.md b/docs/publications/2022-08-26-Phenopackets-practical-introduction-AdvGen.md new file mode 100644 index 0000000..404b640 --- /dev/null +++ b/docs/publications/2022-08-26-Phenopackets-practical-introduction-AdvGen.md @@ -0,0 +1,18 @@ +--- +title: "GA4GH Phenopackets: A Practical Introduction" +template: post.html +authors: + - '@mbaudis' +description: Phenopackets v2 introduction with practical examples +date: 2022-08-26 +links: + - "[Shareable article at Wiley](https://onlinelibrary.wiley.com/share/WSZCRZE29EKJIJVKYZES?target=10.1002/ggn2.202200016)" +--- + +![](/img/logo_AdvancedGenetics.png){: style="float: right; width: 200px; margin-top: -35px;"} +#### Ladewig MS, Jacobsen JO, Wagner AH, Danis D, Kassaby BE, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA and Robinson PN +##### Advanced Genetics 2022, 2200016. [LINK](https://doi.org/10.1002/ggn2.202200016) + +**Abstract** The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases. + +The Phenopacket software is available at . \ No newline at end of file diff --git a/docs/publications/2022-08-29-B2RI-software-tools-Beacon-paper.md b/docs/publications/2022-08-29-B2RI-software-tools-Beacon-paper.md new file mode 100644 index 0000000..aaab01d --- /dev/null +++ b/docs/publications/2022-08-29-B2RI-software-tools-Beacon-paper.md @@ -0,0 +1,26 @@ +--- +title: 'Beacon reference implementtaion in Bioinformatics' +date: 2022-08-29 +template: post.html +author: + - "@AnaT-DCO" +--- + +#### Beacon V2 Reference Implementation: a Toolkit to enable federated sharing of genomic and phenotypic data +##### Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla + +The Beacon team at the [European Genome-phenome Archive (EGA)](https://ega-archive.org/) presents the [**Beacon v2 Reference Implementation (B2RI)**](https://doi.org/10.1093/bioinformatics/btac568), a set of open-source software tools to enable federated sharing of genomic and phenotypic data. + +
+ +
+ + + +B2RI follows the **Beacon v2 specification**, which since April 2022 defines an open [Global Alliance for Genomics and Health (GA4GH)](https://www.ga4gh.org/) standard for secure federated discovery of genomic and phenotypic data in biomedical esearch and clinical applications. + +This toolkit will facilitate the "beaconization" of data as implementing a [Beacon v2 API](https://beacon-project.io/) can be challenging for centers that may not have allocated resources for this purpose. + +#### Links: + +- [Beacon publication in *Bioinformatics*](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac568/6671215?redirectedFrom=fulltext) diff --git a/docs/publications/index.md b/docs/publications/index.md new file mode 100644 index 0000000..9442a4b --- /dev/null +++ b/docs/publications/index.md @@ -0,0 +1,9 @@ +--- +template: publications_list.html +--- + +# Beacon and Related Publications + +This page lists publications about the Beacon protocol as well as related articles +(e.g. GA4GH standards, publications of resources using the Beacon protocol ...). + diff --git a/extras/.icons/ORCID/ORCID-iD_icon-128x128.png b/extras/.icons/ORCID/ORCID-iD_icon-128x128.png new file mode 100644 index 0000000..d73bdcb Binary files /dev/null and b/extras/.icons/ORCID/ORCID-iD_icon-128x128.png differ diff --git a/extras/.icons/ORCID/ORCID-iD_icon-16x16.png b/extras/.icons/ORCID/ORCID-iD_icon-16x16.png new file mode 100644 index 0000000..ef10914 Binary files /dev/null and b/extras/.icons/ORCID/ORCID-iD_icon-16x16.png differ diff --git a/extras/.icons/ORCID/ORCID-iD_icon-bw-128x128.png b/extras/.icons/ORCID/ORCID-iD_icon-bw-128x128.png new file mode 100644 index 0000000..b8c7732 Binary files /dev/null and b/extras/.icons/ORCID/ORCID-iD_icon-bw-128x128.png differ diff --git a/extras/.icons/ORCID/ORCID-iD_icon-bw-16x16.png b/extras/.icons/ORCID/ORCID-iD_icon-bw-16x16.png new file mode 100644 index 0000000..1c14640 Binary files /dev/null and b/extras/.icons/ORCID/ORCID-iD_icon-bw-16x16.png differ diff --git a/extras/.icons/ORCID/icon-bw.svg b/extras/.icons/ORCID/icon-bw.svg new file mode 100644 index 0000000..f348b9b --- /dev/null +++ b/extras/.icons/ORCID/icon-bw.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/extras/.icons/ORCID/icon-green.svg b/extras/.icons/ORCID/icon-green.svg new file mode 100644 index 0000000..2bddf44 --- /dev/null +++ b/extras/.icons/ORCID/icon-green.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/extras/contacts_list.html b/extras/contacts_list.html new file mode 100644 index 0000000..0ab4eb5 --- /dev/null +++ b/extras/contacts_list.html @@ -0,0 +1,44 @@ +{% extends "base.html" %} + +{% block content %} + {{ page.content }} + {% set contacts_pages = [] %} + {% for this_file in pages %} + {% set this_page = this_file.page %} + {% if this_page.meta is defined %} + {% if this_page.url.startswith(config.extra.contacts.dir) %} + + {% if not this_page.url.endswith(config.extra.contacts.dir+"/") %} + {{ contacts_pages.append( this_page ) or "" }} + {% endif %} + {% endif %} + {% endif %} + {% endfor %} + +

Project Leads and Contacts

+ + {% for page in contacts_pages %} + {% if page.meta.is_contact %} + {% include "partials/blog_contact.html" %} + {% endif %} + {% endfor %} + +

Project Members

+ + {% for page in (contacts_pages|sort(attribute="meta.date") | reverse ) %} + {% if not page.meta.is_contact %} + {% if not page.meta.is_gone %} + {% include "partials/blog_contact.html" %} + {% endif %} + {% endif %} + {% endfor %} + +

Alumni and Former Contributors

+ + {% for page in (contacts_pages|sort(attribute="meta.date") | reverse ) %} + {% if page.meta.is_gone %} + {% include "partials/blog_contact.html" %} + {% endif %} + {% endfor %} + +{% endblock %} diff --git a/extras/minutes_list.html b/extras/minutes_list.html new file mode 100644 index 0000000..b9e65f1 --- /dev/null +++ b/extras/minutes_list.html @@ -0,0 +1,36 @@ +{% extends "base.html" %} + +{% block content %} + + {{ page.content }} + + {% set news_posts = [] %} + {% for this_file in pages %} + {% set this_page = this_file.page %} + {% if this_page.meta is defined %} + {% if this_page.url.startswith(config.extra.minutes.dir) and this_page.meta.date is defined %} + {{ news_posts.append( this_page ) or "" }} + {% endif %} + {% endif %} + {% endfor %} + + {% for page in (news_posts|sort(attribute="meta.date", reverse=True))[:config.extra.blog_list_length] %} + + {% include "partials/date_separator.html" %} + +

{{ page.title }}

+ {% if page.meta.description is defined %} +
{{ page.meta.description }}
+ {% endif %} + + {{ page.content.split(config.extra.excerpt_separator, 1)[0] }} + + + {% include ".icons/octicons/arrow-right-24.svg" %} + + Continue reading + + + {% endfor %} + +{% endblock %} diff --git a/extras/news_list.html b/extras/news_list.html new file mode 100644 index 0000000..a583a1b --- /dev/null +++ b/extras/news_list.html @@ -0,0 +1,36 @@ +{% extends "base.html" %} + +{% block content %} + {{ page.content }} + {% set news_posts = [] %} + + {% for this_file in pages %} + {% set this_page = this_file.page %} + {% if this_page.meta is defined %} + {% if this_page.url.startswith(config.extra.news.dir) or this_page.url.startswith(config.extra.presentations.dir) or this_page.url.startswith(config.extra.publications.dir) %} + {% if this_page.meta.date is defined %} + {{ news_posts.append( this_page ) or "" }} + {% endif %} + {% endif %} + {% endif %} + {% endfor %} + + {% for page in (news_posts|sort(attribute="meta.date", reverse=True))[:config.extra.blog_list_length] %} + + {% include "partials/date_separator.html" %} + +

{{ page.title }}

+ {% if page.meta.description is defined %} +
{{ page.meta.description }}
+ {% endif %} + + {{ page.content.split(config.extra.excerpt_separator, 1)[0] }} + + + {% include ".icons/octicons/arrow-right-24.svg" %} + + Continue reading + + + {% endfor %} +{% endblock %} diff --git a/extras/partials/blog_contact.html b/extras/partials/blog_contact.html new file mode 100644 index 0000000..6800c1b --- /dev/null +++ b/extras/partials/blog_contact.html @@ -0,0 +1,18 @@ +

{{ page.title }}

+{% if page.meta.description is defined %} +
{{ page.meta.description }}
+{% endif %} + +{{ page.content.split(config.extra.excerpt_separator, 1)[0] }} + +{% if page.meta.excerpt_link is defined %} + + External Page {% include ".icons/octicons/link-24.svg" %} + +{% else %} + + Contact Details {% include ".icons/octicons/kebab-horizontal-24.svg" %} + +
+
+{% endif %} \ No newline at end of file diff --git a/extras/partials/blog_social.html b/extras/partials/blog_social.html new file mode 100644 index 0000000..cad4111 --- /dev/null +++ b/extras/partials/blog_social.html @@ -0,0 +1,17 @@ +{% if config.extra.social %} + {% set ns = namespace() %} + {% for social in config.extra.social %} + {% set title = social.name %} + {% if not title and "//" in social.link %} + {% set _,url = social.link.split("//") %} + {% set title = url.split("/")[0] %} + {% endif %} + {% if ns.line_break is defined %} + {{ ns.line_break }} + {% endif %} + + {% include ".icons/" ~ social.icon ~ ".svg" %} + + {% set ns.line_break = " · " %} + {% endfor %} +{% endif %} \ No newline at end of file diff --git a/extras/partials/date_separator.html b/extras/partials/date_separator.html new file mode 100644 index 0000000..083cd78 --- /dev/null +++ b/extras/partials/date_separator.html @@ -0,0 +1,10 @@ + diff --git a/extras/partials/post_preview.html b/extras/partials/post_preview.html new file mode 100644 index 0000000..c8bd474 --- /dev/null +++ b/extras/partials/post_preview.html @@ -0,0 +1,15 @@ +
+{% include "partials/date_separator.html" %} +

{{ post_page.title }}

+ {% if post_page.meta.description is defined %} +
{{ post_page.meta.description }}
+ {% endif %} + + {{ post_page.content.split(config.extra.excerpt_separator, 1)[0] }} + + + {% include ".icons/octicons/arrow-right-24.svg" %} + + Continue reading + +
diff --git a/extras/post.html b/extras/post.html new file mode 100644 index 0000000..02641b8 --- /dev/null +++ b/extras/post.html @@ -0,0 +1,38 @@ +{% extends "base.html" %} + +{% block content %} +

{{ page.title }}

+

+ {{ page.meta.description }} +

+ {{ page.content }} + {% if page.meta.pdf_file_name or page.meta.links %} +

Links

+ +
    + {% if page.meta.pdf_file_name %} + {% set pdfLab = "PDF" %} + {% if ".pdf" in page.meta.pdf_file_name %} +
  • Download {{ pdfLab }} {% include ".icons/fontawesome/regular/file-pdf.svg" %}
    • + {% endif %} + {% endif %} + {% if page.meta.links %} + {% if page.meta.links|length > 0 %} + {% for link in page.meta.links %} + {% if link.startswith('{{ link }} + {% elif link.startswith('[') %} + {% set label = link.split('](', 1)[0] | replace('[', '') %} + {% set target = link.split('](', 1)[1] | replace(')', '') %} +
  • [{{label}}]
    • + {% else %} +
  • [LINK]
    • + {% endif %} + {% endfor %} + {% endif %} + {% endif %} + {% endif %} +
+ {% set post_page = page %} + {% include "partials/date_separator.html" %} +{% endblock %} diff --git a/extras/post_list.html b/extras/post_list.html new file mode 100644 index 0000000..0d910ef --- /dev/null +++ b/extras/post_list.html @@ -0,0 +1,67 @@ +{% extends "base.html" %} + +-------------------------------------------------------------------------------- +The list page will process individual pages which: + +* have a match of the list page's `page.meta.path_element` in their url + - alternatively the last path element of the calling page will be used + - this is accessed through `page.url.split('/')[-2]` since the `-1` would + be the page file name or empty (index page) +* have a date in their `meta` +* have "post.html" in their `meta.template` + +-------------------------------------------------------------------------------- + +{% block content %} + + {{ page.content }} + {% set path_element = page.url.split('/')[-2] %} + {% if page.meta.path_element is defined %} + {% set path_element = page.meta.path_element %} + {% endif %} + + {% set today = build_date_utc.strftime('%Y%m%d') | int %} + + {% set future_posts = [] %} + {% set news_posts = [] %} + + {% for this_file in pages %} + {% set this_page = this_file.page %} + {% if this_page.meta is defined %} + {% if this_page.meta.date is defined and this_page.meta.template is defined %} + {% if path_element in this_page.url and "post" in this_page.meta.template %} + {% set page_date = this_page.meta.date.strftime('%Y%m%d') | int %} + {% if page_date >= today %} + {{ future_posts.append( this_page ) or "" }} + {% else %} + {{ news_posts.append( this_page ) or "" }} + {% endif %} + {% endif %} + {% endif %} + {% endif %} + {% endfor %} + + + + {% if future_posts|length > 0 %} +

Upcoming

+ {% for post_page in (future_posts |sort(attribute="meta.date", reverse=False))[:config.extra.blog_list_length] %} + {% include "partials/post_preview.html" %} + {% endfor %} + {% endif %} + + + + {% if news_posts|length > 0 %} +

Recent

+ {% for post_page in (news_posts|sort(attribute="meta.date", reverse=True))[:config.extra.blog_list_length] %} + {% include "partials/post_preview.html" %} + {% endfor %} + {% endif %} + +{% endblock %} diff --git a/extras/publications_list.html b/extras/publications_list.html new file mode 100644 index 0000000..6779995 --- /dev/null +++ b/extras/publications_list.html @@ -0,0 +1,35 @@ +{% extends "base.html" %} + +{% block content %} + + {{ page.content }} + + {% set news_posts = [] %} + {% for this_file in pages %} + {% set this_page = this_file.page %} + {% if this_page.meta is defined %} + {% if this_page.url.startswith(config.extra.publications.dir) and this_page.meta.date is defined %} + {{ news_posts.append( this_page ) or "" }} + {% endif %} + {% endif %} + {% endfor %} + + {% for page in (news_posts|sort(attribute="meta.date", reverse=True))[:config.extra.blog_list_length] %} + {% include "partials/date_separator.html" %} + +

{{ page.title }}

+ {% if page.meta.description is defined %} +
{{ page.meta.description }}
+ {% endif %} + + {{ page.content.split(config.extra.excerpt_separator, 1)[0] }} + + + {% include ".icons/octicons/arrow-right-24.svg" %} + + Continue reading + + + {% endfor %} + +{% endblock %} diff --git a/mkdocs.yaml b/mkdocs.yaml new file mode 100644 index 0000000..683006a --- /dev/null +++ b/mkdocs.yaml @@ -0,0 +1,106 @@ +site_name: Beacon v2 Project Website +site_description: 'Website for Beacon v2' +site_author: 'Michael Baudis, Laureen Fromont & Beacon Developers' +copyright: '© Copyright 2021-2023, Beacon v2 Documentation Contributors' +repo_name: 'ga4gh-beacon.github.io' +repo_url: https://github.com/ga4gh-beacon/ga4gh-beacon.github.io +edit_uri: edit/main/docs/ + +repo_icon: " [:fontawesome-brands-github:](https://github.com/ga4gh-beacon/ga4gh-beacon.github.io/tree/main/docs)" +extra_css: [css/theme_overrides.css] + +plugins: + - search + - macros + - mermaid2 + +markdown_extensions: + - toc: + toc_depth: 2-3 + permalink: true + - admonition + - attr_list + - footnotes + - md_in_html + - pymdownx.critic + - pymdownx.caret + - pymdownx.details + - pymdownx.keys + - pymdownx.mark + - pymdownx.tilde + - pymdownx.saneheaders + - pymdownx.superfences + - pymdownx.magiclink: + hide_protocol: true + - pymdownx.tabbed: + alternate_style: true + - pymdownx.tasklist: + custom_checkbox: true + - tables + - mdx_gh_links: + user: ga4gh-beacon + repo: beacon-v2 + - pymdownx.emoji: + emoji_index: !!python/name:materialx.emoji.twemoji + emoji_generator: !!python/name:materialx.emoji.to_svg + - pymdownx.superfences: + custom_fences: + - name: mermaid + class: mermaid + format: !!python/name:mermaid2.fence_mermaid + +nav: + - Introduction: / + - News: news + - FAQ: FAQ + - Publications: publications + - People: people + - Protocols & Minutes: minutes + - External Links: + - Beacon API Documentation ↗: http://docs.genomebeacons.org + - Github Repositories ↗: https://github.com/ga4gh-beacon/ + - Beacon v2 service registry ↗: https://ga4gh-approval-service-registry.ega-archive.org + - ELIXIR BeaconNetwork ↗: https://beacon-network.elixir-europe.org + - Beacon @ ELIXIR ↗: http://www.elixir-europe.org/about-us/implementation-studies/beacons + - '
Progenetix Beacon+ ↗
': https://progenetix.org/search/ + - GA4GH ↗: http://ga4gh.org + - GA4GH::SchemaBlocks ↗: http://schemablocks.org + - GA4GH::Discovery ↗: http://ga4gh-discovery.github.io + +theme: + custom_dir: extras + name: material + palette: + primary: teal + logo: img/GA-logo.png + favicon: img/ga4gh_circle.ico + icon: + repo: fontawesome/brands/github-alt + features: + - content.tabs.link + - search.highlight + - search.share + - navigation.instant + - navigation.tracking + - navigation.sections + - toc.integrate + +# Options +extra: + excerpt_separator: + blog_list_length: 100 + news: + dir: news + minutes: + dir: minutes + publications: + dir: publications + contacts: + dir: people + social: + - icon: fontawesome/brands/twitter + link: https://twitter.com/genomebeacons + - icon: fontawesome/brands/github + link: https://github.com/ga4gh-beacon + +# https://pypi.org/project/mkdocs-with-pdf/ for more PDF configuration ...