Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond

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

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.

@rahelp 2022-03-17: more ...


The GA4GH Beacon Protocol at BC2

A Standardized Format for Federated Genomic Data Exchange

Michael Baudis

BC2 Basel 2021

Session “Federating computational analyses with GA4GH standards”

BC2 logoDuring 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.

2021-09-13: more ...

A cancer genomics reference resource and implementation toolkit around GA4GH standards

Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis

ESHG 2021

ESHG LogoThis poster presentation at the European Society of Human Genetics meeting 2021 discusses the integration and development of GA4GH standards by the Progenetix oncogenomics resource.

2021-08-31: more ...

hCNV Community and Implementation Studies

Michael Baudis

ELIXIR All Hands 2021 Human Data Day

At the Human Data Day Michael presents a very brief overview of the ending and upcoming ELIXIR hCNV implementation studies.

2021-06-11: more ...

hCNV data and the Progenetix Beacon

Michael Baudis

ELIXIR All Hands 2021

This presentation gives a brief overview of the use of the Progenetix resource to test and implement a genomics reference resource using the emerging Beacon v2 protocol.

2021-06-08: more ...

ELIXIR Beacon Project

Concepts | Status | History | Outlook

Michael Baudis

Research Data Alliance - RDA Virtual Plenary 17

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).

2021-04-20: more ...

GA4GH Connect - Beacon v2 and SchemaBlocks

GA4GH Connect 2020

Michael Baudis

Beacon v2 Structural Variants [slides]
SchemaBlocks {S}[B] [slides]

2021-03-02: more ...

Copy number variant heterogeneity among cancer types reflects inconsistent concordance with diagnostic classifications

Paula Carrio Cordo and Michael Baudis

bioRxiv. doi: https://doi.org/10.1101/2021.03.01.433348

This article explores the correlation between subsets of cancer entities, grouped by their somatic CNV patterns, and levels of diagnostic classification systems.

2021-03-01: more ...


Welcome to Ziying

Today Ziying Yang arrived as a new member of the baudisgroup.

Welcome Ziying!

mbaudis 2020-10-26: more ...

GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange

GA4GH 8th Plenary

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

2020-09-30: more ...

Swissnex SF: Laura & Michael Baudis - Life & Family

Originally planned for their stays at UCB and LBNL, Laura & Michael were interviewed by Tabea Stoeckel from swissnex San Francisco about their stay in the Bay Area and their research & family life as internationally active scientists.

mbaudis 2020-05-06: more ...

Michael @ BBOP

Between 2020-02-08 and 2020-04-10, Michael has switched his office for a desk at the Berkeley Bioinformatics Open-source Projects (BBOP) where he will work with members of Chris Mungall’s team on projects related to biomedical ontologies, data standards and the analysis of cancer genome data.

mbaudis 2020-02-08: more ...

ELIXIR Open Day - Wellcome Trust Genome Campus Hinxton

ELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities

Michael Baudis

2020-02-06: more ...



Public site removed from Github

The info.baudisgroup.org site noe resides on Dropbox and is locally created/updated.

mbaudis 2018-06-09: more ...