Poster ID
P-04
Poster Title
The Progenetix oncogenomic CNV reference database as example for federation-enabled data resources built around the GA4GH Beacon protocol
Authors
Worawich Phornsiricharoenphant
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Anaïs Mottaz
Haute Ecole Spécialisée de Suisse Occidentale, Geneva
Swiss Institute of Bioinformatics, Geneva, Switzerland
Jiahui Yu
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
Patrick Ruch
Haute Ecole Spécialisée de Suisse Occidentale, Geneva
Swiss Institute of Bioinformatics, Geneva, Switzerland
Michael Baudis
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Anaïs Mottaz
Haute Ecole Spécialisée de Suisse Occidentale, Geneva
Swiss Institute of Bioinformatics, Geneva, Switzerland
Jiahui Yu
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
Patrick Ruch
Haute Ecole Spécialisée de Suisse Occidentale, Geneva
Swiss Institute of Bioinformatics, Geneva, Switzerland
Michael Baudis
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
Abstract
The current production version of the Progenetix oncogenomic reference resource (progenetix.org) provides genomic copy number variation (CNV) profiles and associated pheno-clinical data from more than 240’000 individual samples, curated from more than 1’600 publications reference projects and resources such as TCGA, GENIE or cBioPortal. The data in Progenetix as well as some other resources (e.g. cancercelllines.org) is accessible through the Beacon API (v2.n) and supports the Beacon data model as well as Beacon handover data delivery.
Progenetix' Beacon support – developed through the Python based `bycon` package - has been instrumental in developing the protocol in a matter of "implementation driven design" and the resource had been one of the demonstrators in the Beacon v2 approval process. In ongoing work, design proposals for advancement of the Beacon protocol towards its next iterations are directly tested through rapid, iterative integration into the `bycon` stack, against the full Progenetix data content. Here, the current focus is in the design and implementation of "aggregation" features - i.e. single or multi-dimensional, static and dynamically generated data summaries - but especially in advancing genomic variant queries and representation based on the GA4GH VRS and CatVRS standards. For the ongoing development Swiss GA4GH members have been contributors through VRS evaluation and testing as well as through providing expertise for biomedical data annotations, vocabularies and resource retrieval, but also in the presentation and evaluation of those standards in the Swiss bioinformatics community.
Here we will inform about the status and future directions of Progenetix, related resources, the technologies underlying their implementation as well as current and future aspects of the Beacon protocol, especially its use for data delivery, resource content summaries and ongoing GA4GH standards integration, including work on a VRS-aligned Variant Query Standard (VQS).
Links:
· Progenetix https://progenetix.org
· bycon https://codeberg.org/progenetix/bycon
Progenetix' Beacon support – developed through the Python based `bycon` package - has been instrumental in developing the protocol in a matter of "implementation driven design" and the resource had been one of the demonstrators in the Beacon v2 approval process. In ongoing work, design proposals for advancement of the Beacon protocol towards its next iterations are directly tested through rapid, iterative integration into the `bycon` stack, against the full Progenetix data content. Here, the current focus is in the design and implementation of "aggregation" features - i.e. single or multi-dimensional, static and dynamically generated data summaries - but especially in advancing genomic variant queries and representation based on the GA4GH VRS and CatVRS standards. For the ongoing development Swiss GA4GH members have been contributors through VRS evaluation and testing as well as through providing expertise for biomedical data annotations, vocabularies and resource retrieval, but also in the presentation and evaluation of those standards in the Swiss bioinformatics community.
Here we will inform about the status and future directions of Progenetix, related resources, the technologies underlying their implementation as well as current and future aspects of the Beacon protocol, especially its use for data delivery, resource content summaries and ongoing GA4GH standards integration, including work on a VRS-aligned Variant Query Standard (VQS).
Links:
· Progenetix https://progenetix.org
· bycon https://codeberg.org/progenetix/bycon