Pages tagged "Beacon"

Services: collations

  • Documentation Link
  • Source Link

  • provides access to information about data “subsets” in the Progenetix project databases
    • typically aggregations of samples sharing an ontology code (e.g. NCIT) or external identifier (e.g. PMID)

2020-10-20: more ...

Services: Schemas

Examples

2020-10-20: more ...

Services: Geolocations

geolocations

This service provides geographic location mapping for cities above 25’000 inhabitants (~22750 cities), through either:

  • matching of the (start-anchored) name
  • providing GeoJSON compatible parameters:
    • geolongitude
    • geolatitude
    • geodistance
      • optional, in meters; a default of 10’000m (10km) is provided
      • can be used for e.g. retrieving all places (or data from places if used with publication or sample searches) in an approximate region (e.g. for Europe using 2500000 around Heidelberg…)

2020-10-20: more ...

Services: Genespans

  • Documentation Link
  • Source Link

  • genomic mappings of gene coordinats
  • initially limited to GRCh38 and overall CDS extension
  • responds to (start-anchored) text input of HUGO gene symbols using the geneId parameter
  • returns a list of matching gene objects (see below under Response Formats)
Examples

2020-10-20: more ...

Services: Cytomapper

cytomapper Service

This script parses either:

  • a properly formatted cytoband annotation (assemblyId, cytoBands)
    • “8”, “9p11q21”, “8q”, “1p12qter”
  • a concatenated chroBases parameter
    • 7:23028447-45000000
    • X:99202660

2020-10-20: more ...

Progenetix at GA4GH 2020 Plenary

GA4GH 8th Plenary

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.

2020-09-30: more ...

Progenetix Source Code

With exception of some utility scripts and external dependencies (e.g. MongoDB) the following projects provide the vast majority of the software (from database interaction to website) behind Progenetix and Beacon+.

  • bycon
    • Python based service based on the GA4GH Beacon protocol
    • software powering the Progenetix resource
    • Beacon+ implementation(s) use the same code base
  • progenetix-web
    • website for Progenetix and its Beacon+ implementations
    • provides Beacon interfaces for the bycon server, as well as other Progenetix sevices (e.g. the publications repository)
    • implemented as React / Next.js project
  • PGX
    • a Perl ibrary providing utility functions for Progenetix CNV data
    • used for data transformation, e.g. binning of segmental CNV data
    • main purpose now in providing the various plots (CNV histograms, clusterd CNV profiles, array plots)

Additional Projects

  • schemas
    • Progenetix data schemas
    • represent an accessible/stable version of the schemas used in bycon
  • icdot2uberon
    • mappings between ICD-O 3 topographies and UBERON anatomical sites
  • ICDOntologies
    • mappings between ICD-O 3 morphology / topography pairs and NCIt neoplasm core cancer ontology

2021-02-06: 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

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:

2020-09-30: more ...

Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project provides a combination of a Beacon-protocol based API with additional API services, used as backend and middleware for the Progenetix resource.

bycon has been developed to support Beacon protocol development following earlier implementations of Beacon+ (“beaconPlus”) with now deprected Perl libraries. The work tightly integrates with the ELIXIR Beacon project.

2021-04-16: more ...

Bycon Services

The bycon environment provides a number of data services which make use of resources in the Progenetix environment. Please refer to their specific documentation.

Note: As of 2021-04-07 there are some changes - typical Beacon endpoints such as biosamples have been moved to the /beacon/__service-name__ path:

services.py and URL Mapping

The service URL format progenetix.org/services/__service-name__?parameter=value is a shorthand for progenetix.org/cgi-bin/bycon/services/__service-name__.py?parameter=value.

2020-10-20: more ...

Beaconplus Data / Query Model

The Progenetix / Beaconplus query model utilises the GA4GH core data model for genomic and (biomedical, procedural) queries and data delivery.

2020-05-26: more ...

BeaconPlus in ELIXIR Beacon Network

The Beacon+ implementation of the GA4GH Beacon protocol has become a part of the ELIXIR Beacon Network, an expanding Beacon service to query multiple Beacon resources and aggregate their query results.

@mbaudis 2020-01-20: more ...

BeaconPlus Changes

This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.

2021-04-30: Closing in on Beacon v2

As one of the drivers of the Beacon protocol and to drive the Beacon v2 protocol process we have now started the documentation of Beacon v2 endpoints which are supported in Progenetix as part of the implementations-v2 project:

2021-04-30: more ...

Beacon: Variants

This endpoint is mostly aimed at providing variants Beacon functionality. The app uses the same query processing mechanism as the other bycon applications.

2021-04-16: more ...

Beacon: Biosamples

This endpoint is mostly aimed at providing biosamples handover functionality. However, the app uses the same query processing mechanism as the main byconplus application.

2021-04-16: more ...

Beacon+ and Progenetix Queries by Gene Symbol

Gene Symbol Selector ExampleWe have introduced a simple option to search directly by Gene Symbol, which will match to any genomic variant with partial overlap to the specified gene. This works by expanding the Gene Symbol (e.g. TP53, CDKN2A …) into a range query for its genomic coordinates (maximum CDR).

Such queries - which would e.g. return all whole-chromosome CNV events covering the gene of interest, too - should be narrowed by providing e.g. Variant Type and Maximum Size (e.g. 2000000) values.

@mbaudis 2021-02-22: more ...

API: Beacon Paths Updates

For testing the rapidly evolving Beacon v2 API, we have now implemented more paths/endpoints which mostly conform to the brand new & still “flexible” v2.0.0-draft.4 version. Please check the documentation and examples.

@mbaudis 2021-07-02: more ...