Pages tagged "Beacon"

Beacon - Discovery Services for Genomic Data

The Beacon protocol defines an open standard for genomics data discovery, developed by members of the Global Alliance for Genomics & Health. Since 2016, the Beacon protocols is being developed through the ELIXIR Beacon project as a GA4GH driver project.

2016-07-01: more ...

Beacon Variants in UCSC Browser

The response element of the Beacon+ interface now contains a link for displaying the matched variants e.g. of e.g. a CNV query in the UCSC genome browser.

@mbaudis 2019-10-14: 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 ...

Coordinate use for Beacon Queries

more ...

BeaconPlus Changes

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

2020-10-01: 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 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 ...

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.

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 ...

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

The bycon project provides implementation of middleware & server for the Beacon API, for use with the Progenetix (i.e. GA4GH object model derived, MongoDB implemented) environment. In this project, the byconplus.py application and its libraries provide the necessary functionality to run a Beacon instance, provided the given environment.

Future versions will add methods to set-up necessary database structures from various variant and metadata files. Please contact us for further information.

2020-10-20: 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 ...

Progenetix - A cancer genomics reference resource around GA4GH standards

GA4GH 8th Plenary

Michael Baudis

2020-09-30: more ...

Progenetix Projects Code

  • 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 ...

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-next
    • 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 ...

Services: 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.

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 ...

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: 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: Ontolgymaps

The ontologymaps service provides equivalency mapping between ICD-O and other classification systems, notably NCIt. The mappings are represented in the ICDOntologies project and accessible trough a front-end in the Progenetix Services area.

2020-10-20: more ...

Services: Phenopackets

The phenopackets service is usually called as a handover endpoint, to wrap & deliver penopackets from samples & variants … matched by a Beacon query.

2020-10-20: more ...

Services: Publications

The publications service serves as backend API for the display of genome screening publications through the Progenetix Publications DB.

2020-10-20: more ...

Services: Schemas
Examples

2020-10-20: more ...

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: dbstats

2020-10-20: more ...

Services: deliveries

  • a simple app which only provides data deliveries from handover objects
  • requires a (locally existing) accessid parameter
  • optionally limiting the response content by supplying a deliveryKeys list (can be comma-concatenated or multiple times parameter)

2020-10-20: more ...

Services: ids

The ids service forwards compatible, prefixed ids (see config/ids.yaml) to specific website endpoints. There is no check if the id exists; this is left to the web page handling itself. Stacking with the “pgx:” prefix is allowed.

2020-10-20: more ...

byconplus.md Python Code Documentation

2020-10-20: more ...