Pages tagged "bycon"

Beacon v2: Path Examples

The Beacon v2 protocol uses a REST path structure for consistant data access.

The Beacon+ implementation - developed oin the bycon project implements an expanding set of those Beacon v2 paths for the Progenetix resource.

2021-04-23: 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: 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 ...

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 ...

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 ...

Clustering

The Progenetix CNV visualization includes some default clustering for sample CNV profiles and collation CNV frequencies.

Michael Baudis 2021-06-22: more ...

Genomic Intervals and Binning

The resource uses a standard CNV binning model with (in GRCh38) 3102 intervals of 1MB default size. Binned genome CNV values are available for all individual analyses (genome profiles), indicating the interval’s involvement in one or more CNV events, separated for gains and losses.

Additionally, for all all collations (e.g. profiles of a tumor type, or from the same publication), pre-computed interval CNV frequencies are available Alternatively, interval frequency maps can be generated on the fly from e.g. search results.

Michael Baudis 2021-06-22: 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

  • 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: 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: IntervalFrequencies

This service provides access to binned CNV frequency information of data “collations” in the Progenetix project databases. A typical use would be the retrieval of data for a single collation, e.g. by its identifier (e.g. NCIT:C7376, PMID:22824167, pgxcohort-TCGAcancers).

2021-05-06: 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 ...

Tools: pgxRpi, an R Library to Access Progenetix Data

pgxRpi is an API wrapper package to access data from Progenetix database. You can use it to

2021-09-16: more ...