Pages tagged "services"

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 ...

Legacy API Documentation

The current implementation of the Progenetix APIs uses 2 URL endpoints:

Legacy API

  • progenetix.org/api/ has been deprecated
    • based on the original Perl libraries
    • stepwise deprecation in favour of services
    • documentation removed

2020-06-20: 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 ...

Progenetix project Namespace

Since July 2017, the Progenetix project has a registered namespace prefix at EBI’s identifiers.org.

This prefix will gradually be used to implement a REST syntax with stable endpoints for all Progenetix resources (e.g. arraymap.org, cnvar.org …), as well as to guide to our code mapping resources.

Michael Baudis 2018-05-10: more ...

Services: Cytomapper

cytomapper Service

This services parses either:

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

While the return object is JSON by default, specifying text=1, together with the cytoBands or chroBases parameter will return the text version of the opposite.

There is a fallback to GRCh38 if no assembly is being provided.

The cytobands and chrobases parameters can be used for running the script on the command line (see examples below). Please be aware of the “chrobases” (command line) versus “chroBases” (cgi) use.

Examples

Response

As in other bycon services, API responses are in JSON format with the main content being contained in the data field.

As of v2020-09-29, the ChromosomeLocation response is compatible to the GA4GH VRS standard. The GenomicLocation object is a wrapper around a VRS SimpleInterval.

{
  "data": {
    "ChromosomeLocation": {
      "chr": "8",
      "interval": {
        "end": "q24.13",
        "start": "q24.11",
        "type": "CytobandInterval"
      },
      "species_id": "taxonomy:9606",
      "type": "ChromosomeLocation"
    },
    "GenomicLocation": {
      "chr": "8",
      "interval": {
        "end": 127300000,
        "start": 117700000,
        "type": "SimpleInterval"
      },
      "species_id": "taxonomy:9606",
      "type": "GenomicLocation"
    },
    "info": {
      "bandList": [
        "8q24.11",
        "8q24.12",
        "8q24.13"
      ],
      "chroBases": "8:117700000-127300000",
      "cytoBands": "8q24.11q24.13",
      "referenceName": "8",
      "size": 9600000
    }
  },
  "errors": [],
  "parameters": {
    "assemblyId": "NCBI36.1",
    "cytoBands": "8q24.1"
  },
  "response_type": "cytomapper",
  "warnings": []
}

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: 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 ...

pgx namespace and persistant identifiers

While the pgx prefix had been registered in 2017 with identifiers.org we recently changed the resolver and target mappings on the Progenetix server. This went hand-in-hand with the generation of unique & persistant identifiers for the main data items.

2020-10-09: more ...