Pages tagged "Python"

2021

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 ...

2020

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 ...

Services: Schemas

Examples

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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

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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

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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: 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 ...

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 ...