Pages tagged "code"

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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.

Examples

The first examples are for “standard” Beacon (v1) queries and may become deprecated/remapped during the ongoing development.

2021-04-16: more ...

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Filter Documentation

For non-genomic parameters, the Progenetix resource uses a query syntax based around the Beacon v2 “filters” concept.

@qingyao 2021-04-14: more ...

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Legacy API Documentation

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

2020-06-20: more ...

Ontology Term Contributions

The group is an active contributor to several public ontologies, both through mapping efforts (ICDOntologies, icdot2uberon) and by requesting terms relevant for genomic and metadata e.g. for EFO.

@mbaudis 2021-01-14: more ...

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Progenetix File Formats

Progenetix Segment Files .pgxseg

Progenetix uses a variation of a standard tab-separated columnar text file such as produced by array or sequencing CNV software, with an optional metadata header for e.g. plot or grouping instructions.

Wile the first edition only was geared towards sample-linked segment annotations, a variation is now being provided for CNV frequencies.

@mbaudis 2021-04-16: more ...

Progenetix Image Formats

The standard format for (plot-)images generated on Progenetix is Scalable Vector Graphics (SVG). As the name implies, SVG is scalable, i.e. images can be scaled up without loosing quality or expanding in storage size. However, some of teh generated images use also embedded rastered components which will deteriorate during scaling - this is e.g. the case for array probe plots.

According to Wikipedia

All major modern web browsers—including Mozilla Firefox, Internet Explorer, Google Chrome, Opera, Safari, and Microsoft Edge—have SVG rendering support

On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.

@mbaudis 2021-02-12: 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 ...

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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.

2021-04-16: 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 ...

Structure of geographic data

Note: This page has been uppdated to reflect the new GeoJSON complete schema version from January 2021.

We have now a new standard structure for geo_location objects, which has been implemented for biosamples and publications.

@mbaudis 2021-01-25: more ...

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byconplus.md Python Code Documentation

2020-10-20: more ...