Pages tagged "Python"

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.

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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.

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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: 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: 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…)

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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.

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Services: Publications

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

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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)

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Services: dbstats

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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

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