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Change Log

This page lists changes for the Beacon+ implementation of the "Beacon" genomics API, as well as related updates for the Progenetix front-end.

2024-06-18 Switching ontology use for

While we had previously used the PATO terms for genotypic sex (PATO:0020001 or PATO:0020002) we have now recoded those to "NCIT:C16576": "female" and "NCIT:C20197": "male" to stay in line with the Beacon v2 documentation examples (which will probably drive implementations).

    label: Genotypic Sex
    infoText: |
      Genotypic sex of the individual.
    defaultValue: ""
    isHidden: true
      - value: ""
        label: "(no selection)"
      - value: NCIT:C16576
        label: female
      - value: NCIT:C20197
        label: male

2024-02-24 Adding analysis_operation to analyses

This new parameter with its (so far) values

  • "":"EDAM:operation_3961", "analysis_operation.label":"Copy number variation detection"
  • "":"EDAM:operation_3227", "analysis_operation.label":"Variant Calling"

... allows now the filtering of analyses based on the type of genomic profiling performed.

2023-06-12: Some schema changes...

Schema changes are now extensively tracked in

The latest changes of the database schemas involve e.g.:

  • several field changes in biosamples, to align w/ main Beacon v2 default schema:
  • sampledTissue => sampleOriginDetail
  • description => notes
  • timeOfCollection.age => collectionMoment

2022-12-22: Various API fixes & extensions

  • the genespans responses contain now a cytobands parameter (i.e. the cytogenetic mapping of the gene's locus)
  • FIXED: the beacon response meta now has the standard receivedRequestSummary.requestParameters instead of before receivedRequestSummary.variantPars

2022-01-17: Term-specific queries

includeDescendantTerms selectorSo far (and still as standard), any selected filter will also include matches on its child terms; i.e. "NCIT:C3052 - Digestive System Neoplasm" will include results from gastric, esophagus, colon ... cancer. Here we introduce a selector for the search panel to make use of the Beacon v2 filters includeDescendantTerms pragma, which can be set to false if one only wants to query for the term itself and exclude any child terms from the matching.

Please be aware that this can only be applied globally and will affect all filtering terms used in a query. More information is available in the Filtering Terms documentation.

2022-01-17: Introducing variant_state classes for CNVs

More information can be found in the description of ontology use for CNVs.

2022-01-10: BUG FIX Frequency Maps

Pre-computed Progenetix CNV frequency histograms (e.g. for NCIT codes) are based samples from all child terms; e.g. NCIT:C3262 will display an overview of all neoplasias, although no single case has this specific code.

However, there had been a bu when under specific circumstances (code has some mapped samples and code has more samples in child terms) only the direct matches were used to compute the frequencies although the full number of samples was indicated in the plot legend. FIXED.