This page lists changes for the Beacon+ implementation of the "Beacon" genomics API, as well as related updates for the Progenetix front-end.
2022-12-22: Various API fixes & extensions¶
genespansresponses contain now a
cytobandsparameter (i.e. the cytogenetic mapping of the gene's locus)
- FIXED: the beacon response meta now has the standard
receivedRequestSummary.requestParametersinstead of before
2022-01-17: Term-specific queries¶
So 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
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.
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.