This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.
2020-10-01: more ...
The Progenetix / Beaconplus query model utilises the GA4GH core data model for genomic and (biomedical, procedural) queries and data delivery.
2020-05-26: more ...
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 MappingThe 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 ...
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 ...
Wherever possible, data annotation in Progenetix uses {S}[B] OntologyClass
objects for categorical values, with CURIEs as id values. So far, the
Progenetix databases had used pubmed: for PubMed identifiers and ncit:
for NCI Metathesaurus (Neoplasm) ids.
@mbaudis 2020-03-30: more ...
The Progenetix Jekyll template modifies the standard Jekyll file structure.
@mbaudis 2019-03-14: more ...
The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.
@mbaudis 2019-03-14: more ...
The current implementation of the Progenetix APIs uses 2 URL endpoints:
2020-06-20: more ...
The Progenetix website has been completely rebuilt using a JavaScript / React based framework and API based content delivery. At its core, the site is built around the Beacon standard, with some extensions for data colections and advanced query options.
@mbaudis 2020-09-21: more ...
Loss of heterozygosity (LOH) is a phenomenon frequently observed in cancer genomes where the selective pressure to keep only the susceptible gene product from one allele removes the other healthy allele from the pool; In this context, copy neutral - loss of heterozygosity (CN-LOH) is commonly observed in haematological malignancies (O’keefe et al., 2010 and Mulligan et al., 2007). To Progenetix oncogenomic resource, comprising of nearly 800 cancer types (by NCIt classification) as of 2021, we expanded the new feature of LOH in our data collection, in addition to the total copy number, to open the door for the analysis of frequency and impact of this phenomenon.
Update 2021-01-28:
LOH variants can now be queried through the Search and Beacon+ interfaces, either as specific variants or together with deletions.
Please be aware that in contrast to the “complete for chromosomes 1-22” DUP and DEL calls, LOH is only determined for a subset of samples and therefore will be underreported in the statistics section.
@qingyao 2021-01-14: more ...
schemas
byconicdot2uberon
ICDOntologies
2021-02-06: more ...
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
progenetix-next
bycon server, as well as other Progenetix sevices (e.g. the publications repository)PGX
schemas
byconicdot2uberon
ICDOntologies
2021-02-06: more ...
After many years of using a CreativeCommons CC-BY-SA (“attribution + share alike”), the Progenetix resource has dropped the “SA - share alike” attribute and is now “attribution” only. This may facilitate the use of the data in more complex and/or commercial scenarios - enjoy!
@mbaudis 2020-08-05: more ...
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 ...
This script parses either:
assemblyId, cytoBands)
chroBases parameter
7:23028447-45000000X:992026602020-10-20: more ...
geneId
parameter2020-10-20: more ...
This service provides geographic location mapping for cities above 25’000 inhabitants (~22750 cities), through either:
geolongitudegeolatitudegeodistance
2500000 around Heidelberg…)2020-10-20: more ...
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 ...
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 ...
The publications service serves as backend API for the display of genome
screening publications through the Progenetix Publications DB.
2020-10-20: more ...
2020-10-20: more ...
2020-10-20: more ...
accessid parameterdeliveryKeys list
(can be comma-concatenated or multiple times parameter)2020-10-20: more ...
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 ...
The new year brings some refinements to biosamples search and display:
@mbaudis 2021-01-04: more ...
2020-10-20: more ...