For testing the rapidly evolving Beacon v2 API, we have now implemented more paths/endpoints which mostly conform to the brand new & still “flexible” v2.0.0-draft.4 version. Please check the documentation and examples.
@mbaudis 2021-07-02: more ...
The Biosample schema used for exporting Progenetix data has been adjusted with respect to representation of “bio-“classifications. The previous biocharacteristics list parameter has been deprecated and its previous content is now expressed in1:
histologicalDiagnosis (PXF)sampledTissue (PXF)icdoMorphology (pgx)icdoTopography (pgx)Here, “PGX” means that the attribute is part of the Phenopackets standard, while “pgx” labels it as specific to Progenetix. ↩
@mbaudis 2021-08-31: more ...
In “forward-looking” conformity with the Beacon v2
API, the JSON attributes of the API responses has been changed from snake_cased
to camelCased. Please adjust your code, where necessary.
@mbaudis 2021-07-01: more ...
The Beacon v2 protocol uses a REST path structure for consistant data access.
The Beacon+ implementation - developed oin the bycon project
implements an expanding set of those Beacon v2 paths for the Progenetix
resource.
2021-04-23: 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.
2021-04-16: more ...
This endpoint is mostly aimed at providing variants Beacon functionality. The app uses the same query processing mechanism as the other bycon applications.
2021-04-16: more ...
This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.
As one of the drivers of the Beacon protocol and to drive the Beacon v2 protocol process we have now started the documentation of Beacon v2 endpoints which are supported in Progenetix as part of the implementations-v2 project:
2021-04-30: 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.
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 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 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.
2021-04-16: 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 CNV visualization includes some default clustering for sample CNV profiles and collation CNV frequencies.
Michael Baudis 2021-06-22: more ...
For gene coordinates, we use a mapping of the genes’ maximum CDR as derived from mapping resources.
Michael Baudis 2018-05-08: more ...
The resource uses a standard CNV binning model with (in GRCh38) 3102 intervals of 1MB default size. Binned genome CNV values are available for all individual analyses (genome profiles), indicating the interval’s involvement in one or more CNV events, separated for gains and losses.
Additionally, for all all collations (e.g. profiles of a tumor type, or from the same publication), pre-computed interval CNV frequencies are available Alternatively, interval frequency maps can be generated on the fly from e.g. search results.
Michael Baudis 2021-06-22: more ...
Geographic point coordinates are assigned to each sample after review of existing information from associated publications or repository information for their ”best available” geographic origin using a precedence of:
Michael Baudis 2021-03-26: more ...
@mbaudis 2021-04-29: more ...
The current implementation of the Progenetix APIs uses 2 URL endpoints:
progenetix.org/beacon/
progenetix.org/services/
progenetix.org/api/ has been deprecated
services2020-06-20: 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 ...
Contents
.pgxsegProgenetix 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 ...
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 ...
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-web
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 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 ...
This service provides access to binned CNV frequency information of data
“collations” in the Progenetix project databases. A typical use would be the
retrieval of data for a single collation, e.g. by its identifier (e.g.
NCIT:C7376, PMID:22824167, pgxcohort-TCGAcancers).
2021-05-06: 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 ...
pgxRpi is an API wrapper package to access data from Progenetix database.
TBD
2021-09-16: more ...
The Progenetix resource provides pre-computed CNV frequencies for all its “collations” such as
This data can be accessed through the Progenetix API in data and image format.
@mbaudis 2021-05-14: more ...
One of the main use cases for the Progenetix resource is the exploration of frequency and disease specificity of genes of interest. Traditionally, the relevance of somatic CNVs hitting a gene in the context of cancer are judged by
@mbaudis 2021-04-20: more ...
The Progenetix resource has a limited option to visualize CNV data provided by the users. Data has to be formatted in a standard tab-delimited columnar format, preferably using the .pgxseg file format. Additional information can be found on the upload service page:
The data is only temporary stored on the server with a randomiized access path. At this time we do not provide any long term or login protected data storage and do not store access data.
TBD
@mbaudis 2021-04-20: more ...