Services
/byconschemas
¶
This helper service reads and serves local schema definition files. The name of
the schema (corresponding to the file name minus extension) is provided either
as an id
query parameter or as the first part of the path after schemas/
.
/cnvstats
¶
TBD
/collationplots
¶
The collationplots
function is a service to provide plots for CNV data aggregated
for samples matching individual filter values such as diagnostic codes or experimental
series id values. The default response is an SVG histogram ("histoplot"). Please refer
to the plot parameters documentation and the ByconPlot
class for other options.
For a single plot one can provide the entity id as path id value.
Examples (using the Progenetix resource as endpoint):¶
- progenetix.org/services/collationplots/pgx:cohort-TCGAcancers
- progenetix.org/services/collationplots/?filters=NCIT:C7376,PMID:22824167,pgx:icdom-85003
- progenetix.org/services/collationplots/?filters=NCIT:C7376,PMID:22824167&plotType=histoheatplot
- progenetix.org/services/collationplots/?collationTypes=icdom&minNumber=1000&plotType=histoheatplot
/collations
¶
The collations
service provides access to information about data "subsets"
in the project databases. Collations typically are aggregations of samples
sharing an ontology code (e.g. NCIT) or external identifier (e.g. PMID). Therefore,
in the context of Beacon the collations in bycon
provide the filtering_terms
available through Beacon queries, but also additional information e.g. about
child terms and statistics related to the terms.
In the case of the web projects the main purpose of the `services/collations/ endpoin is in providing the child terms and path relations for generating ontology trees in the UI.
Parameters¶
collationTypes=...
includeDescendantTerms=false
- only delivers data about codes with direct matches, i.e. excluding such where only a child term had a direct match
- this is especially useful for e.g. getting a fast overview about mappings
of deeply nested coding systems like
NCIT
deliveryKeys=...
Examples¶
- progenetix.org/services/collations?deliveryKeys=id,count&collationTypes=cellosaurus
- progenetix.org/services/collations?collationTypes=NCIT
- progenetix.org/services/collations?collationTypes=NCIT&includeDescendantTerms=false
/cytomapper
¶
The cytomapper
function provides a JSON response with cytoband information
such as matched cytobands and the genome coordinates of their extend.
There is currently only support for GRCh38.
Response Schema¶
Parameters¶
cytoBands
(path default)- a properly formatted cytoband annotation
- "8", "9p11q21", "8q", "1p12qter"
- or
chroBases
7:23028447-45000000
X:99202660
Examples (using the Progenetix resource as endpoint):¶
- progenetix.org/services/cytomapper/8q21q24
- progenetix.org/services/cytomapper/13q
- progenetix.org/services/cytomapper?chroBases=12:10000000-45000000
/dbstats
¶
This service endpoint provides statistic information about the resource's datasets.
Examples¶
/endpoints
¶
The service provides the schemas for the BeaconMap
OpenAPI endpoints.
Examples (using the Progenetix resource as endpoint):¶
/genespans
¶
The genespans
function provides a JSON response with the coordinates of
matching gene IDs.
Examples (using the Progenetix resource as endpoint):¶
/geolocations
¶
TBD
Examples¶
- progenetix.org/services/geolocations?city=zurich
- progenetix.org/services/geolocations?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000
- progenetix.org/services/geolocations?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000&output=map
- progenetix.org/services/geolocations?inputfile=https://raw.githubusercontent.com/progenetix/pgxMaps/main/rsrc/locationtest.tsv&debug=&output=map&
- progenetix.org/cgi/bycon/services/geolocations.py?city=New&ISO3166alpha2=UK&output=map&markerType=marker
/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.
Examples (using the Progenetix resource as endpoint):¶
- progenetix.org/services/ids/pgxbs-kftva5zv
- progenetix.org/services/ids/PMID:28966033
- progenetix.org/services/ids/NCIT:C3262
/intervalFrequencies
¶
None
/ontologymaps
¶
Examples¶
/pgxsegvariants
¶
None
/publications
¶
The publications service provides API functionality for accessing the Progenetix publications collection, which represents curated information about several thousand articles reporting genome-wide screening experiments in cancer.
Examples¶
- progenetix.org/services/publications/?filters=PMID
- progenetix.org/services/publications/?filters=PMID,genomes:>200,arraymap:>1
- progenetix.org/services/publications/?filters=PMID:22824167&method=details
- progenetix.org/services/publications/?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000
/samplemap
¶
TBD
/samplematrix
¶
The service uses the standard bycon data retrieval pipeline with analysis
as entity type. Therefore, all standard Beacon query parameters work and also
the path is interpreted for an biosample id
value if there is an entry at
.../biosamples/{id}
/sampleplots
¶
The plot service uses the standard bycon data retrieval pipeline with biosample
as entity type. Therefore, all standard Beacon query parameters work and also
the path is interpreted for an biosample id
value if there is an entry at
.../sampleplots/{id}
The plot type can be set with plotType=samplesplot
(or histoplot
but that is
the fallback). Plot options are available as usual.
Examples (using the Progenetix resource as endpoint):¶
- progenetix.org/services/sampleplots/pgxbs-kftvjv8w
- progenetix.org/services/sampleplots/pgxbs-kftvjv8w?plotType=samplesplot&datasetIds=cellz
- progenetix.org/services/sampleplots?plotType=samplesplot&datasetIds=cellz&filters=cellosaurus:CVCL_0030
- progenetix.org/services/sampleplots?filters=pgx:icdom-81703
- progenetix.org/services/sampleplots/?testMode=true&plotType=samplesplot
- progenetix.org/services/sampleplots?filters=pgx:icdom-81703&plotType=histoplot&plotPars=plot_chro_height=0::plot_title_font_size=0::plot_area_height=18::plot_margins=0::plot_axislab_y_width=0::plot_grid_stroke=0::plot_footer_font_size=0::plot_width=400
- progenetix.org/services/sampleplots?datasetIds=progenetix&plotMinLength=1000&plotMaxLength=3000000&geneId=CDKN2A&variantType=EFO:0020073&plotPars=plotChros=9::plotGeneSymbols=CDKN2A::plotWidth=300&plotType=histoplot
/sampletable
¶
The service uses the standard bycon data retrieval pipeline with biosample
as entity type. Therefore, all standard Beacon query parameters work and also
the path is interpreted for an biosample id
value if there is an entry at
.../sampletable/{id}
The table type can be changed with tableType=individuals
(or analyses
).
Examples¶
- progenetix.org/services/sampletable/pgxbs-kftvjv8w
- progenetix.org/services/sampletable?datasetIds=cellz&filters=cellosaurus:CVCL_0030
- progenetix.org/services/sampletable?filters=pgx:icdom-81703
/services
¶
The services
application deparses a request URI and calls the respective
script. The functionality is combined with the correct configuration of a
rewrite in the server configuration for creation of canonical URLs.
/uploader
¶
This service is used by UI implementations to upload user provided .pgxseg
files
for visualization of the variants using the packages plotting functions.
As exception to the general rule the uploader
service does not make use of standard
argument parsing but directly uses cgi.FieldStorage()
and ....file.read()
.
/variantsbedfile
¶
The variantsbedfile
function provides a BED file with the matched genomic
variants from a Beacon query or a sample id.
Examples¶
/vcfvariants
¶
The VCF service uses the standard bycon data retrieval pipeline with biosample
as entity type. Therefore, all standard Beacon query parameters work and also
the path is interpreted for an biosample id
value if there is an entry at
.../vcfvariants/{id}