The bycon package supports number of parameters for filtering and querying the data which includes and extends
+standard Beacon parameters and can - depending on the parameter and the current scope - in general be
+invoked through HTTP requests and as command line arguments.
Only parameters defined in config/argument_definitions.yaml will be
+interpreted.
Parameters are listed in snake_case format although for command line arguments
+(and also optionally web requests) camelCase versions are required (see the cmdFlags).
user_name¶type: string
+pattern: ^\w+$
+cmdFlags: --userName
+description:
+faking a user name
test_mode¶type: boolean
+cmdFlags: -t,--testMode
+description:
+test setting, i.e. returning some random documents
+default: False
skip¶type: integer
+cmdFlags: --skip
+description:
+pages to be skipped
+default: 0
limit¶type: integer
+cmdFlags: -l,--limit
+description:
+limit number of documents; a value of 0 sets to unlimited
+default: 200
+local: 0
requested_granularity¶type: string
+pattern: ^\w+$
+description:
+The requested granularity of the beacon
+cmdFlags: --requestedGranularity
+default: record
request_entity_path_id¶type: string
+cmdFlags: --requestEntityPathId
+description:
response_entity_path_id¶type: string
+cmdFlags: --responseEntityPathId
+description:
indviduals
+ in /sampletable/) include_resultset_responses¶type: string
+cmdFlags: --includeResultsetResponses
+description:
HIT dataset_ids¶type: array
+items:
+ - type: string
+cmdFlags: -d,--datasetIds
+description:
+dataset ids
cohort_ids¶type: array
+items:
+ - type: string
+cmdFlags: --cohortIds
+description:
+cohort ids
filters¶type: array
+items:
+ - type: string
+cmdFlags: --filters
+description:
+prefixed filter values, comma concatenated; or objects in POST
filter_precision¶type: string
+cmdFlags: --filterPrecision
+description:
+either start or exact for matching filter values
+default: exact
filter_logic¶type: string
+cmdFlags: --filterLogic
+description:
+Global for either OR or AND (translated to the MongoDB $and etc.). The Beacon protocol only knows AND.
+default: AND
include_descendant_terms¶type: boolean
+cmdFlags: --includeDescendantTerms
+description:
+global treatment of descendant terms
+default: True
assembly_id¶type: string
+pattern: ^\w+?[\w\-\.]*?\w*?$
+db_key: assembly_id
+cmdFlags: --assemblyId
+description:
+assembly id; currently not used in bycon's version
reference_name¶type: string
+db_key: location.sequence_id
+pattern: ^\w+.*?\w?$
+cmdFlags: --referenceName
+description:
+chromosome
mate_name¶type: string
+db_key: adjoined_sequences.sequence_id
+pattern: ^\w+.*?\w?$
+cmdFlags: --mateName
+description:
+chromosome
reference_bases¶type: string
+db_key: reference_sequence
+pattern: ^[ACGTN]+$
+cmdFlags: --referenceBases
+description:
+reference bases
alternate_bases¶type: string
+db_key: sequence
+pattern: ^[ACGTN]+$
+cmdFlags: --alternateBases
+description:
+alternate bases
variant_type¶type: string
+db_key: variant_state.id
+pattern: ^\w+[\w \-\:]\w+?$
+cmdFlags: --variantType
+description:
+variant type, e.g. DUP
start¶type: array
+db_key: location.start
+items:
+ - type: integer
+ - pattern: ^\d+?$
+cmdFlags: --start
+description:
+genomic start position
end¶type: array
+db_key: location.end
+items:
+ - type: integer
+ - pattern: ^\d+?$
+cmdFlags: --end
+description:
+genomic end position
mate_start¶type: integer
+db_key: adjoined_sequences.start
+pattern: ^\d+?$
+cmdFlags: --mateStart
+description:
+genomic start position of fusion partner breakpoint region
mate_end¶type: integer
+db_key: adjoined_sequences.end
+pattern: ^\d+?$
+cmdFlags: --MateEnd
+description:
+genomic end position of fusion partner breakpoint region
variant_min_length¶type: integer
+db_key: info.var_length
+pattern: ^\d+?$
+cmdFlags: --variantMinLength
+description:
+The minimal variant length in bases e.g. for CNV queries.
variant_max_length¶type: integer
+db_key: info.var_length
+pattern: ^\d+?$
+cmdFlags: --variantMaxLength
+description:
+The maximum variant length in bases e.g. for CNV queries.
gene_id¶type: array
+items:
+ - type: string
+ - pattern: ^\w+?(\w+?(\-\w+?)?)?$
+db_key: None
+cmdFlags: --geneId
+description:
+gene id
aminoacid_change¶type: string
+db_key: molecular_attributes.aminoacid_changes
+pattern: ^\w+?$
+examples: V600E,M734V,G244A
+cmdFlags: --aminoacidChange
+description:
+Aminoacid alteration in 1 letter format
genomic_allele_short_form¶type: string
+db_key: identifiers.genomicHGVS_id
+pattern: ^\w+.*\w$
+examples: NC_000017.11:g.7674232C>G
+cmdFlags: --genomicAlleleShortForm
+description:
+Genomic HGVSId descriptor
variant_query_digests¶type: array
+db_key: None
+items:
+ - type: string
+ - pattern: ^(?:chro?)?([12]?[\dXY]):(\d+?(?:-\d+?)?)(?:--(\d+?(?:-\d+?)?))?(?::([\w\:\>]+?))?$
+cmdFlags: --variantQueryDigests
+examples: 9:9000001-21975098--21967753-24000000:DEL
+description:
+EXPERIMENTAL Variant query digest-style short form
variant_multi_pars¶type: array
+db_key: None
+items:
+ - type: object
+cmdFlags: --variantMultiPars
+description:
+EXPERIMENTAL List of multiple variant queries, for POST
variant_internal_id¶type: string
+db_key: variant_internal_id
+pattern: ^\w[\w\:\-\,]+?\w$
+examples: 11:52900000-134452384:EFO_0030067
+cmdFlags: --variantInternalId
+description:
+An id value used for all variant instances of the same composition; a kind of digest
accessid¶type: string
+db_key: id
+pattern: ^\w[\w\-]+?\w$
+examples: b59857bc-0c4a-4ac8-804b-6596c6566494
+cmdFlags: --accessid
+description:
+An accessid for retrieving handovers etc.
file_id¶type: string
+pattern: ^\w[\w\-]+?\w$
+examples: 90e19951-1443-4fa8-8e0b-6b5d8c5e45cc
+cmdFlags: --fileId
+description:
+A file id e.g. as generated by the uploader service
id¶type: string
+db_key: id
+pattern: ^\w[\w\:\-\,]+?\w$
+examples: pgxvar-5bab576a727983b2e00b8d32,pgxind-kftx25eh
+cmdFlags: --id
+description:
+An id; this parameter only makes sense for specific REST entry types
ids¶type: array
+items:
+ - type: string
+ - pattern: ^\w[\w:-]+\w$
+cmdFlags: --ids
+description:
+One or more ids; this parameter only makes sense for specific REST entry types
biosample_ids¶type: array
+items:
+ - type: string
+ - pattern: ^\w[\w:-]+\w$
+byc_entity: biosample
+cmdFlags: --biosampleIds
+description:
+biosample ids
analysis_ids¶type: array
+items:
+ - type: string
+ - pattern: ^\w[\w:-]+\w$
+byc_entity: analysis
+cmdFlags: --analysisIds
+description:
+analysis ids
individual_ids¶type: array
+items:
+ - type: string
+ - pattern: ^\w[\w:-]+\w$
+byc_entity: individual
+cmdFlags: --individualIds
+description:
+subject ids
variant_ids¶type: array
+items:
+ - type: string
+ - pattern: ^\w[\w:-]+\w$
+byc_entity: genomicVariant
+cmdFlags: --variantIds
+description:
+variant ids
debug_mode¶type: boolean
+cmdFlags: --debugMode
+description:
+debug setting
+default: False
show_help¶type: boolean
+cmdFlags: --showHelp
+description:
+specific help display
+default: False
test_mode_count¶type: integer
+cmdFlags: --testModeCount
+description:
+setting the number of documents reurned in test mode
+default: 5
output¶type: string
+cmdFlags: --output
+description:
+For defining a special output format, mostly for byconaut services use. Examples:
cnvstats, for analyses, to present some CNV statistics pgxseg, using the .pgxseg variant file format text, for some services to deliver a text table instead of JSON include_handovers¶type: boolean
+default: True
+cmdFlags: --includeHandovers
+description:
+only used for web requests & testing
method¶type: string
+cmdFlags: --method
+description:
+special method
+default: None
group_by¶type: string
+cmdFlags: --groupBy
+description:
+group parameter e.g. for subset splitting
+default: text
mode¶type: string
+cmdFlags: -m,--mode
+description:
+mode, e.g. file type
update¶type: boolean
+cmdFlags: -u,--update
+description:
+update existing records - might be deprecated; only used for publications
+default: False
force¶type: boolean
+cmdFlags: --force
+description:
+force mode, e.g. for update or insert (cmd line)
+default: False
inputfile¶type: string
+cmdFlags: -i,--inputfile
+description:
+a custom file to specify input data, usually tab-delimited with special header
outputdir¶type: string
+cmdFlags: --outputdir
+description:
+output directory where supported (cmd line)
outputfile¶type: string
+cmdFlags: -o,--outputfile
+description:
+output file where supported (cmd line)
min_number¶type: integer
+cmdFlags: --minNumber
+description:
+minimal number, e.g. for collations, where supported
+default: 0
delivery_keys¶type: array
+items:
+ - type: string
+cmdFlags: --deliveryKeys
+description:
+delivery keys to force only some parameters in custom exporters
collation_types¶type: array
+items:
+ - type: string
+cmdFlags: --collationTypes
+description:
+selected collation types, e.g. "EFO"
selected_beacons¶type: array
+items:
+ - type: string
genome_binning¶type: string
+default: 1Mb
+cmdFlags: --genomeBinning
+description:
+one of the predefined genome binning keys - default 1Mb
cyto_bands¶type: string
+pattern: ^(?:chro?)?([12]?[\dXY])([pq](generated?:(?:ter)|(?:cen)|(?:[1-4](generated?:\d(?:\.\d\d*?)?)?)?))?\-?([pq](generated?:(?:cen)|(?:ter)|(?:[1-4](generated?:\d(?:\.\d\d*?)?)?)?))?$
+db_key: None
+cmdFlags: --cytoBands
+description:
+cytobands, e.g. 8q21q24.1
chro_bases¶type: string
+pattern: ^(chro?)?([12]?[\dXY])\:(\d+?)(\-(\d+?))?$
+db_key: None
+cmdFlags: --chroBases
+description:
+only for the cytoband converter ... e.g. 8:0-120000000
city¶type: string
+cmdFlags: -c,--city
+description:
+only for the geolocations...
geo_latitude¶type: number
+cmdFlags: --geoLatitude
+description:
+only for the geolocations...
geo_longitude¶type: number
+cmdFlags: --geoLongitude
+description:
+only for the geolocations...
geo_distance¶type: integer
+cmdFlags: --geoDistance
+description:
+only for the geolocations...
plot_pars¶type: string
+cmdFlags: --plotPars
+description:
+plot parameters in form par=value concatenated by ::
plot_type¶type: string
+cmdFlags: --plotType
+description:
+plot type (histoplot, samplesplot, arrayplot - more?)
+default: None
The byconServices package inside bycon provides a number of plotting functions which can be used to visualize the data in the database. Generally
+plot functionality is focussed on generating CNV visualizations for per-sample and
+aggregated CNV data (e.g. frequencyplots). Additionally some geographic map projectins are provided e.g. for samples and metadata.
More information can be found on these pages:
+histoplot¶description:
+The default option, used to plot histograms of the CNV frequencies per data collection ("collation") or aggregated sample data.
+data_key: interval_frequencies_bundles
+data_type: collations
histoheatplot¶description:
+A "heatmap" style version of the histogram plot, where a single gain/loss frequency result is transformed into a small heat color strip.
+data_key: interval_frequencies_bundles
+data_type: collations
histosparkplot¶description:
+A version of the histogram with predefined parameters for representing a small and unlabeled plot, e.g. for use in hover previews. As in the normal histogram parameters can be overridden.
+data_key: interval_frequencies_bundles
+data_type: collations
+mods:
+ - 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: 480
+ - plot_area_opacity: 0
+ - plot_dendrogram_width: 0
+ - plot_labelcol_width: 0
+ - plot_axis_y_max: 80
+modded: histoplot
histocircleplot¶description:
+A version circular of the histogram.
+data_key: interval_frequencies_bundles
+data_type: collations
+mods:
+ - plot_width: 640
+ - plot_chro_height: 16
+ - plot_axislab_y_width: 0
+ - plot_area_opacity: 0
+ - plot_dendrogram_width: 0
+ - plot_labelcol_width: 0
samplesplot¶description:
+A plot of the called CNV segments per sample, with the samples ordered by their clustering (i.e. similarity of binned CNV data).
+data_key: analyses_variants_bundles
+data_type: samples
geomapplot¶description:
+A leaflet based plot of geolocations.
+data_key: geolocs_list
+data_type: geolocs
plot_id¶default: genomeplot
plot_title¶description: +title above the plot
+plot_group_by¶description:
+group samples in histograms by a filter type (NCIT, PMID...)
+default: ``
plot_filter_empty_samples¶description:
+By setting to true samples w/o data can be removed e.g. from sample plots
+type: boolean
+default: False
force_empty_plot¶description:
+By setting to true a plot strip will be forced even if there are no CNV samples
+type: boolean
+default: False
plot_cluster_results¶description:
+By setting to false clustering can be suppressed
+type: boolean
+default: True
plot_samples_cluster_type¶description: +Selection of which measurees are used to generate the clustering matrix
+intcoverage uses the ~2x3k (gain, loss) 1MB intervals chrostats only uses the CNV coverage per chromosomal arm (separately
+ for gains and losses) intcoverage chrostats,intcoverage plot_cluster_metric¶default: ward
+oneOf: average,centroid,complete,median,single,ward,weighted
plot_dup_color¶default: #FFC633
plot_hldup_color¶default: #FF6600
plot_del_color¶default: #33A0FF
plot_hldel_color¶default: #0033CC
plot_loh_color¶default: #0066FF
plot_snv_color¶default: #FF3300
plot_chros¶type: array
+items: string
+default: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
plot_width¶description:
+plot_width - 2
+*plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width 1024 plot_area_height¶description:
+height of the plot area (applies only to histogram plots)
+type: integer
+default: 100
plot_axis_y_max¶description:
+100 plot_samplestrip_height¶description:
+height of a single sample strip
+type: integer
+default: 12
plot_margins¶description:
+outer plot margins, in px
+type: integer
+default: 25
plot_labelcol_width¶description:
+width of the space for left text labels (e.g. sample ids, collation + labels)
+defaults to 0 when only one item
+type: integer
+default: 220
plot_axislab_y_width¶description:
+width of the space for histogram percentage markers
+type: integer
+default: 30
plot_dendrogram_width¶description:
+50 plot_dendrogram_color¶description:
+color of the cluster tree stroke
+default: #333333
plot_dendrogram_stroke¶description:
+thickness of the cluster tree stroke
+type: number
+default: 0.5
plot_chro_height¶description:
+height (well, width...) of the chromosomes in the ideogram strip
+type: integer
+default: 14
plot_region_gap_width¶type: integer
+default: 3
plot_canvas_color¶description:
+color of the document background
+default: #ffffff
plot_area_color¶description:
+color of the plot area background
+default: #eef6ff
plot_area_opacity¶description:
+opacity of the plot background
+type: number
+default: 0.8
plot_heat_intensity¶description:
+factor for frequency heatmap value brightness
+type: number
+default: 1
plot_grid_stroke¶type: integer
+default: 1
plot_grid_color¶description:
+color of grid lines
+default: #c0e3ee
plot_grid_opacity¶type: float
+default: 0.8
plot_font_color¶default: #000000
plot_font_size¶description:
+font size, in px
+type: integer
+default: 10
plot_title_font_size¶description:
+title font size, in px
+type: integer
+default: 16
plot_labelcol_font_size¶description:
+label font size (left column), in px
+type: integer
+default: 12
plot_label_y_font_size¶description:
+font size for Y-axis labels (percents ...)
+type: integer
+default: 8
plot_label_y_font_color¶description:
+font color for Y-axis labels (percents ...)
+default: #666666
plot_label_y_values¶type: array
+items: integer
+default: 25,50,75
plot_label_y_unit¶type: string
+default: %
circ_start_gap¶description:
+in degrees; top (usually) gap providing separation & space for labels
+type: integer
+default: 20
circ_start_angle¶description:
+in degrees; start of plot circle from 12 o'clock position
+type: integer
+default: 0
plot_probe_y_factor¶description:
+relative y-scaling of the probes in array-/probeplots
+type: integer
+default: 1
plot_probe_label_y_values¶type: array
+items: number
+default: 1,2,3,4,5,6,7,8,9
plot_probedot_size¶type: integer
+default: 1
plot_probedot_opacity¶type: integer
+default: 222
plot_region_labels¶description:
+8:120000000-124000000:Region+of+Interest plot_regionlabel_color¶default: #ddceff
plot_gene_symbols¶description:
+plot_cytoregion_labels¶description:
+plot_cytoregion_color¶default: #ffe3ee
plot_marker_font_color¶description:
+font color for gene and region markers
+default: #dd3333
plot_marker_font_size¶type: integer
+default: 10
plot_marker_label_padding¶description:
+text padding of markers versus background/box
+type: integer
+default: 4
plot_marker_lane_padding¶type: integer
+default: 2
plot_footer_font_size¶type: integer
+default: 10
plot_footer_font_color¶default: #999999
cytoband_shades¶type: object
+default:
+ - gpos100: {'0%': 'rgb(39,39,39)', '100%': 'rgb(0,0,0)'}
+ - gpos75: {'0%': 'rgb(87,87,87)', '100%': 'rgb(39,39,39)'}
+ - gpos50: {'0%': 'rgb(196,196,196)', '100%': 'rgb(111,111,111)'}
+ - gpos25: {'0%': 'rgb(223,223,223)', '100%': 'rgb(196,196,196)'}
+ - gneg: {'0%': 'white', '100%': 'rgb(223,223,223)'}
+ - gvar: {'0%': 'rgb(196,196,196)', '100%': 'rgb(111,111,111)'}
+ - stalk: {'0%': 'rgb(39,39,39)', '100%': 'rgb(0,0,0)'}
+ - acen: {'0%': 'rgb(163,55,247)', '100%': 'rgb(138,43,226)'}
histoval_directions¶type: object
+default:
+ - gain_frequency: 1
+ - gain_hlfrequency: 1
+ - loss_frequency: -1
+ - loss_hlfrequency: -1
histoval_colorkeys¶type: object
+default:
+ - gain_frequency: plot_dup_color
+ - gain_hlfrequency: plot_hldup_color
+ - loss_frequency: plot_del_color
+ - loss_hlfrequency: plot_hldel_color
tiles_source¶default: https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png
attribution¶default: Map data © <a href="https://www.openstreetmap.org/">OpenStreetMap</a> contributors, <a href="https://creativecommons.org/licenses/by-sa/2.0/">CC-BY-SA</a>
init_latitude¶default: 30
init_longitude¶default: 9
zoom¶default: 1
head¶default: <meta charset="utf-8"> <link rel="stylesheet" href="https://unpkg.com/leaflet@1.8.0/dist/leaflet.css" integrity="sha512-hoalWLoI8r4UszCkZ5kL8vayOGVae1oxXe/2A4AO6J9+580uKHDO3JdHb7NzwwzK5xr/Fs0W40kiNHxM9vyTtQ==" crossorigin="" />
map_w_px¶default: 800
map_h_px¶default: 512
marker_type¶default: marker
bubble_stroke_color¶default: #dd6633
bubble_stroke_weight¶default: 1
bubble_fill_color¶default: #cc9966
bubble_opacity¶default: 0.4
marker_scale¶default: 2
marker_max_r¶default: 1000
zoom_min¶default: 2
zoom_max¶default: 14
The bycon environment provides a number of data services beyond typical Beacon +functionality. These services can be loosely grouped into two major types:
+API Parameters
+A complete list of parameters accepted by the API is provided on the Web and Command Line Parameters page.
+Standard responses are provided as Content-Type: application/json. The wrapper
+format is based on the Beacon v2 response format, with the data returned in the
+results array:
meta:
+ api_version: ...
+ returned_schemas: [ ]
+response:
+ exists: true | false
+ info: { }
+ resultSets: [ ]
+This (incomplete) example response may help with understanding the general
+format. Here, the data is a dictionary/object with a single key (genes):
The byconServices package inside bycon provides a number of plotting functions which can be used to visualize the data in the database. Generally
+plot functionality is focussed on generating CNV visualizations for per-sample and
+aggregated CNV data (e.g. frequencyplots). Additionally some geographic map projectins are provided e.g. for samples and metadata.
More information can be found in the plot documentation on this page.
+/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.
+/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.
+collationTypes=...includeDescendantTerms=falseNCITdeliveryKeys=.../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.
+cytoBands (path default)chroBases7:23028447-45000000X:99202660/dbstats¶This service endpoint provides statistic information about the resource's +datasets.
+/endpoints¶The service provides the schemas for the BeaconMap OpenAPI endpoints.
/genespans¶The genespans function provides a JSON response with the coordinates of
+matching gene IDs.
/geolocations¶TBD
+/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.
+/intervalFrequencies¶None
+/ontologymaps¶/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.
+/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.
/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).
/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.
/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}
The following is a list of standard Beacon responses supported by the bycon package.
+Responses for individual entities or endpoints are grouped by their Beacon framework
+response classes (e.g. beaconResultsetsResponse for biosamples, g_variants etc.).\n\n
+Please be reminded about the general syntax used in Beacon: A path element such
+as /biosamples corresponds to an entity (here biosample). Below these relations
+are indicated by the @ symbol.\n\n
API Parameters
+A complete list of parameters accepted by the API is provided on the Web and Command Line Parameters page.
+Tests, examples and schemas are run from the server defined in this site's build instructions
+(see the current progenetix.org entry for reference_server_url entry in the github.com/progenetix/bycon/blob/main/mkdocs.yaml configuration file.
Complete definition for a minimal response that provides only an aggregate Boolean "exists": true or "exists": false answer to the query.
+Additional information - which should not consist of record-level information - can be provided through beaconHandovers.
For a list of entities potentially served by beaconBooleanResponse depending on
+the selected or granted responseGranularity please check beaconResultsetsResponse.
Complete definition for a minimal response that provides an aggregate Boolean "exists": true or "exists": false answer to the query as well as the count of the matched records.
+Additional information - which should not consist of record-level information - can be provided through beaconHandovers.
For a list of entities potentially served by beaconCountResponse depending on
+the selected or granted responseGranularity please check beaconResultsetsResponse.
A beaconResultsetsResponse returns the results of a query against a beacon or beacon aggregator. Beyond the responseSummary for overall matches the response contains details about the matches in individual collections in the beacon or beacon network. This type of response is required when serving a request with a "record" level responseGranularity, and beaconResultsets typically contain a list of records matched by the query.
+The types of beaconResultsets objects are defined in the beacon's configuration; e.g. if using the Beacon v2+ default model the types dataset and cohort are supported as result sets.
/g_variants¶The type of response used for the endpoint depends on the requested and granted responseGranularity.
{E} progenetix.org/beacon/g_variants/pgxvar-5bab576a727983b2e00b8d32
+{E} progenetix.org/beacon/g_variants/pgxvar-5bab576a727983b2e00b8d32/individuals
+{E} progenetix.org/beacon/g_variants?geneId=CDKN2A&variantMaxSize=100000&limit=5
+/analyses¶The analysis schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s).
The type of response used for the endpoint depends on the requested and granted responseGranularity.
/runs¶Schema for the experimental run (e.g. sequencing run, array processing...) leading to the raw data for the (computational) analysis. NOTE: In the bycon environment run parameters are stored in the analysis documents and rewritten into this schema at export time.
+The type of response used for the endpoint depends on the requested and granted responseGranularity.
/biosamples¶A Biosample refers to a unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue biopsy, a single cell from a culture for single cell genome sequencing or a protein fraction from a gradient centrifugation. Several instances (e.g. technical replicates) or types of experiments (e.g. genomic array as well as RNA-seq experiments) may refer to the same Biosample.
+The type of response used for the endpoint depends on the requested and granted responseGranularity.
{E} progenetix.org/beacon/biosamples?filters=NCIT:C4017&limit=3
+/individuals¶None
+The type of response used for the endpoint depends on the requested and granted responseGranularity, i.e. while a "record" level responseGranularity has to be served through a beaconResultsetsResponse other granularities might employ summary response types.
{E} progenetix.org/beacon/individuals?filters=EFO:0030049&limit=5
+A type of Beacon response that includes details about the collections in a beacon. The types of collections are defined in each beacon's configuration; if using the Beacon v2+ default model usually the types dataset and cohort are supported.
/datasets¶A dataset available in the beacon.
+/cohorts¶A cohort available in the beacon.
+The filtering terms response provides information about available individual filters for a beacon's entry types as well as optional information about the ontologies the filters belong to.
+ +/filtering_terms¶Schema for the Filtering Terms list related to the hosting entry type. It is kept separated to allow updating it independently.
+The beaconInfoResponse provides metadata describing a Beacon instance, such as its name, the organization responsible for the Beacon, contact information, site logo and alternative URLs and importantly the beacon's API version. It is based on the GA4GH service-info standard.
+The content of the beaconInfoResponse can be used by clients such as web front ends or beacon aggregators to evaluate potential access patterns and to display information about the beacon.
/info¶Metadata describing a Beacon instance.
+The beaconConfigurationResponse returns information about configuration parameters of a given beacon instance such as maturity or security attributes or supported entry types. It is directed towards Beacon clients like web pages or network aggregators.
/configuration¶The Beacon configuration reports several attributes of the beacon instance related to security, maturity and available entry types. Where appropriate the details returned in service-info should mirror the ones in this configuration.
{S} progenetix.org/services/schemas/beaconConfigurationSchema
+A beaconMapResponse provides information about the beacon instance such as the different endpoints supported by this implementation of the Beacon API. This response is aimed to allow Beacon clients such as web front ends and Beacon network aggregators to evaluate which access patterns can be implemented against individual beacons.
/map¶Map of a Beacon, its entry types and endpoints. It isconceptually similar to a website sitemap.
+The beaconEntryTypesResponse provides information about the entry types served through a beacon, including their definitions and pointers to their schemas.
/entry_types¶Schema for the entry types list.
+