Progenetix Tools#

Configuration File: progenetix_tools.json Tool Type: Local Tools Count: 6

This page contains all tools defined in the progenetix_tools.json configuration file.

Available Tools#

Progenetix_cnv_search (Type: ProgenetixTool)#

Search for cancer biosamples with copy number variations (CNVs) in a specific genomic region. Com…

Progenetix_cnv_search tool specification

Tool Information:

  • Name: Progenetix_cnv_search

  • Type: ProgenetixTool

  • Description: Search for cancer biosamples with copy number variations (CNVs) in a specific genomic region. Combines disease and genomic filters and returns complete external-reference metadata (id, label, description, URL/reference, and notes) instead of only reference IDs.

Parameters:

  • reference_name (string) (required) RefSeq chromosome accession. Examples: ‘refseq:NC_000007.14’ (chr7/GRCh38), ‘refseq:NC_000017.11’ (chr17/GRCh38), ‘refseq:NC_000001.11’ (chr1/GRCh38).

  • start (integer) (required) Start position (1-based, GRCh38). Example: 55019017 for EGFR start.

  • end (integer) (required) End position (1-based, GRCh38). Example: 55211628 for EGFR end.

  • variant_type (string) (optional) CNV type: ‘DUP’ for amplification/duplication, ‘DEL’ for deletion. Leave empty for any CNV type.

  • filters (string) (optional) Optional NCIt ontology code to filter by cancer type. Example: ‘NCIT:C4017’ for breast cancer.

  • limit (integer) (optional) Maximum number of biosamples to return (default: 10).

Example Usage:

query = {
    "name": "Progenetix_cnv_search",
    "arguments": {
        "reference_name": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

Progenetix_get_cnv_frequencies (Type: ProgenetixTool)#

Get the genome-wide aggregate CNV frequency profile for a cancer type from Progenetix — the signa…

Progenetix_get_cnv_frequencies tool specification

Tool Information:

  • Name: Progenetix_get_cnv_frequencies

  • Type: ProgenetixTool

  • Description: Get the genome-wide aggregate CNV frequency profile for a cancer type from Progenetix — the signature Progenetix output. For each genomic interval bin (cytoband), returns the gain frequency and loss frequency aggregated across all samples of a Progenetix collation, selected by NCIt code. Example: NCIT:C4017 (Breast Ductal Carcinoma) returns sampleCount 13869 across 3106 interval bins; NCIT:C3058 (Glioblastoma) bin 1p36.33 has gain_frequency 4.258 and loss_frequency 5.278.

Parameters:

  • filters (string) (required) NCIt ontology code identifying the cancer-type collation. Examples: ‘NCIT:C4017’ (Breast Ductal Carcinoma), ‘NCIT:C3058’ (Glioblastoma), ‘NCIT:C9145’ (AML), ‘NCIT:C3224’ (Melanoma), ‘NCIT:C4872’ (Lung Adenocarcinoma).

  • dataset_ids (string) (optional) Progenetix dataset to query (default ‘progenetix’).

  • max_intervals (integer) (optional) Optional cap on the number of interval bins returned (default: all ~3000 bins).

Example Usage:

query = {
    "name": "Progenetix_get_cnv_frequencies",
    "arguments": {
        "filters": "example_value"
    }
}
result = tu.run(query)

Progenetix_list_cohorts (Type: ProgenetixTool)#

List Progenetix cohorts with IDs, names, sizes, types, and data types. Returns exact total_cohort…

Progenetix_list_cohorts tool specification

Tool Information:

  • Name: Progenetix_list_cohorts

  • Type: ProgenetixTool

  • Description: List Progenetix cohorts with IDs, names, sizes, types, and data types. Returns exact total_cohorts and recoverable offset pagination; continue with data.next_offset while has_more is true.

Parameters:

  • limit (integer) (optional) Maximum number of cohorts to return (default: 10).

  • offset (integer) (optional) Zero-based offset in the complete cohort list. Continue with data.next_offset.

Example Usage:

query = {
    "name": "Progenetix_list_cohorts",
    "arguments": {
    }
}
result = tu.run(query)

Progenetix_list_filtering_terms (Type: ProgenetixTool)#

List Progenetix filtering terms (ontology codes) with matching-sample counts. Prefix filtering is…

Progenetix_list_filtering_terms tool specification

Tool Information:

  • Name: Progenetix_list_filtering_terms

  • Type: ProgenetixTool

  • Description: List Progenetix filtering terms (ontology codes) with matching-sample counts. Prefix filtering is applied client-side before exact total_terms and recoverable offset pagination; continue with data.next_offset while has_more is true. The live NCIT catalog currently contains more than 600 terms.

Parameters:

  • prefixes (string) (optional) Ontology prefix to filter terms by. Use ‘NCIT’ for NCI Thesaurus cancer types (default), ‘EDAM’ for operation types, ‘HP’ for HPO phenotypes.

  • limit (integer) (optional) Maximum number of terms to return (default: 25).

  • offset (integer) (optional) Zero-based offset after prefix filtering. Continue with data.next_offset.

Example Usage:

query = {
    "name": "Progenetix_list_filtering_terms",
    "arguments": {
    }
}
result = tu.run(query)

Progenetix_search_biosamples (Type: ProgenetixTool)#

Search cancer tumor biosamples in Progenetix by NCIt disease code. Returns diagnoses, stage, and …

Progenetix_search_biosamples tool specification

Tool Information:

  • Name: Progenetix_search_biosamples

  • Type: ProgenetixTool

  • Description: Search cancer tumor biosamples in Progenetix by NCIt disease code. Returns diagnoses, stage, and every external reference with its id, label, description, URL/reference, and notes; reference metadata is not discarded. Use skip/limit and next_skip while has_more is true to retrieve all results.

Parameters:

  • filters (string) (required) NCIt ontology code to filter biosamples by cancer type. Examples: ‘NCIT:C3058’ (Glioblastoma), ‘NCIT:C4017’ (Breast Carcinoma), ‘NCIT:C9145’ (Acute Myeloid Leukemia), ‘NCIT:C3224’ (Melanoma), ‘NCIT:C4872’ (Lung Adenocarcinoma), ‘NCIT:C3167’ (Neuroblastoma).

  • limit (integer) (optional) Maximum number of biosamples to return (default: 10).

  • skip (integer) (optional) Number of results to skip for pagination (default: 0).

Example Usage:

query = {
    "name": "Progenetix_search_biosamples",
    "arguments": {
        "filters": "example_value"
    }
}
result = tu.run(query)

Progenetix_search_individuals (Type: ProgenetixTool)#

Search individuals (patients) in the Progenetix cancer CNV database by NCIt disease code. Returns…

Progenetix_search_individuals tool specification

Tool Information:

  • Name: Progenetix_search_individuals

  • Type: ProgenetixTool

  • Description: Search individuals (patients) in the Progenetix cancer CNV database by NCIt disease code. Returns sex, diagnosis, onset, and every external reference with id, label, description, URL/reference, and notes. Use skip/limit and next_skip while has_more is true; broad diseases can contain hundreds of patients.

Parameters:

  • filters (string) (required) NCIt ontology code to filter individuals by cancer type. Examples: ‘NCIT:C9145’ (AML), ‘NCIT:C3058’ (Glioblastoma), ‘NCIT:C4017’ (Breast Carcinoma), ‘NCIT:C3224’ (Melanoma).

  • limit (integer) (optional) Maximum number of individuals to return (default: 10).

  • skip (integer) (optional) Number of matching individuals to skip. Use next_skip from the preceding response for the next page.

Example Usage:

query = {
    "name": "Progenetix_search_individuals",
    "arguments": {
        "filters": "example_value"
    }
}
result = tu.run(query)