Hubmap Sample Tools#

Configuration File: hubmap_sample_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

HuBMAP_get_sample (Type: HuBMAPSampleTool)#

Get the full record for a single HuBMAP tissue Sample by its HuBMAP ID, including its CCF/RUI spa…

HuBMAP_get_sample tool specification

Tool Information:

  • Name: HuBMAP_get_sample

  • Type: HuBMAPSampleTool

  • Description: Get the full record for a single HuBMAP tissue Sample by its HuBMAP ID, including its CCF/RUI spatial registration. For spatially-registered blocks and sections this returns rui_location: the 3-D dimensions (x/y/z + units) of the tissue, the placement_target reference organ in the Common Coordinate Framework (e.g. a 3-D kidney/heart/lung model), and ccf_annotations – the list of CCF/UBERON anatomical structures the specimen overlaps. Also returns sample_category, organ, owning group, protocol URL, and the parent donor’s HuBMAP ID. Obtain valid sample IDs from HuBMAP_search_samples. Example: HBM658.BXNB.873.

Parameters:

  • hubmap_id (string) (required) HuBMAP Sample identifier (e.g. ‘HBM658.BXNB.873’). Obtain from HuBMAP_search_samples.

Example Usage:

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

HuBMAP_search_donors (Type: HuBMAPSampleTool)#

Search HuBMAP human Donors with normalized demographics, exact totals, and Elasticsearch offset p…

HuBMAP_search_donors tool specification

Tool Information:

  • Name: HuBMAP_search_donors

  • Type: HuBMAPSampleTool

  • Description: Search HuBMAP human Donors with normalized demographics, exact totals, and Elasticsearch offset pagination. Continue with metadata.next_offset while metadata.has_more is true.

Parameters:

  • group_name (string) (optional) Filter by the data-providing group/TMC name (partial match, e.g. ‘Stanford’, ‘Vanderbilt TMC’, ‘University of California San Diego TMC’).

  • query (string) (optional) Free-text search across donor description and demographic values (e.g. ‘female’, ‘White’, ‘diabetes’).

  • limit (integer) (optional) Maximum number of results (1-50, default 10).

  • offset (integer) (optional) Number of matching donors to skip. Continue with metadata.next_offset.

Example Usage:

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

HuBMAP_search_samples (Type: HuBMAPSampleTool)#

Search HuBMAP biospecimen Samples with exact totals and Elasticsearch offset pagination. Continue…

HuBMAP_search_samples tool specification

Tool Information:

  • Name: HuBMAP_search_samples

  • Type: HuBMAPSampleTool

  • Description: Search HuBMAP biospecimen Samples with exact totals and Elasticsearch offset pagination. Continue with metadata.next_offset while metadata.has_more is true. Filter by organ, sample category, and CCF/RUI registration.

Parameters:

  • organ (string) (optional) 2-letter RUI organ code to filter by (e.g. ‘LK’ left kidney, ‘HT’ heart, ‘SK’ skin, ‘BR’ brain). Case-insensitive.

  • sample_category (string) (optional) Tissue granularity: ‘block’, ‘section’, ‘organ’, or ‘suspension’. Case-insensitive.

  • registered_only (boolean) (optional) If true, return only spatially-registered samples that carry CCF/RUI coordinates (rui_location). Default false.

  • limit (integer) (optional) Maximum number of results (1-50, default 10).

  • offset (integer) (optional) Number of matching samples to skip. Continue with metadata.next_offset.

Example Usage:

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