Hubmap Tools

Configuration File: hubmap_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

HuBMAP_get_dataset (Type: HuBMAPTool)

Get detailed metadata for a specific HuBMAP dataset by its HuBMAP ID. Returns comprehensive infor…

HuBMAP_get_dataset tool specification

Tool Information:

  • Name: HuBMAP_get_dataset

  • Type: HuBMAPTool

  • Description: Get detailed metadata for a specific HuBMAP dataset by its HuBMAP ID. Returns comprehensive information including title, description, data type, organ, group, contacts, contributors, DOI, and data access level. Use HuBMAP_search_datasets first to find HuBMAP IDs.

Parameters:

  • hubmap_id (string) (required) HuBMAP dataset identifier (e.g., ‘HBM626.FHJD.938’)

Example Usage:

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

HuBMAP_get_dataset_provenance (Type: HuBMAPTool)

Retrieve a HuBMAP dataset’s biological provenance lineage: the ordered chain of ancestor entities…

HuBMAP_get_dataset_provenance tool specification

Tool Information:

  • Name: HuBMAP_get_dataset_provenance

  • Type: HuBMAPTool

  • Description: Retrieve a HuBMAP dataset’s biological provenance lineage: the ordered chain of ancestor entities from which the dataset was derived. The lineage runs Dataset -> Sample(s) (anatomical granularity section -> block -> organ) -> Donor, each entry giving entity_type, hubmap_id, uuid, sample_category, organ, and dataset_type. This answers ‘which donor, organ, and tissue blocks/sections produced this dataset?’. Provide the dataset UUID (32-char hex) or HuBMAP ID; obtain these from HuBMAP_search_datasets or HuBMAP_get_dataset. Example: uuid b1ca0a28b39e5ee6a252403e03247db6 returns 5 ancestors: Dataset HBM386.RVHN.555, Sample HBM522.MQPX.944 (section), Sample HBM364.WDPC.959 (block), Sample HBM865.MWHF.489 (organ, LK), Donor HBM758.JRSC.348.

Parameters:

  • uuid (string) (required) HuBMAP dataset UUID (32-char hex, e.g. ‘b1ca0a28b39e5ee6a252403e03247db6’) or HuBMAP ID (e.g. ‘HBM329.JZJG.469’). Obtain from HuBMAP_search_datasets.

Example Usage:

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

HuBMAP_list_organs (Type: HuBMAPTool)

List all organs available in the HuBMAP (Human BioMolecular Atlas Program) atlas. Returns organ n…

HuBMAP_list_organs tool specification

Tool Information:

  • Name: HuBMAP_list_organs

  • Type: HuBMAPTool

  • Description: List all organs available in the HuBMAP (Human BioMolecular Atlas Program) atlas. Returns organ names, codes (for use in HuBMAP_search_datasets), UBERON ontology IDs, and CUI codes. HuBMAP maps 43 organs including kidney, heart, liver, lung, brain, spleen, intestine, skin, and more.

Parameters:

No parameters required.

Example Usage:

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

HuBMAP_search_datasets (Type: HuBMAPTool)

Search HuBMAP (Human BioMolecular Atlas Program) published datasets by organ, assay type, or free…

HuBMAP_search_datasets tool specification

Tool Information:

  • Name: HuBMAP_search_datasets

  • Type: HuBMAPTool

  • Description: Search HuBMAP (Human BioMolecular Atlas Program) published datasets by organ, assay type, or free text. HuBMAP provides spatial biology and single-cell atlas datasets across 43 human organs with data types including scRNA-Seq, CODEX, MALDI, LC-MS, snATAC-Seq, and more. Organ codes: LK=Left Kidney, RK=Right Kidney, LI=Large Intestine, SI=Small Intestine, HT=Heart, LV=Liver, LU=Lung, SP=Spleen, TH=Thymus, LY=Lymph Node, BL=Bladder, PA=Pancreas, SK=Skin, BR=Brain, BM=Bone Marrow, MU=Muscle.

Parameters:

  • organ (string) (optional) Organ code to filter by (e.g., ‘LK’ for left kidney, ‘HT’ for heart, ‘LV’ for liver, ‘LU’ for lung, ‘BR’ for brain, ‘SP’ for spleen). Use HuBMAP_list_organs to see all codes.

  • dataset_type (string) (optional) Filter by assay/data type (e.g., ‘RNAseq’, ‘CODEX’, ‘MALDI’, ‘snATACseq’, ‘LC-MS’, ‘scRNAseq-10xGenomics-v3’)

  • query (string) (optional) Free text search across title, description, and anatomy fields

  • status (string) (optional) Dataset status filter. Default: ‘Published’

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

Example Usage:

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