Idr Searchengine Tools

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

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

Available Tools

IDR_list_metadata_keys (Type: IDRSearchEngineTool)

List the curated metadata attribute keys available for searching the Image Data Resource (IDR), f…

IDR_list_metadata_keys tool specification

Tool Information:

  • Name: IDR_list_metadata_keys

  • Type: IDRSearchEngineTool

  • Description: List the curated metadata attribute keys available for searching the Image Data Resource (IDR), for a given resource type. These are the valid ‘key’ arguments for IDR_search_images and IDR_search_studies, e.g. ‘Gene Symbol’, ‘Gene Identifier’, ‘Organism’, ‘Cell Line’, ‘Compound Name’, ‘Antibody Name’, ‘Phenotype’, ‘Pathology’, ‘Sex’, ‘Age’. Use this first to discover what can be queried before building a search.

Parameters:

  • resource ([‘string’, ‘null’]) (optional) Resource type whose metadata keys to list. Default ‘image’. Other values: ‘screen’, ‘project’, ‘well’, ‘plate’.

Example Usage:

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

IDR_list_values_for_key (Type: IDRSearchEngineTool)

List every distinct value (and the number of images annotated with it) for one IDR metadata key, …

IDR_list_values_for_key tool specification

Tool Information:

  • Name: IDR_list_values_for_key

  • Type: IDRSearchEngineTool

  • Description: List every distinct value (and the number of images annotated with it) for one IDR metadata key, across the whole Image Data Resource. For example key=’Organism’ returns ‘homo sapiens’ (13M+ images), ‘mus musculus’, ‘danio rerio’, etc.; key=’Phenotype’ returns 300+ phenotype terms with their image counts; key=’Compound Name’ returns the screened compounds. Use this to discover valid values before calling IDR_search_images / IDR_search_studies, or to survey the contents of IDR for a given attribute.

Parameters:

  • key (string) (required) The metadata attribute whose values to enumerate, e.g. ‘Organism’, ‘Phenotype’, ‘Cell Line’, ‘Compound Name’. Required. Use IDR_list_metadata_keys to find valid keys.

  • resource ([‘string’, ‘null’]) (optional) Resource type. Default ‘image’.

  • max_results ([‘integer’, ‘null’]) (optional) Optional client-side cap on the number of values returned.

Example Usage:

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

IDR_search_images (Type: IDRSearchEngineTool)

Search the Image Data Resource (IDR) for individual images across ALL published studies at once b…

IDR_search_images tool specification

Tool Information:

  • Name: IDR_search_images

  • Type: IDRSearchEngineTool

  • Description: Search the Image Data Resource (IDR) for individual images across ALL published studies at once by curated metadata, using the IDR searchengine (Elasticsearch-backed). This is the cross-study entry point that the project-tree tools (IDR_list_studies / IDR_list_dataset_images) cannot provide. Filter by a metadata key (e.g. ‘Gene Symbol’, ‘Organism’, ‘Compound Name’, ‘Cell Line’, ‘Phenotype’, ‘Antibody Name’; use IDR_list_metadata_keys to see all keys) and a value (e.g. Gene Symbol = ‘TP53’). Each returned image includes its IDR image ID, a webclient URL, and its flattened key/value metadata pairs (gene, cell line, organism, antibody, etc.). Use operator=’contains’ for substring matching. Note: value matching is case-sensitive on the stored form regardless of case_sensitive (e.g. organism must be ‘Homo sapiens’, not ‘homo sapiens’); call IDR_list_values_for_key to get the exact stored values, which are reported lower-cased there but matched with their original capitalization in search. Example: key=’Gene Symbol’, value=’TP53’ returns thousands of images annotated with the TP53 gene.

Parameters:

  • value (string) (required) The metadata value to search for, e.g. ‘TP53’, ‘homo sapiens’, ‘HeLa’, ‘paclitaxel’. Required.

  • key ([‘string’, ‘null’]) (optional) The metadata attribute to match the value against, e.g. ‘Gene Symbol’, ‘Organism’, ‘Compound Name’, ‘Cell Line’, ‘Phenotype’. If omitted, the value is searched across all keys. Use IDR_list_metadata_keys to list available keys.

  • operator ([‘string’, ‘null’]) (optional) Match operator: ‘equals’ (default) or ‘contains’ for substring matching.

  • case_sensitive ([‘boolean’, ‘null’]) (optional) Whether the value match is case sensitive. Default false.

  • study ([‘string’, ‘null’]) (optional) Optional study-name filter, e.g. ‘idr0001-graml-sysgro/screenA’, to restrict results to one study.

  • resource ([‘string’, ‘null’]) (optional) Resource type to search. Default ‘image’. Other values: ‘screen’, ‘project’, ‘well’, ‘plate’.

  • max_results ([‘integer’, ‘null’]) (optional) Optional client-side cap on the number of image rows returned (the API returns up to 1000).

Example Usage:

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

IDR_search_studies (Type: IDRSearchEngineTool)

Find which IDR studies (screens and projects) contain images matching a metadata key/value, searc…

IDR_search_studies tool specification

Tool Information:

  • Name: IDR_search_studies

  • Type: IDRSearchEngineTool

  • Description: Find which IDR studies (screens and projects) contain images matching a metadata key/value, searching across the entire Image Data Resource. This answers the question ‘which published imaging studies involve gene X / organism Y / compound Z / phenotype W?’. Returns the containing screens (high-content screens) and projects, each with its IDR container ID, name (e.g. ‘idr0028-pascualvargas-rhogtpases/screenA’), type (‘screen’ or ‘project’), image count, and study-level key/value metadata. Use the returned container name/id with IDR_get_study or IDR_get_study_datasets to drill down. Example: key=’Phenotype’, value=’spindly’ returns the RhoGTPase screens (idr0028).

Parameters:

  • value (string) (required) The metadata value to search for, e.g. ‘TP53’, ‘spindly’, ‘homo sapiens’. Required.

  • key ([‘string’, ‘null’]) (optional) The metadata attribute to match against, e.g. ‘Gene Symbol’, ‘Phenotype’, ‘Organism’, ‘Compound Name’. If omitted, the value is searched across all keys.

  • operator ([‘string’, ‘null’]) (optional) Match operator: ‘equals’ (default) or ‘contains’.

  • case_sensitive ([‘boolean’, ‘null’]) (optional) Whether the value match is case sensitive. Default false.

  • study ([‘string’, ‘null’]) (optional) Optional study-name filter to restrict to one study.

  • resource ([‘string’, ‘null’]) (optional) Resource type to search. Default ‘image’.

Example Usage:

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