Synapse Tools#

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

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

Available Tools#

Synapse_get_entity (Type: SynapseTool)#

Get metadata and annotations of one public Synapse entity by its Synapse ID (e.g. syn22364283): n…

Synapse_get_entity tool specification

Tool Information:

  • Name: Synapse_get_entity

  • Type: SynapseTool

  • Description: Get metadata and annotations of one public Synapse entity by its Synapse ID (e.g. syn22364283): name, type (Project, Folder, File, Table, Dataset), description, parent, creation/modification dates, version, and the annotation key/value pairs curators attached (assay, species, disease, tissue, consortium …). Restricted or private entities return a clear ‘not public’ error; nothing is downloaded and no login is used.

Parameters:

  • entity_id (string) (required) Synapse ID, e.g. ‘syn22364283’

Example Usage:

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

Synapse_list_children (Type: SynapseTool)#

List what a public Synapse project or folder contains: the child folders, files, tables and datas…

Synapse_list_children tool specification

Tool Information:

  • Name: Synapse_list_children

  • Type: SynapseTool

  • Description: List what a public Synapse project or folder contains: the child folders, files, tables and datasets with their Synapse IDs, names, types, versions and dates. Paged: when metadata.next_page_token is set, pass it back as next_page_token for the next page. Restricted containers return a clear ‘not public’ error.

Parameters:

  • entity_id (string) (required) Synapse ID of a project or folder, e.g. ‘syn22364283’

  • include_types ([‘array’, ‘null’]) (optional) Child types to list (default: folder, file, table, dataset)

  • next_page_token ([‘string’, ‘null’]) (optional) Token from the previous page’s metadata.next_page_token

Example Usage:

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

Synapse_search_entities (Type: SynapseTool)#

Search public Synapse.org (Sage Bionetworks) content by keyword: projects, folders, files, tables…

Synapse_search_entities tool specification

Tool Information:

  • Name: Synapse_search_entities

  • Type: SynapseTool

  • Description: Search public Synapse.org (Sage Bionetworks) content by keyword: projects, folders, files, tables and datasets shared by consortia such as AD Knowledge Portal, NF-OSI, PsychENCODE, HTAN and DREAM challenges. Returns id (synNNN), name, type, a description excerpt and dates for each hit, plus the total number of matches. Anonymous and read-only: only public entities are searchable and no file contents are downloaded. Follow up with Synapse_get_entity for metadata/annotations and Synapse_list_children to browse a project.

Parameters:

  • query (string) (required) Search words, e.g. ‘alzheimer proteomics’ (all words are matched)

  • node_type ([‘string’, ‘null’]) (optional) Restrict to one entity type: project, folder, file, table, dataset

  • size ([‘integer’, ‘null’]) (optional) Hits per page (1-100, default 10)

  • start ([‘integer’, ‘null’]) (optional) Offset of the first hit, for paging (default 0)

Example Usage:

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