Unibind Tools

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

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

Available Tools

UniBind_get_dataset (Type: UniBindRESTTool)

Retrieve full direct transcription factor (TF)-DNA binding-site detail for one UniBind dataset by…

UniBind_get_dataset tool specification

Tool Information:

  • Name: UniBind_get_dataset

  • Type: UniBindRESTTool

  • Description: Retrieve full direct transcription factor (TF)-DNA binding-site detail for one UniBind dataset by its dataset_id (e.g. ‘EXP030726.neural_stem_cells.SMAD3’, obtained from UniBind_search_datasets). Returns the TF name, cell line/tissue, biological condition, source identifiers (GEO/ENCODE/PubMed), the JASPAR motif IDs used, and a list of TFBS model blocks. Each TFBS model gives the JASPAR motif (jaspar_id + version), total number of predicted binding sites (total_tfbs), the PWM score threshold, the centrality distance threshold, the CentriMo adjusted enrichment p-value, and direct download URLs for the binding sites in BED format, the underlying sequences in FASTA, and a summary plot. These are motif-anchored, base-pair-resolution, experimentally supported direct binding sites - distinct from raw ChIP-seq peaks. Public, no API key.

Parameters:

  • operation (string) (optional) Operation selector. Must be ‘get_dataset’.

  • dataset_id (string) (required) UniBind dataset identifier, e.g. ‘EXP030726.neural_stem_cells.SMAD3’. Obtain from UniBind_search_datasets (the ‘dataset_id’ field).

Example Usage:

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

UniBind_list_tfs (Type: UniBindRESTTool)

List the catalog of transcription factors (TFs) profiled in the UniBind database of direct TF-DNA…

UniBind_list_tfs tool specification

Tool Information:

  • Name: UniBind_list_tfs

  • Type: UniBindRESTTool

  • Description: List the catalog of transcription factors (TFs) profiled in the UniBind database of direct TF-DNA binding sites. Optionally filter by a case-insensitive substring of the TF gene symbol via ‘search’ (e.g. ‘SMAD’ returns SMAD2, SMAD3, SMAD4…). Returns a sorted, de-duplicated list of TF gene symbols. Use this to discover valid tf_name values for UniBind_search_datasets. Public, no API key.

Parameters:

  • operation (string) (optional) Operation selector. Must be ‘list_tfs’.

  • search ([‘string’, ‘null’]) (optional) Case-insensitive substring filter applied client-side to TF gene symbols, e.g. ‘SMAD’, ‘FOX’, ‘GATA’. Optional; omit to list all TFs.

  • limit (integer) (optional) Maximum number of TF names to return after filtering.

Example Usage:

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

UniBind_search_datasets (Type: UniBindRESTTool)

Search the UniBind catalog of curated, experimentally derived direct transcription factor (TF)-DN…

UniBind_search_datasets tool specification

Tool Information:

  • Name: UniBind_search_datasets

  • Type: UniBindRESTTool

  • Description: Search the UniBind catalog of curated, experimentally derived direct transcription factor (TF)-DNA binding-site datasets (one dataset = one ChIP-seq experiment for one TF in one cell type/condition). Filter by TF gene symbol (tf_name), species scientific name (species, e.g. ‘Homo sapiens’), cell type/tissue (cell_line), and collection (‘Robust’ or ‘Permissive’). All filters are optional and compose. Returns a paginated list of matching datasets with their TF name, total peak count, and dataset_id (use UniBind_get_dataset for full binding-site detail). UniBind provides motif-anchored, base-pair-resolution direct binding sites derived from ChIP-seq via the DAMO/ChIP-eat pipeline with JASPAR motifs - distinct from JASPAR/HOCOMOCO motif matrices and from ReMap raw ChIP-seq peaks. Public, no API key.

Parameters:

  • operation (string) (optional) Operation selector. Must be ‘search_datasets’.

  • tf_name ([‘string’, ‘null’]) (optional) Transcription factor gene symbol to filter by, e.g. ‘CTCF’, ‘SMAD3’, ‘ESR1’. Exact match on UniBind’s TF name. Optional.

  • species ([‘string’, ‘null’]) (optional) Species scientific name to filter by, e.g. ‘Homo sapiens’, ‘Mus musculus’, ‘Drosophila melanogaster’. Optional.

  • cell_line ([‘string’, ‘null’]) (optional) Cell type / tissue / condition name to filter by, e.g. ‘neural stem cells’, ‘MCF7’. Optional.

  • collection ([‘string’, ‘null’]) (optional) UniBind collection: ‘Robust’ (high-confidence, metadata-curated) or ‘Permissive’ (broader). Optional.

  • order ([‘string’, ‘null’]) (optional) Field to order results by, e.g. ‘tf_name’ or ‘-tf_name’ (prefix ‘-’ for descending). Optional.

  • page (integer) (optional) 1-based page number for pagination.

  • page_size (integer) (optional) Number of datasets per page (max 1000).

Example Usage:

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